Citrus Sinensis ID: 032044

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------15
Protein Sequence
MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRRS
Secondary Structure (PSIPRED)
cEEEEEEEEcccccccccEEEEEcccHHHHHHHHHHHcccEEccEEEEEEcccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccEEccEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEEEEcccccccccEEEEEcccHHHHHHHHHHHcccEEcccEEEEEcccccccccccccccccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHccccccccEEEEEccccccc
Coil and Loop (DISEMBL)
MLSKLTVlydretgrsrgFAFVTMSTVEDCNAVIENLDGREYLGRILRvnfsdkpkpklplyaetDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVlydgesgrsrgygfvcYSTKAEMETALESLNGVELEGRAMRVSLAQGRRS
Flexible Loop (DISEMBL)
mlskltvlydretgrsrgfafvtmstveDCNAVIENLDGREYLGRILrvnfsdkpkpkLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLydgesgrsrGYGFVCYSTKAEMETALEslngvelegramrvslaqgrrs
Low Complexity Region (SEG)
MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRRS
Disordered region (IsUnstruct)
*****TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME**************************
Disordered Region (DISOPRED)
MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR*********************FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV*LA*G***
Disordered Region (DISEMBL)
MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRRS
Disordered Region (DISPRO)
MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP********ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRRS
Positional Conservation
no confident homologs detected

---

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	148	2.2.26 [Sep-21-2011]
Q08935	273	29 kDa ribonucleoprotein	N/A	no	0.959	0.520	0.453	1e-30
P49313	279	30 kDa ribonucleoprotein,	N/A	no	0.959	0.508	0.436	8e-30
P19682	276	28 kDa ribonucleoprotein,	N/A	no	0.939	0.503	0.451	1e-29
Q04836	329	31 kDa ribonucleoprotein,	no	no	0.939	0.422	0.458	2e-29
P19683	315	31 kDa ribonucleoprotein,	N/A	no	0.939	0.441	0.437	3e-29
P28644	233	28 kDa ribonucleoprotein,	N/A	no	0.939	0.596	0.479	3e-29
Q08937	291	29 kDa ribonucleoprotein	N/A	no	0.959	0.487	0.409	4e-29
P19684	324	33 kDa ribonucleoprotein,	N/A	no	0.959	0.438	0.396	7e-29
P49314	292	31 kDa ribonucleoprotein,	N/A	no	0.959	0.486	0.397	1e-28
Q9ZUU4	289	Ribonucleoprotein At2g372	no	no	0.925	0.474	0.414	4e-28

>sp|Q08935|ROC1_NICSY 29 kDa ribonucleoprotein A, chloroplastic OS=Nicotiana sylvestris PE=2 SV=1

 Score =  131 bits (330), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 69/152 (45%), Positives = 97/152 (63%), Gaps = 10/152 (6%)

Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK------ 58
           + V+YD+ TGRSRGF FVTMS+ E+  A  +  +G E  GR LRVN    P+ +      
Sbjct: 116 VEVIYDKLTGRSRGFGFVTMSSKEEVEAACQQFNGYELDGRALRVNSGPPPEKRENSSFR 175

Query: 59  ----LPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVC 114
                    ++  +++VGNL+W V  ++L   F E G VV A+V+YD +SGRSRG+GFV 
Sbjct: 176 GGSRGGGSFDSSNRVYVGNLAWGVDQDALETLFSEQGKVVDAKVVYDRDSGRSRGFGFVT 235

Query: 115 YSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
           YS+  E+  A+ESL+GV+L GRA+RVS A+ R
Sbjct: 236 YSSAEEVNNAIESLDGVDLNGRAIRVSPAEAR 267

Could be involved in splicing and/or processing of chloroplast RNA's.
Nicotiana sylvestris (taxid: 4096)

>sp|P49313|ROC1_NICPL 30 kDa ribonucleoprotein, chloroplastic OS=Nicotiana plumbaginifolia PE=2 SV=1

 Score =  129 bits (323), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 69/158 (43%), Positives = 97/158 (61%), Gaps = 16/158 (10%)

Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK------ 58
           + V+YD+ TGRSRGF FVTMS+ E+  A  +  +G E  GR LRVN    P+ +      
Sbjct: 116 VEVIYDKLTGRSRGFGFVTMSSKEEVEAACQQFNGYELDGRALRVNSGPPPEKRENSSFR 175

Query: 59  ----------LPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSR 108
                          ++  +++VGNL+W V  ++L   F E G VV A+V+YD +SGRSR
Sbjct: 176 ENSSFRGGSRGGGSFDSSNRVYVGNLAWGVDQDALETLFSEQGKVVDAKVVYDRDSGRSR 235

Query: 109 GYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
           G+GFV YS+  E+  A+ESL+GV+L GRA+RVS A+ R
Sbjct: 236 GFGFVTYSSAEEVNNAIESLDGVDLNGRAIRVSPAEAR 273

Could be involved in splicing and/or processing of chloroplast RNA's.

Nicotiana plumbaginifolia (taxid: 4092)

>sp|P19682|ROC3_NICSY 28 kDa ribonucleoprotein, chloroplastic OS=Nicotiana sylvestris PE=1 SV=1

 Score =  128 bits (321), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 65/144 (45%), Positives = 96/144 (66%), Gaps = 5/144 (3%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS----DKPKPKLPLY 62
           V+Y+RET RSRGF FVTMSTVE+ +  +E     +  GR+L VN +     +P+ + P  
Sbjct: 128 VIYNRETDRSRGFGFVTMSTVEEADKAVELYSQYDLNGRLLTVNKAAPRGSRPE-RAPRT 186

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
            +  ++++VGN+ W +    L Q F E+G VV ARV++D ESGRSRG+GFV  S++AEM 
Sbjct: 187 FQPTYRIYVGNIPWDIDDARLEQVFSEHGKVVSARVVFDRESGRSRGFGFVTMSSEAEMS 246

Query: 123 TALESLNGVELEGRAMRVSLAQGR 146
            A+ +L+G  L+GR +RV+ A+ R
Sbjct: 247 EAIANLDGQTLDGRTIRVNAAEER 270

Probably involved in the 3'-end processing of chloroplast mRNA's.

Nicotiana sylvestris (taxid: 4096)

>sp|Q04836|ROC3_ARATH 31 kDa ribonucleoprotein, chloroplastic OS=Arabidopsis thaliana GN=RBP31 PE=1 SV=1

 Score =  127 bits (319), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 66/144 (45%), Positives = 95/144 (65%), Gaps = 5/144 (3%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS----DKPKPKLPLY 62
           V+Y+RET +SRGF FVTMS+V++    +E  +  +  GR+L VN +     +P+ + P  
Sbjct: 181 VIYNRETDQSRGFGFVTMSSVDEAETAVEKFNRYDLNGRLLTVNKAAPRGSRPE-RAPRV 239

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
            E  F+++VGNL W V    L Q F E+G VV ARV+YD E+GRSRG+GFV  S   E+ 
Sbjct: 240 YEPAFRVYVGNLPWDVDNGRLEQLFSEHGKVVEARVVYDRETGRSRGFGFVTMSDVDELN 299

Query: 123 TALESLNGVELEGRAMRVSLAQGR 146
            A+ +L+G  LEGRA+RV++A+ R
Sbjct: 300 EAISALDGQNLEGRAIRVNVAEER 323

Probably involved in the 3'-end processing of chloroplast mRNA's.

Arabidopsis thaliana (taxid: 3702)

>sp|P19683|ROC4_NICSY 31 kDa ribonucleoprotein, chloroplastic OS=Nicotiana sylvestris PE=1 SV=1

 Score =  127 bits (319), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 63/144 (43%), Positives = 98/144 (68%), Gaps = 5/144 (3%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS----DKPKPKLPLY 62
           V+Y+R+T +SRGF FVTMSTVE+    +E  +  +  GR+L VN +    ++P+ + P  
Sbjct: 167 VIYNRDTDQSRGFGFVTMSTVEEAEKAVEMYNRYDVNGRLLTVNKAARRGERPE-RPPRT 225

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
            E  ++++VGN+ W +    L Q F E+G VV ARV+YD E+GRSRG+GFV  +++AEM 
Sbjct: 226 FEQSYRIYVGNIPWGIDDARLEQLFSEHGKVVSARVVYDRETGRSRGFGFVTMASEAEMS 285

Query: 123 TALESLNGVELEGRAMRVSLAQGR 146
            A+ +L+G  L+GR +RV++A+ R
Sbjct: 286 DAIANLDGQSLDGRTIRVNVAEDR 309

Could be involved in splicing and/or processing of chloroplast RNA's.

Nicotiana sylvestris (taxid: 4096)

>sp|P28644|ROC1_SPIOL 28 kDa ribonucleoprotein, chloroplastic OS=Spinacia oleracea PE=1 SV=1

 Score =  127 bits (318), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 69/144 (47%), Positives = 96/144 (66%), Gaps = 5/144 (3%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           V+Y+RET RSRGF FVTMSTVE+    +E L+G +  GR L VN +  P+         D
Sbjct: 86  VIYNRETDRSRGFGFVTMSTVEEAEKAVELLNGYDMDGRQLTVNKA-APRGSPERAPRGD 144

Query: 67  F----KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           F    +++VGNL W V T  L Q F E+G VV ARV+ D E+GRSRG+GFV  S+++E+ 
Sbjct: 145 FEPSCRVYVGNLPWDVDTSRLEQLFSEHGKVVSARVVSDRETGRSRGFGFVTMSSESEVN 204

Query: 123 TALESLNGVELEGRAMRVSLAQGR 146
            A+ +L+G  L+GRA+RV++A+ R
Sbjct: 205 DAIAALDGQTLDGRAVRVNVAEER 228

Probably involved in the 3'-end processing of chloroplast mRNA's.

Spinacia oleracea (taxid: 3562)

>sp|Q08937|ROC2_NICSY 29 kDa ribonucleoprotein B, chloroplastic OS=Nicotiana sylvestris PE=2 SV=1

 Score =  126 bits (317), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 70/171 (40%), Positives = 98/171 (57%), Gaps = 29/171 (16%)

Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLY-- 62
           + V+YD+ TGRSRGF FVTMST E+  A  +  +G E  GR +RVN    P  +      
Sbjct: 116 VEVIYDKLTGRSRGFGFVTMSTKEEVEAAEQQFNGYEIDGRAIRVNAGPAPAKRENSSFG 175

Query: 63  ---------------------------AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVG 95
                                       ++  +++VGNLSW V   +L + F E GNVV 
Sbjct: 176 GGRGGNSSYGGGRDGNSSFGGARGGRSVDSSNRVYVGNLSWGVDDLALKELFSEQGNVVD 235

Query: 96  ARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
           A+V+YD +SGRSRG+GFV YS+  E+  A++SLNGV+L+GR++RVS A+ R
Sbjct: 236 AKVVYDRDSGRSRGFGFVTYSSSKEVNDAIDSLNGVDLDGRSIRVSAAEER 286

Could be involved in splicing and/or processing of chloroplast RNA's.

Nicotiana sylvestris (taxid: 4096)

>sp|P19684|ROC5_NICSY 33 kDa ribonucleoprotein, chloroplastic OS=Nicotiana sylvestris PE=1 SV=1

 Score =  125 bits (315), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 61/154 (39%), Positives = 97/154 (62%), Gaps = 12/154 (7%)

Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK----- 56
           ++ + ++YDR T RSRGFAFVTM +VE+    I   DG +  GR ++VNF + P+     
Sbjct: 140 VANVEIVYDRVTDRSRGFAFVTMGSVEEAKEAIRLFDGSQVGGRTVKVNFPEVPRGGERE 199

Query: 57  -------PKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRG 109
                       + ++  KL+V NLSW++T++ L  AF +    + A+V+YD  SGRSRG
Sbjct: 200 VMSAKIRSTYQGFVDSPHKLYVANLSWALTSQGLRDAFADQPGFMSAKVIYDRSSGRSRG 259

Query: 110 YGFVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
           +GF+ +S+   M +AL+++N VELEGR +R+++A
Sbjct: 260 FGFITFSSAEAMNSALDTMNEVELEGRPLRLNVA 293

Could be involved in splicing and/or processing of chloroplast RNA's.

Nicotiana sylvestris (taxid: 4096)

>sp|P49314|ROC2_NICPL 31 kDa ribonucleoprotein, chloroplastic OS=Nicotiana plumbaginifolia PE=2 SV=1

 Score =  124 bits (312), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 68/171 (39%), Positives = 98/171 (57%), Gaps = 29/171 (16%)

Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLY-- 62
           + V+YD+ +GRSRGF FVTMST E+  A  +  +G E  GR +RVN    P  +      
Sbjct: 117 VEVIYDKLSGRSRGFGFVTMSTKEEVEAAEQQFNGYEIDGRAIRVNAGPAPAKRENSSFG 176

Query: 63  ---------------------------AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVG 95
                                       ++  +++VGNLSW V   +L + F E GNVV 
Sbjct: 177 GGRGGNSSYGGGRDGNSSFGGARGGRSVDSSNRVYVGNLSWGVDDLALKELFSEQGNVVD 236

Query: 96  ARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
           A+V+YD +SGRSRG+GFV YS+  E+  A++SLNG++L+GR++RVS A+ R
Sbjct: 237 AKVVYDRDSGRSRGFGFVTYSSAKEVNDAIDSLNGIDLDGRSIRVSAAEER 287

Nicotiana plumbaginifolia (taxid: 4092)

>sp|Q9ZUU4|ROC1_ARATH Ribonucleoprotein At2g37220, chloroplastic OS=Arabidopsis thaliana GN=At2g37220 PE=1 SV=1

 Score =  123 bits (309), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 70/169 (41%), Positives = 96/169 (56%), Gaps = 32/169 (18%)

Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAE 64
           + V+YD+ TGRSRGF FVTMS+V +  A  +  +G E  GR LRVN +  P PK     E
Sbjct: 120 VEVIYDKITGRSRGFGFVTMSSVSEVEAAAQQFNGYELDGRPLRVN-AGPPPPKR----E 174

Query: 65  TDF---------------------------KLFVGNLSWSVTTESLTQAFQEYGNVVGAR 97
             F                           +++VGNLSW V   +L   F E G VV AR
Sbjct: 175 DGFSRGPRSSFGSSGSGYGGGGGSGAGSGNRVYVGNLSWGVDDMALESLFSEQGKVVEAR 234

Query: 98  VLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
           V+YD +SGRS+G+GFV Y +  E++ A++SL+G +L+GR +RVS A+ R
Sbjct: 235 VIYDRDSGRSKGFGFVTYDSSQEVQNAIKSLDGADLDGRQIRVSEAEAR 283

Could be involved in splicing and/or processing of chloroplast RNA's.

Arabidopsis thaliana (taxid: 3702)

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	148
296083731	283	unnamed protein product [Vitis vinifera]	0.959	0.501	0.880	1e-69
255574887	285	ribonucleoprotein, chloroplast, putative	0.959	0.498	0.852	5e-68
224099981	279	predicted protein [Populus trichocarpa]	0.959	0.508	0.838	8e-68
224107511	279	predicted protein [Populus trichocarpa]	0.959	0.508	0.845	4e-67
225433269	751	PREDICTED: uncharacterized protein LOC10	0.918	0.181	0.867	7e-66
356534904	282	PREDICTED: 29 kDa ribonucleoprotein, chl	0.972	0.510	0.812	6e-65
449432502	276	PREDICTED: 28 kDa ribonucleoprotein, chl	0.972	0.521	0.784	4e-64
558629	287	chloroplast RNA binding protein [Phaseol	0.972	0.501	0.812	7e-64
388500434	273	unknown [Lotus japonicus]	0.972	0.527	0.791	3e-63
357439793	387	31 kDa ribonucleoprotein [Medicago trunc	0.972	0.372	0.763	4e-63

>gi|296083731|emb|CBI23720.3| unnamed protein product [Vitis vinifera]

 Score =  267 bits (682), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 125/142 (88%), Positives = 136/142 (95%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           VLY+R+TGRSRGFAFVTMS+VEDCNAVIENLDG EY GR LRVNFSDKPKPKLPLY ET+
Sbjct: 142 VLYNRDTGRSRGFAFVTMSSVEDCNAVIENLDGSEYGGRTLRVNFSDKPKPKLPLYPETE 201

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           +KLFVGNLSWSVT+ESL Q FQEYGNV+GARVLYDGE+GRSRGYGFVCYSTKAEM+TALE
Sbjct: 202 YKLFVGNLSWSVTSESLNQVFQEYGNVIGARVLYDGETGRSRGYGFVCYSTKAEMDTALE 261

Query: 127 SLNGVELEGRAMRVSLAQGRRS 148
           SLNGVELEGRA+R+SLAQGRRS
Sbjct: 262 SLNGVELEGRAIRISLAQGRRS 283

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255574887|ref|XP_002528350.1| ribonucleoprotein, chloroplast, putative [Ricinus communis] gi|223532218|gb|EEF34022.1| ribonucleoprotein, chloroplast, putative [Ricinus communis]

 Score =  261 bits (668), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 121/142 (85%), Positives = 135/142 (95%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           VLYDR+TGRSRGFAFVTMSTVEDCNAVIENLDG +++GRILRVNFSDKPKPK PLY ET+
Sbjct: 144 VLYDRDTGRSRGFAFVTMSTVEDCNAVIENLDGSQFMGRILRVNFSDKPKPKEPLYPETE 203

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
            KLFVGNLSWSVT+ESL +AFQEYGN+VGARVLYDGE+GRSRGYGFVCY+T++EME AL 
Sbjct: 204 HKLFVGNLSWSVTSESLVEAFQEYGNIVGARVLYDGETGRSRGYGFVCYATRSEMENALV 263

Query: 127 SLNGVELEGRAMRVSLAQGRRS 148
           SLNGVELEGRAMRVSLAQG++S
Sbjct: 264 SLNGVELEGRAMRVSLAQGKKS 285

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224099981|ref|XP_002311696.1| predicted protein [Populus trichocarpa] gi|118486835|gb|ABK95252.1| unknown [Populus trichocarpa] gi|222851516|gb|EEE89063.1| predicted protein [Populus trichocarpa]

 Score =  261 bits (666), Expect = 8e-68,   Method: Compositional matrix adjust.
 Identities = 119/142 (83%), Positives = 135/142 (95%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           VLY RETGRSRGFAFVTMS++EDC  VIENLDG +Y+GRILRVNF+DKPKPK PLY ET+
Sbjct: 138 VLYHRETGRSRGFAFVTMSSIEDCETVIENLDGSQYMGRILRVNFADKPKPKEPLYPETE 197

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           +KLF+GNLSWSVT+ESLTQAFQEYGNVVGARVLYDGE+G+SRGYGFVCYSTK E+ETAL+
Sbjct: 198 YKLFIGNLSWSVTSESLTQAFQEYGNVVGARVLYDGETGKSRGYGFVCYSTKEELETALQ 257

Query: 127 SLNGVELEGRAMRVSLAQGRRS 148
           SLNGVELEGRA+RVSLA+GR+S
Sbjct: 258 SLNGVELEGRALRVSLAEGRKS 279

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224107511|ref|XP_002314506.1| predicted protein [Populus trichocarpa] gi|222863546|gb|EEF00677.1| predicted protein [Populus trichocarpa]

 Score =  258 bits (660), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 120/142 (84%), Positives = 134/142 (94%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           VLY RETGRSRGFAFVTMS++EDCNAVIENLD  +Y+GRILRVNFSD PKPK PLY ET+
Sbjct: 138 VLYHRETGRSRGFAFVTMSSIEDCNAVIENLDESQYMGRILRVNFSDNPKPKEPLYPETE 197

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           +KLFVGNLSWS T+ESLTQAFQEYGNVVGARVLYDGE+G+SRGYGFVCYSTKAEM+TAL 
Sbjct: 198 YKLFVGNLSWSATSESLTQAFQEYGNVVGARVLYDGETGKSRGYGFVCYSTKAEMQTALV 257

Query: 127 SLNGVELEGRAMRVSLAQGRRS 148
           SL+GVELEGRA+RVSLA+GR+S
Sbjct: 258 SLDGVELEGRALRVSLAEGRKS 279

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225433269|ref|XP_002285469.1| PREDICTED: uncharacterized protein LOC100261382 [Vitis vinifera]

 Score =  254 bits (650), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 118/136 (86%), Positives = 129/136 (94%)

Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAE 64
           + VLY+R+TGRSRGFAFVTMS+VEDCNAVIENLDG EY GR LRVNFSDKPKPKLPLY E
Sbjct: 140 VEVLYNRDTGRSRGFAFVTMSSVEDCNAVIENLDGSEYGGRTLRVNFSDKPKPKLPLYPE 199

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           T++KLFVGNLSWSVT+ESL Q FQEYGNV+GARVLYDGE+GRSRGYGFVCYSTKAEM+TA
Sbjct: 200 TEYKLFVGNLSWSVTSESLNQVFQEYGNVIGARVLYDGETGRSRGYGFVCYSTKAEMDTA 259

Query: 125 LESLNGVELEGRAMRV 140
           LESLNGVELEGRA+RV
Sbjct: 260 LESLNGVELEGRAIRV 275

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356534904|ref|XP_003535991.1| PREDICTED: 29 kDa ribonucleoprotein, chloroplastic-like [Glycine max]

 Score =  251 bits (641), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 117/144 (81%), Positives = 131/144 (90%)

Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAE 64
           + VLYDR++G+SRGFAFVTMS +EDCNAVIENLDG+E+LGR LRVNFS KPKPK PLY E
Sbjct: 139 IEVLYDRDSGKSRGFAFVTMSCIEDCNAVIENLDGKEFLGRTLRVNFSSKPKPKEPLYPE 198

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           T+ KLFVGNLSWSVT E LTQAFQEYG VVGARVLYDGE+GRSRGYGFVCYST+AEME A
Sbjct: 199 TEHKLFVGNLSWSVTNEILTQAFQEYGTVVGARVLYDGETGRSRGYGFVCYSTQAEMEAA 258

Query: 125 LESLNGVELEGRAMRVSLAQGRRS 148
           + +LN VELEGRAMRVSLAQG+R+
Sbjct: 259 VAALNDVELEGRAMRVSLAQGKRA 282

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449432502|ref|XP_004134038.1| PREDICTED: 28 kDa ribonucleoprotein, chloroplastic-like [Cucumis sativus] gi|449487476|ref|XP_004157645.1| PREDICTED: 28 kDa ribonucleoprotein, chloroplastic-like [Cucumis sativus]

 Score =  248 bits (634), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 113/144 (78%), Positives = 133/144 (92%)

Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAE 64
           + VLYDR TG+SRGFAFVTMS++EDCN VIENLDG  Y+GRILRVNFSDKPKPK PLY E
Sbjct: 131 IEVLYDRNTGKSRGFAFVTMSSIEDCNKVIENLDGSAYMGRILRVNFSDKPKPKEPLYPE 190

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           T++KLFVGNLSWSVT+E LTQAFQEYGNVVGARV+YDGE+G+SRGYGFV YSTK+EMETA
Sbjct: 191 TEYKLFVGNLSWSVTSEILTQAFQEYGNVVGARVIYDGETGKSRGYGFVSYSTKSEMETA 250

Query: 125 LESLNGVELEGRAMRVSLAQGRRS 148
           LE++N +ELEGR +RVSLA+G+++
Sbjct: 251 LETINELELEGRVIRVSLAEGKQA 274

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|558629|emb|CAA57551.1| chloroplast RNA binding protein [Phaseolus vulgaris]

 Score =  248 bits (632), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 117/144 (81%), Positives = 130/144 (90%)

Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAE 64
           + VLYDR+TG+SRGFAFVTMS +EDCNAVIENLDG+EYLGR LRVNFS+KPK K PLY E
Sbjct: 142 IEVLYDRDTGKSRGFAFVTMSCIEDCNAVIENLDGKEYLGRTLRVNFSNKPKAKEPLYPE 201

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           T+ KLFVGNLSWSVT E LTQAFQEYG VVGARVLYDGE+GRSRGYGFVC+STK EME A
Sbjct: 202 TEHKLFVGNLSWSVTNEILTQAFQEYGTVVGARVLYDGETGRSRGYGFVCFSTKEEMEAA 261

Query: 125 LESLNGVELEGRAMRVSLAQGRRS 148
           L +LN VELEGRAMRVSLA+G+R+
Sbjct: 262 LGALNDVELEGRAMRVSLAEGKRA 285

Source: Phaseolus vulgaris

Species: Phaseolus vulgaris

Genus: Phaseolus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388500434|gb|AFK38283.1| unknown [Lotus japonicus]

 Score =  245 bits (626), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 114/144 (79%), Positives = 130/144 (90%)

Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAE 64
           + VLYDR++G+SRGFAFVTMS VEDCN VIENLDG+E+LGR LRVN SDKPKPK PLY E
Sbjct: 130 IEVLYDRDSGKSRGFAFVTMSCVEDCNTVIENLDGKEFLGRTLRVNLSDKPKPKEPLYPE 189

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           T+ KLFVGNLSW+VT+ESL Q FQEYG VVGARVLYDGE+GRSRGYGFVCYS ++E+ETA
Sbjct: 190 TEHKLFVGNLSWTVTSESLIQVFQEYGTVVGARVLYDGETGRSRGYGFVCYSKRSELETA 249

Query: 125 LESLNGVELEGRAMRVSLAQGRRS 148
           L SLN VELEGRA+RVSLA+G+RS
Sbjct: 250 LISLNNVELEGRAIRVSLAEGKRS 273

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357439793|ref|XP_003590174.1| 31 kDa ribonucleoprotein [Medicago truncatula] gi|355479222|gb|AES60425.1| 31 kDa ribonucleoprotein [Medicago truncatula]

 Score =  245 bits (626), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 110/144 (76%), Positives = 133/144 (92%)

Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAE 64
           + VLYDR+TG+SRGFAFVTMS VEDCNAVI+NLDG+E++GR LRVNFSDKPKPK PLY E
Sbjct: 244 IEVLYDRDTGKSRGFAFVTMSCVEDCNAVIQNLDGKEFMGRTLRVNFSDKPKPKEPLYPE 303

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           T++KLFVGNL+W+VT+ESLTQAFQE+G VVGARVL+DGE+G+SRGYGFV Y+TK+EM+TA
Sbjct: 304 TEYKLFVGNLAWTVTSESLTQAFQEHGTVVGARVLFDGETGKSRGYGFVSYATKSEMDTA 363

Query: 125 LESLNGVELEGRAMRVSLAQGRRS 148
           L  ++ VELEGR +RVSLAQG+RS
Sbjct: 364 LAIMDNVELEGRTLRVSLAQGKRS 387

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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	148
TAIR|locus:2202740	258	AT1G60000 [Arabidopsis thalian	0.952	0.546	0.760	2.3e-55
TAIR|locus:2049721	289	AT2G37220 [Arabidopsis thalian	0.533	0.273	0.506	6.8e-30
TAIR|locus:2122009	329	RBP31 "AT4G24770" [Arabidopsis	0.939	0.422	0.458	3.1e-28
TAIR|locus:2157702	289	CP31B "chloroplast RNA-binding	0.939	0.480	0.444	7.3e-27
TAIR|locus:2079874	329	CP33 "chloroplast RNA-binding	0.945	0.425	0.368	8.4e-26
TAIR|locus:2083810	253	PSRP2 "plastid-specific	0.959	0.561	0.401	2e-24
TAIR|locus:2062379	308	AT2G35410 [Arabidopsis thalian	0.932	0.448	0.4	1.3e-20
TAIR|locus:2200975	294	AT1G01080 [Arabidopsis thalian	0.959	0.482	0.348	3.6e-18
UNIPROTKB|Q43472	161	blt801 "Glycine-rich RNA-bindi	0.581	0.534	0.430	2e-17
ASPGD|ASPL0000076731	524	AN4865 [Emericella nidulans (t	0.520	0.146	0.423	3.8e-12

TAIR|locus:2202740 AT1G60000 [Arabidopsis thaliana (taxid:3702)]

 Score = 571 (206.1 bits), Expect = 2.3e-55, P = 2.3e-55
 Identities = 108/142 (76%), Positives = 130/142 (91%)

Query:     7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP-KLPLYAET 65
             VLY+R+TG+SRGFAFVTMS VEDCN +I+NLDG EYLGR L+VNF+DKPKP K PLY ET
Sbjct:   116 VLYNRDTGQSRGFAFVTMSNVEDCNIIIDNLDGTEYLGRALKVNFADKPKPNKEPLYPET 175

Query:    66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
             + KLFVGNLSW+VT+ESL  AF+E G+VVGARV++DG++GRSRGYGFVCYS+KAEMETAL
Sbjct:   176 EHKLFVGNLSWTVTSESLAGAFRECGDVVGARVVFDGDTGRSRGYGFVCYSSKAEMETAL 235

Query:   126 ESLNGVELEGRAMRVSLAQGRR 147
             ESL+G ELEGRA+RV+LAQG++
Sbjct:   236 ESLDGFELEGRAIRVNLAQGKK 257

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0019344 "cysteine biosynthetic process" evidence=RCA

TAIR|locus:2049721 AT2G37220 [Arabidopsis thaliana (taxid:3702)]

 Score = 216 (81.1 bits), Expect = 6.8e-30, Sum P(2) = 6.8e-30
 Identities = 40/79 (50%), Positives = 58/79 (73%)

Query:    68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
             +++VGNLSW V   +L   F E G VV ARV+YD +SGRS+G+GFV Y +  E++ A++S
Sbjct:   205 RVYVGNLSWGVDDMALESLFSEQGKVVEARVIYDRDSGRSKGFGFVTYDSSQEVQNAIKS 264

Query:   128 LNGVELEGRAMRVSLAQGR 146
             L+G +L+GR +RVS A+ R
Sbjct:   265 LDGADLDGRQIRVSEAEAR 283

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009409 "response to cold" evidence=IEP;RCA

GO:0010319 "stromule" evidence=IDA

GO:0045087 "innate immune response" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0009737 "response to abscisic acid stimulus" evidence=IEP

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0009814 "defense response, incompatible interaction" evidence=RCA

GO:0019684 "photosynthesis, light reaction" evidence=RCA

GO:0042742 "defense response to bacterium" evidence=RCA

TAIR|locus:2122009 RBP31 "AT4G24770" [Arabidopsis thaliana (taxid:3702)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 66/144 (45%), Positives = 95/144 (65%)

Query:     7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS----DKPKPKLPLY 62
             V+Y+RET +SRGF FVTMS+V++    +E  +  +  GR+L VN +     +P+ + P  
Sbjct:   181 VIYNRETDQSRGFGFVTMSSVDEAETAVEKFNRYDLNGRLLTVNKAAPRGSRPE-RAPRV 239

Query:    63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
              E  F+++VGNL W V    L Q F E+G VV ARV+YD E+GRSRG+GFV  S   E+ 
Sbjct:   240 YEPAFRVYVGNLPWDVDNGRLEQLFSEHGKVVEARVVYDRETGRSRGFGFVTMSDVDELN 299

Query:   123 TALESLNGVELEGRAMRVSLAQGR 146
              A+ +L+G  LEGRA+RV++A+ R
Sbjct:   300 EAISALDGQNLEGRAIRVNVAEER 323

GO:0003723 "RNA binding" evidence=ISS;IDA;TAS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0045087 "innate immune response" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0009451 "RNA modification" evidence=IMP

GO:0009073 "aromatic amino acid family biosynthetic process" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0016226 "iron-sulfur cluster assembly" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0045036 "protein targeting to chloroplast" evidence=RCA

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

GO:0009631 "cold acclimation" evidence=IMP

GO:0016553 "base conversion or substitution editing" evidence=IMP

GO:0043489 "RNA stabilization" evidence=IMP

GO:0006396 "RNA processing" evidence=TAS

TAIR|locus:2157702 CP31B "chloroplast RNA-binding protein 31B" [Arabidopsis thaliana (taxid:3702)]

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 64/144 (44%), Positives = 96/144 (66%)

Query:     7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS----DKPKPKLPLY 62
             V+Y+R+T +SRGF FVTMSTVE+    +E  +  E  GR L VN +     +P+ +  +Y
Sbjct:   144 VIYNRDTDQSRGFGFVTMSTVEEAEKAVEKFNSFEVNGRRLTVNRAAPRGSRPERQPRVY 203

Query:    63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
              +  F+++VGNL W V +  L + F E+G VV ARV+ D E+GRSRG+GFV  S + E+ 
Sbjct:   204 -DAAFRIYVGNLPWDVDSGRLERLFSEHGKVVDARVVSDRETGRSRGFGFVQMSNENEVN 262

Query:   123 TALESLNGVELEGRAMRVSLAQGR 146
              A+ +L+G  LEGRA++V++A+ R
Sbjct:   263 VAIAALDGQNLEGRAIKVNVAEER 286

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0045087 "innate immune response" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009451 "RNA modification" evidence=IMP

GO:0000023 "maltose metabolic process" evidence=RCA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0009409 "response to cold" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0009814 "defense response, incompatible interaction" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0019684 "photosynthesis, light reaction" evidence=RCA

GO:0042742 "defense response to bacterium" evidence=RCA

TAIR|locus:2079874 CP33 "chloroplast RNA-binding protein 33" [Arabidopsis thaliana (taxid:3702)]

 Score = 292 (107.8 bits), Expect = 8.4e-26, P = 8.4e-26
 Identities = 56/152 (36%), Positives = 98/152 (64%)

Query:     7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK--------PK 58
             ++YD+ T RSRGF FVTM ++E+    ++  +  +  GR ++VNF + P+         K
Sbjct:   147 IVYDKVTDRSRGFGFVTMGSIEEAKEAMQMFNSSQIGGRTVKVNFPEVPRGGENEVMRTK 206

Query:    59 LP----LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVC 114
             +      Y ++  K++ GNL W++T++ L  AF +   V+GA+V+Y+  +GRSRG+GF+ 
Sbjct:   207 IRDNNRSYVDSPHKVYAGNLGWNLTSQGLKDAFGDQPGVLGAKVIYERNTGRSRGFGFIS 266

Query:   115 YSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
             + +   +++AL ++NGVE+EGRA+R++LA  R
Sbjct:   267 FESAENVQSALATMNGVEVEGRALRLNLASER 298

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0009579 "thylakoid" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009793 "embryo development ending in seed dormancy" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0016226 "iron-sulfur cluster assembly" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0048481 "ovule development" evidence=RCA

TAIR|locus:2083810 PSRP2 "plastid-specific ribosomal protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 61/152 (40%), Positives = 96/152 (63%)

Query:     2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP---KPK 58
             + K+ V+YD+ +GRSR F F TM +VED NAV+E L+G    GR ++VN ++KP    P 
Sbjct:   102 VEKVQVMYDKYSGRSRRFGFATMKSVEDANAVVEKLNGNTVEGREIKVNITEKPIASSPD 161

Query:    59 LPL-------YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
             L +       + ++ +K++VGNL+ +VT E L   F E G VV A+V     + +S G+G
Sbjct:   162 LSVLQSEDSAFVDSPYKVYVGNLAKTVTKEMLENLFSEKGKVVSAKVSRVPGTSKSTGFG 221

Query:   112 FVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
             FV +S++ ++E A+ +LN   LEG+ +RV+ A
Sbjct:   222 FVTFSSEEDVEAAIVALNNSLLEGQKIRVNKA 253

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009773 "photosynthetic electron transport in photosystem I" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0045036 "protein targeting to chloroplast" evidence=RCA

TAIR|locus:2062379 AT2G35410 [Arabidopsis thaliana (taxid:3702)]

 Score = 243 (90.6 bits), Expect = 1.3e-20, P = 1.3e-20
 Identities = 60/150 (40%), Positives = 86/150 (57%)

Query:    11 RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS---DKPKPK----LPLYA 63
             ++ G++RGFAFVTM++ E+  A I+  D  +  GRI+ V+F+    KP PK    LP  A
Sbjct:   129 QKDGKNRGFAFVTMASGEEAQAAIDKFDTFQVSGRIISVSFARRFKKPTPKSPNDLPSPA 188

Query:    64 --ETDFKLFVGNLSWSVTTESLTQAFQEYG-NVVGARVLYDGESGRSRGYGFVCYSTKAE 120
               +T  KL+V NL+W   +  L + F     N V ARV++    GRS GYGFV ++T+ E
Sbjct:   189 PGDTRHKLYVSNLAWKARSTHLRELFTAADFNPVSARVVFADPEGRSSGYGFVSFATREE 248

Query:   121 METALESLNGVELEGR--AMRVSLAQGRRS 148
              E A+  LNG E+ GR   ++ SL     S
Sbjct:   249 AENAITKLNGKEIMGRPITLKFSLRSASES 278

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0006364 "rRNA processing" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0015979 "photosynthesis" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0042793 "transcription from plastid promoter" evidence=RCA

TAIR|locus:2200975 AT1G01080 [Arabidopsis thaliana (taxid:3702)]

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 55/158 (34%), Positives = 87/158 (55%)

Query:     1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS-D------ 53
             ++S   V  + +TG SRG  +VTM ++      I +LDG E  GR +RV +S D      
Sbjct:   134 VISVEVVSRNPQTGESRGSGYVTMGSINSAKIAIASLDGTEVGGREMRVRYSVDMNPGTR 193

Query:    54 -KPK-----PKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRS 107
               P+     PK  L  E+  K++VGNL W    + L   F ++G +V  RVL+D ++GR+
Sbjct:   194 RNPEVLNSTPKKILMYESQHKVYVGNLPWFTQPDGLRNHFSKFGTIVSTRVLHDRKTGRN 253

Query:   108 RGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG 145
             R + F+ +++  E + AL S NG + EGR  R+ + +G
Sbjct:   254 RVFAFLSFTSGEERDAAL-SFNGTQYEGR--RIIVREG 288

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0006655 "phosphatidylglycerol biosynthetic process" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

UNIPROTKB|Q43472 blt801 "Glycine-rich RNA-binding protein blt801" [Hordeum vulgare (taxid:4513)]

 Score = 213 (80.0 bits), Expect = 2.0e-17, P = 2.0e-17
 Identities = 37/86 (43%), Positives = 62/86 (72%)

Query:    63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
             A+ +++ FVG L W+   +SL  AF +YG+V+ ++++ D E+GRSRG+GFV +++   M 
Sbjct:     2 ADVEYRCFVGGLRWATDDQSLQNAFSKYGDVIDSKIITDRETGRSRGFGFVTFASDEAMR 61

Query:   123 TALESLNGVELEGRAMRVSLAQGRRS 148
              A+E++NG +L+GR + V+ AQ RRS
Sbjct:    62 QAIEAMNGQDLDGRNITVNEAQSRRS 87

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

GO:0003723 "RNA binding" evidence=IDA

GO:0009409 "response to cold" evidence=IDA

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

ASPGD|ASPL0000076731 AN4865 [Emericella nidulans (taxid:162425)]

 Score = 172 (65.6 bits), Expect = 3.8e-12, P = 3.8e-12
 Identities = 33/78 (42%), Positives = 54/78 (69%)

Query:    69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
             LFVGNLSW+VT E L Q F+++G +  AR++ + ++GRSRG+G+V ++  A+   A E++
Sbjct:   279 LFVGNLSWNVTEEWLHQEFEQFGEL-SARIMTERDTGRSRGFGYVEFTNAADAAKAYEAM 337

Query:   129 NGVELEGRAMRVSLAQGR 146
                E++GR + +  A GR
Sbjct:   338 KEHEIDGRKINLDYATGR 355

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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:
	GSVIVG00020349001	SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (283 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00012366001	SubName- Full=Chromosome chr4 scaffold_373, whole genome shotgun sequence; (227 aa)			•						0.495
	GSVIVG00034829001	SubName- Full=Chromosome chr4 scaffold_73, whole genome shotgun sequence; (202 aa)			•						0.443
	GSVIVG00019496001	SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (206 aa)			•						0.437
	GSVIVG00006170001	SubName- Full=Chromosome undetermined scaffold_165, whole genome shotgun sequence; (209 aa)			•						0.400

---

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	148
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	4e-28
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	8e-27
smart00360	73	smart00360, RRM, RNA recognition motif	1e-25
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	9e-22
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-21
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-21
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-21
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-20
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	5e-20
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	8e-20
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-19
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-19
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-19
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	9e-19
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	9e-19
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-18
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-18
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	8e-18
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	8e-18
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	1e-17
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	5e-17
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-16
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-16
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	5e-16
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	7e-16
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	9e-16
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	9e-16
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-15
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-15
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-15
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-15
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-15
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-15
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	7e-15
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	9e-15
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	9e-15
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-14
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-14
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	2e-14
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-14
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-14
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	4e-14
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	5e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	5e-14
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-14
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	6e-14
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	7e-14
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	9e-14
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-13
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	1e-13
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-13
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-13
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-13
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	3e-13
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-13
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-13
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	5e-13
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-12
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-12
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-12
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-12
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-12
smart00360	73	smart00360, RRM, RNA recognition motif	3e-12
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-12
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	5e-12
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-12
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-12
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	9e-12
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	9e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-11
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	1e-11
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-11
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-11
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-11
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-11
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-11
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-11
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-11
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-11
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-11
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	3e-11
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	4e-11
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-11
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	4e-11
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	4e-11
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	5e-11
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	5e-11
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	6e-11
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	7e-11
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	7e-11
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	9e-11
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-10
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-10
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	1e-10
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-10
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-10
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	2e-10
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	2e-10
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-10
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-10
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-10
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	3e-10
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	3e-10
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	3e-10
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	3e-10
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	3e-10
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	4e-10
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	5e-10
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	7e-10
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	7e-10
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	8e-10
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	8e-10
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	9e-10
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-09
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-09
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	1e-09
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	1e-09
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-09
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	2e-09
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	2e-09
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-09
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	2e-09
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	3e-09
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	3e-09
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	3e-09
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-09
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	4e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-09
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	4e-09
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	4e-09
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	4e-09
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	4e-09
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	6e-09
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	6e-09
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	6e-09
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	6e-09
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	8e-09
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	9e-09
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	9e-09
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-08
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	1e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-08
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-08
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	2e-08
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-08
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-08
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-08
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	2e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-08
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-08
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-08
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	3e-08
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	4e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	4e-08
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	4e-08
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	5e-08
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	5e-08
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	5e-08
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	5e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	6e-08
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	6e-08
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	6e-08
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	7e-08
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	7e-08
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	7e-08
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	8e-08
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	9e-08
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-07
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-07
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-07
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	2e-07
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-07
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	2e-07
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-07
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-07
cd12600	72	cd12600, RRM2_SRSF4_like, RNA recognition motif 2	3e-07
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	4e-07
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	4e-07
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	4e-07
cd12626	77	cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in	4e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	6e-07
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	6e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	6e-07
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	6e-07
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	7e-07
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	8e-07
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	8e-07
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	9e-07
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-06
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	1e-06
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	1e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-06
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-06
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	2e-06
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	2e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-06
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-06
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	3e-06
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	3e-06
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	3e-06
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	3e-06
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	3e-06
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	4e-06
cd12625	77	cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in	4e-06
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	4e-06
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-06
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	5e-06
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	5e-06
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	5e-06
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	6e-06
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	6e-06
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	6e-06
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	6e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	7e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	7e-06
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	8e-06
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	8e-06
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	8e-06
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	8e-06
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	9e-06
cd12643	77	cd12643, RRM_CFIm68, RNA recognition motif of pre-	9e-06
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-05
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-05
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	1e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-05
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	1e-05
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	1e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-05
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	2e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	2e-05
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	2e-05
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	2e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-05
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	2e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	2e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-05
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	2e-05
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	2e-05
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	2e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-05
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	3e-05
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	3e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	3e-05
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	3e-05
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	3e-05
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	3e-05
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	3e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	4e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	4e-05
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	4e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	4e-05
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	4e-05
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	4e-05
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	5e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	5e-05
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	5e-05
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	6e-05
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	6e-05
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	6e-05
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	6e-05
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	7e-05
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	7e-05
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	8e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	1e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-04
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	1e-04
cd12644	90	cd12644, RRM_CFIm59, RNA recognition motif of pre-	1e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	1e-04
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-04
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	1e-04
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	1e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	1e-04
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	1e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	2e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	2e-04
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	2e-04
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	2e-04
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	2e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	2e-04
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	2e-04
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	2e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	3e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	3e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	3e-04
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	3e-04
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	3e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	3e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	4e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	4e-04
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	4e-04
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	4e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	4e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	5e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	6e-04
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	6e-04
cd12282	91	cd12282, RRM2_TatSF1_like, RNA recognition motif 2	6e-04
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	6e-04
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	7e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	7e-04
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	7e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	8e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.001
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	0.001
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.001
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.001
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	0.001
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.001
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	0.001
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	0.001
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	0.001
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	0.001
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.001
cd12764	72	cd12764, RRM2_SRSF4, RNA recognition motif 2 in ve	0.001
cd12627	77	cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in	0.001
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.001
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.001
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	0.001
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	0.001
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	0.001
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	0.002
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.002
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	0.002
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.002
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.002
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	0.002
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.002
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	0.002
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	0.002
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.002
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	0.003
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	0.003
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	0.003
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	0.003
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	0.003
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.003
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.003
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.003
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.003
cd12695	93	cd12695, RRM3_PTBP1, RNA recognition motif 3 in ve	0.003
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	0.004
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	0.004
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.004
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	0.004
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	0.004
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	0.004

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

 Score = 98.6 bits (246), Expect = 4e-28
 Identities = 37/76 (48%), Positives = 55/76 (72%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            LFVGNLSWSV  E L   F+++G VVGARV+ D E+GRSRG+G+V + +  + + A+E+
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 128 LNGVELEGRAMRVSLA 143
           ++G EL+GR + V  +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 95.4 bits (238), Expect = 8e-27
 Identities = 36/77 (46%), Positives = 49/77 (63%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L+VGNL ++VT E L   F ++G V  ARV+ D E+GRSRG+GFV   T  E   A+E 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 128 LNGVELEGRAMRVSLAQ 144
           LNG +  GR + V+ A+
Sbjct: 61  LNGTDFGGRTLTVNEAR 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|214636 smart00360, RRM, RNA recognition motif

 Score = 92.3 bits (230), Expect = 1e-25
 Identities = 32/73 (43%), Positives = 49/73 (67%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            LFVGNL    T E L + F ++G V   R++ D E+G+S+G+ FV + ++ + E ALE+
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 128 LNGVELEGRAMRV 140
           LNG EL+GR ++V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 89.6 bits (222), Expect = 9e-22
 Identities = 50/142 (35%), Positives = 77/142 (54%), Gaps = 8/142 (5%)

Query: 10  DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK-------LPLY 62
           DR + RS+G A+V    VE     +  L G+  LGR + V  S   K +        P  
Sbjct: 124 DRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGD 182

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
                KL+VGNL +++T + L Q F+ +G++   ++  D E+GRS+G+GF+ +    E +
Sbjct: 183 IPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAK 242

Query: 123 TALESLNGVELEGRAMRVSLAQ 144
            ALE +NG EL GR ++V  AQ
Sbjct: 243 EALEVMNGFELAGRPIKVGYAQ 264

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

 Score = 89.5 bits (222), Expect = 1e-21
 Identities = 52/154 (33%), Positives = 78/154 (50%), Gaps = 22/154 (14%)

Query: 12  ETGRSRGFAFVTMSTVEDCNAVIENLDGRE----------YLGR---------ILRVNFS 52
            +GRSRGFAFV     ED    +E ++G++          Y+GR          LR  F 
Sbjct: 214 GSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFE 273

Query: 53  DKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGF 112
           +  + +       +  L+V NL  +VT E L + F E G +  A+V+ D E G SRG+GF
Sbjct: 274 ELQQERKMKAQGVN--LYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGF 330

Query: 113 VCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
           VC+S   E   A+  ++G  L G+ + V+LAQ +
Sbjct: 331 VCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK 364

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

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

 Score = 80.7 bits (200), Expect = 3e-21
 Identities = 30/74 (40%), Positives = 44/74 (59%)

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           FVGN+ +  T E L + F E G VV  R++ D ++G+ +GYGF  +       +A+ +LN
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 130 GVELEGRAMRVSLA 143
           G E  GRA+RV  A
Sbjct: 62  GYEFNGRALRVDFA 75

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

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

 Score = 80.4 bits (199), Expect = 5e-21
 Identities = 31/73 (42%), Positives = 48/73 (65%), Gaps = 1/73 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFVGNL    T E L + F ++G +   R++ D + G+S+G+ FV + +  + E ALE+L
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 129 NGVELEGRAMRVS 141
           NG EL+GR ++VS
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 83.5 bits (205), Expect = 4e-20
 Identities = 44/113 (38%), Positives = 61/113 (53%), Gaps = 1/113 (0%)

Query: 35  ENLDGREYLGRILRVNFSDKPKPKLPL-YAETDFKLFVGNLSWSVTTESLTQAFQEYGNV 93
           +N   R Y        F     PK      E +  LFVGNL + VT E L + F+++G V
Sbjct: 83  QNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPV 142

Query: 94  VGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
              R++ D E+G+SRG+ FV + ++   E A+E LNG ELEGR +RV  AQ  
Sbjct: 143 KRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPA 195

Length = 306

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

 Score = 77.9 bits (192), Expect = 5e-20
 Identities = 31/72 (43%), Positives = 46/72 (63%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FVG+LS  VT  +L  AF  + +   ARV++D +SGRSRGYGFV + ++ + E A+  +
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 129 NGVELEGRAMRV 140
           NG  L  R +R 
Sbjct: 62  NGKWLGSRPIRC 73

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

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

 Score = 77.2 bits (191), Expect = 8e-20
 Identities = 32/71 (45%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFVGNL    T E L   F ++G +   R++ D E+GRS+G+ FV +  + + E ALE+L
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 129 NGVELEGRAMR 139
           NG EL GR +R
Sbjct: 60  NGKELGGRELR 70

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

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

 Score = 78.9 bits (194), Expect = 1e-19
 Identities = 37/81 (45%), Positives = 52/81 (64%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLF+G LSW     SL  AF  +G+VV A+V+ D E+GRSRG+GFV ++ +     A+  
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           ++G EL GR +RV+ A  R S
Sbjct: 96  MDGKELNGRHIRVNPANDRPS 116

Length = 144

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

 Score = 77.0 bits (190), Expect = 1e-19
 Identities = 33/71 (46%), Positives = 50/71 (70%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FVG+LS  + TE+L  AF  +G +  ARV+ D ++G+S+GYGFV +  K + E A++S+
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 129 NGVELEGRAMR 139
           NG  L GRA+R
Sbjct: 62  NGQWLGGRAIR 72

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

>gnl|CDD|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 = 76.0 bits (187), Expect = 4e-19
 Identities = 30/77 (38%), Positives = 47/77 (61%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLF+G LS+    +SL Q F +YG +    V+ D E+ RSRG+GFV +    + + A+ +
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 128 LNGVELEGRAMRVSLAQ 144
           +NG  ++GR +RV  A 
Sbjct: 62  MNGKSVDGRQIRVDQAG 78

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

 Score = 74.6 bits (184), Expect = 9e-19
 Identities = 29/73 (39%), Positives = 48/73 (65%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VGNL +++T + L   F+ +G +   ++  D E+GRS+GYGF+ ++   + + ALE L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 129 NGVELEGRAMRVS 141
           NG EL GR ++V 
Sbjct: 61  NGFELAGRPIKVG 73

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

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

 Score = 75.0 bits (185), Expect = 9e-19
 Identities = 35/79 (44%), Positives = 49/79 (62%), Gaps = 1/79 (1%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQE-YGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           D  +FVG+L+  VT   L + F+  Y +V GA+V+ D  +GRS+GYGFV +  + E + A
Sbjct: 1   DHSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60

Query: 125 LESLNGVELEGRAMRVSLA 143
           L  +NGV    R MRVS A
Sbjct: 61  LTEMNGVYCSSRPMRVSPA 79

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

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

 Score = 74.6 bits (184), Expect = 1e-18
 Identities = 30/76 (39%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG L +  T +SL + F ++G +  A V+ D ++G+SRGYGFV +  K   E A + 
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 128 LNGVELEGRAMRVSLA 143
            N + ++GR   V+LA
Sbjct: 62  PNPI-IDGRKANVNLA 76

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|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 = 74.2 bits (183), Expect = 2e-18
 Identities = 31/76 (40%), Positives = 45/76 (59%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFV  LS   T + L   F ++G V    ++ D E+G SRG+GFV + +  + + A+  
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 128 LNGVELEGRAMRVSLA 143
           LNG ELEGR ++V  A
Sbjct: 63  LNGKELEGRVIKVEKA 78

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

 Score = 72.3 bits (178), Expect = 8e-18
 Identities = 37/78 (47%), Positives = 50/78 (64%), Gaps = 2/78 (2%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFVGNLSWS   + L + F+E G VV  R+  D + GRS+G+G V ++T+   + ALE  
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALE-K 59

Query: 129 NGVELEGRAMRVSLAQGR 146
           +G EL GR +RV LA  R
Sbjct: 60  SGEELLGREIRVDLATER 77

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

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

 Score = 72.4 bits (178), Expect = 8e-18
 Identities = 30/72 (41%), Positives = 49/72 (68%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFVGNLS+    +S+ +AF EYG +   R+  D +SGR +G+G+V +S++   + AL++L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 129 NGVELEGRAMRV 140
            G +L GR +R+
Sbjct: 61  GGTDLLGRPVRL 72

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

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

 Score = 71.9 bits (177), Expect = 1e-17
 Identities = 29/78 (37%), Positives = 49/78 (62%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           E DF++FVG+L   VT E L +AF +Y +   A+V+ D  +G+S+GYGFV +S   +   
Sbjct: 4   ENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLK 63

Query: 124 ALESLNGVELEGRAMRVS 141
           A++ +NG  +  R +++ 
Sbjct: 64  AMKEMNGKYVGNRPIKLR 81

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

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

 Score = 70.3 bits (173), Expect = 5e-17
 Identities = 27/45 (60%), Positives = 32/45 (71%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
          V+ DRETGRSRGF FV M T E+ NA IE L+G ++ GR L VN 
Sbjct: 31 VITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNE 75

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

 Score = 74.2 bits (181), Expect = 1e-16
 Identities = 44/157 (28%), Positives = 68/157 (43%), Gaps = 19/157 (12%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS---DKPKPKLPLYA 63
           ++ DRETG+SRGFAFV   + E     IE L+G+E  GR LRV  +    +P+ +L    
Sbjct: 147 LVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNL 206

Query: 64  ETDFK----------------LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRS 107
           +  F                 L+VGNL      E L   F+  G++V A +    +    
Sbjct: 207 DASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIP 266

Query: 108 RGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ 144
           +   FV      +   +    N  ++ GR  R + +Q
Sbjct: 267 KSRSFVGNEASKDALESNSRGNKKKILGRGPRKAFSQ 303

Length = 306

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

 Score = 68.7 bits (168), Expect = 2e-16
 Identities = 33/75 (44%), Positives = 46/75 (61%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FVGN+ +  T E L   F E G VV  R++YD E+G+ +GYGF  Y  +    +A+ +L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 129 NGVELEGRAMRVSLA 143
           NG EL GR +RV  A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

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

 Score = 67.7 bits (166), Expect = 5e-16
 Identities = 31/72 (43%), Positives = 46/72 (63%), Gaps = 1/72 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FV NL +SVT + L   F+E GNV+ A V  D + GRS+G+G V + +  + + A+E  
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59

Query: 129 NGVELEGRAMRV 140
           NG +LEGR + V
Sbjct: 60  NGYDLEGRELEV 71

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

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

 Score = 67.6 bits (166), Expect = 7e-16
 Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 1/76 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++V NL   +  E L + F +YG +  A+V+ D + G+S+G+GFV +      + A+E L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 129 NGVELEGRAMRVSLAQ 144
           NG E+ G+ + V  AQ
Sbjct: 63  NGKEVNGKKLYVGRAQ 78

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

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

 Score = 67.2 bits (164), Expect = 9e-16
 Identities = 28/74 (37%), Positives = 41/74 (55%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V NL   +T + L + F+ YGN+V   +L D  +G  RG  FV Y  + E + A+ SL
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 129 NGVELEGRAMRVSL 142
           NG    G  M +S+
Sbjct: 63  NGTIPPGSTMPLSV 76

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

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

 Score = 67.3 bits (165), Expect = 9e-16
 Identities = 31/77 (40%), Positives = 48/77 (62%), Gaps = 1/77 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L+V NL  S+  E L + F  +G +  A+V+ D E GRS+G+GFVC+S+  E   A+  
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVTE 61

Query: 128 LNGVELEGRAMRVSLAQ 144
           +NG  + G+ + V+LAQ
Sbjct: 62  MNGRIIGGKPLYVALAQ 78

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

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

 Score = 66.1 bits (162), Expect = 2e-15
 Identities = 28/70 (40%), Positives = 44/70 (62%), Gaps = 4/70 (5%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES- 127
           LF+G LSW  T ESL + F +YG VV   ++ D  +GRSRG+GFV ++  + ++  L + 
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 128 ---LNGVELE 134
              L+G E++
Sbjct: 61  PHVLDGREID 70

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

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

 Score = 66.1 bits (162), Expect = 2e-15
 Identities = 29/76 (38%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
            +L V NL + VT E L + F   G V   ++ YD  SGRS G   V +  + + E A++
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIK 59

Query: 127 SLNGVELEGRAMRVSL 142
             NGV L+G+ M+V L
Sbjct: 60  QFNGVLLDGQPMQVEL 75

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

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

 Score = 66.3 bits (161), Expect = 2e-15
 Identities = 31/77 (40%), Positives = 49/77 (63%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           F +FVG+LS  +TT+ +  AF  +G +  ARV+ D  +G+S+GYGFV +  K + E A++
Sbjct: 2   FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61

Query: 127 SLNGVELEGRAMRVSLA 143
            + G  L GR +R + A
Sbjct: 62  QMGGQWLGGRQIRTNWA 78

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

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

 Score = 65.6 bits (161), Expect = 3e-15
 Identities = 28/72 (38%), Positives = 47/72 (65%), Gaps = 1/72 (1%)

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           FVGNL + +  E L + F++ G+V   R++ D ++G  +G+G+V + TK  +  AL  LN
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KLN 61

Query: 130 GVELEGRAMRVS 141
           G++L+GR +RV 
Sbjct: 62  GIKLKGRKIRVK 73

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

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

 Score = 70.4 bits (172), Expect = 3e-15
 Identities = 43/140 (30%), Positives = 73/140 (52%), Gaps = 7/140 (5%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           ++ D +TG S G+AFV   +  D    I+NL+G     + L+V+++      +      D
Sbjct: 139 IMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESI-----KD 193

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             L+V NL  ++T + L   F +YG +V   +L D  +G  RG  FV ++ + E + A+ 
Sbjct: 194 TNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAIS 253

Query: 127 SLNGVELEG--RAMRVSLAQ 144
           +LN V  EG  + + V LA+
Sbjct: 254 ALNNVIPEGGSQPLTVRLAE 273

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 70.2 bits (172), Expect = 6e-15
 Identities = 40/145 (27%), Positives = 74/145 (51%), Gaps = 4/145 (2%)

Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPL 61
           +  + V  D  T RS G+ +V      D    +E ++ +   G+ +R+ +S +  P L  
Sbjct: 27  VLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR-DPSLRR 85

Query: 62  YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEM 121
               +  +FV NL  SV  ++L   F ++GN++  +V  D E+G+SRGYGFV +  +   
Sbjct: 86  SGVGN--IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESA 142

Query: 122 ETALESLNGVELEGRAMRVSLAQGR 146
           + A++ +NG+ L  + + V     +
Sbjct: 143 KAAIQKVNGMLLNDKEVYVGRFIKK 167

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

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

 Score = 64.9 bits (159), Expect = 7e-15
 Identities = 25/78 (32%), Positives = 41/78 (52%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV NL +  T E L + F E G +    V+ D  S + RG+G+V ++ + + + ALE  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 129 NGVELEGRAMRVSLAQGR 146
              +  GR + V  A+ +
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

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

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

 Score = 64.7 bits (157), Expect = 9e-15
 Identities = 32/77 (41%), Positives = 48/77 (62%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           F +FVG+LS  +TTE +  AF  +G +  ARV+ D  +G+S+GYGFV +  K + E A+ 
Sbjct: 2   FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61

Query: 127 SLNGVELEGRAMRVSLA 143
            + G  L GR +R + A
Sbjct: 62  HMGGQWLGGRQIRTNWA 78

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

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

 Score = 64.5 bits (157), Expect = 9e-15
 Identities = 33/78 (42%), Positives = 48/78 (61%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV NL++SVT E LT  F +   +  A V+ D E+G SRGYGFV ++   + + AL  L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 129 NGVELEGRAMRVSLAQGR 146
              +L GR +R+ +A+ R
Sbjct: 62  KNKKLHGRILRLDIAERR 79

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

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

 Score = 64.2 bits (157), Expect = 1e-14
 Identities = 24/73 (32%), Positives = 44/73 (60%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LF+ +L    T + L Q F  +GNV+ A+V  D  +G+S+ +GFV Y      + A++++
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 129 NGVELEGRAMRVS 141
           NG ++ G+ ++V 
Sbjct: 61  NGFQVGGKRLKVQ 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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 64.2 bits (157), Expect = 1e-14
 Identities = 25/75 (33%), Positives = 45/75 (60%), Gaps = 3/75 (4%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLY---DGESGRSRGYGFVCYSTKAEMETAL 125
           L+VGNL+  VT E L Q F  +G +   ++++   + E  R+R  GFV +  +A+ E AL
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 126 ESLNGVELEGRAMRV 140
           + L+G ++ G  +++
Sbjct: 64  DELDGKDVMGYELKL 78

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

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

 Score = 63.4 bits (155), Expect = 2e-14
 Identities = 29/76 (38%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
            KL V NL + V+ + + + F E+G +  A V YD  SGRS G   V +  +A+   A++
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYD-RSGRSLGTADVVFERRADALKAMK 59

Query: 127 SLNGVELEGRAMRVSL 142
             NGV L+GR M++ L
Sbjct: 60  QYNGVPLDGRPMKIQL 75

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 67.9 bits (166), Expect = 3e-14
 Identities = 46/146 (31%), Positives = 71/146 (48%), Gaps = 19/146 (13%)

Query: 12  ETGRSRGFAFVTMSTVEDCNAVIENLDG------REYLGRILRVNFSDKPKPKLPLYAET 65
           E G+SRG+ FV     E   A I+ ++G        Y+GR ++     +  P        
Sbjct: 124 ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIK-KHEREAAP------LK 176

Query: 66  DF-KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
            F  L+V NL  SV  + L + F ++G +  A V+ D  SGRSRG+ FV +    +   A
Sbjct: 177 KFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKA 235

Query: 125 LESLNGVEL----EGRAMRVSLAQGR 146
           +E +NG ++    EG+ + V  AQ R
Sbjct: 236 VEEMNGKKIGLAKEGKKLYVGRAQKR 261

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

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

 Score = 63.3 bits (155), Expect = 3e-14
 Identities = 26/72 (36%), Positives = 41/72 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VG+L   VT   L + F   G V+  RV  D  + RS GY +V +   A+ E AL++L
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 129 NGVELEGRAMRV 140
           N   ++G+ +R+
Sbjct: 62  NFDVIKGKPIRI 73

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

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

 Score = 62.7 bits (153), Expect = 4e-14
 Identities = 31/73 (42%), Positives = 48/73 (65%), Gaps = 1/73 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFVGNL W+V ++ L + F ++G V    V +D E+G S+GYGFV +S++  +E AL+ 
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 128 LNGVELEGRAMRV 140
              + LEG  ++V
Sbjct: 61  QKHI-LEGNKLQV 72

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

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 62.7 bits (153), Expect = 5e-14
 Identities = 34/80 (42%), Positives = 51/80 (63%), Gaps = 3/80 (3%)

Query: 66  DFKLFVGNLSWSVTTESLTQAF-QEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           +F LFVG+L+  V    L + F + Y +  GA+V+ D ++G SRGYGFV +S ++E + A
Sbjct: 1   EFSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRA 59

Query: 125 LESLNG-VELEGRAMRVSLA 143
           L  + G   L G+ +RVSLA
Sbjct: 60  LTEMQGASGLGGKPIRVSLA 79

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score = 62.7 bits (153), Expect = 5e-14
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +L V NL +  T   L + F  +G V    +      G+ +G+ FV +++KA+ E A++ 
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRK-PDGKKKGFAFVQFTSKADAEKAIKG 59

Query: 128 LNGVELEGRAMRVSLA 143
           +NG +++GR + V  A
Sbjct: 60  VNGKKIKGRPVAVDWA 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|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 62.3 bits (152), Expect = 6e-14
 Identities = 30/72 (41%), Positives = 45/72 (62%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  LS   T   L + F  YG +   +V+YD ++GRSRG+GFV + +  + + A E L
Sbjct: 2   LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 129 NGVELEGRAMRV 140
           NG+E++GR +RV
Sbjct: 62  NGMEIDGRRIRV 73

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

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

 Score = 62.6 bits (153), Expect = 6e-14
 Identities = 28/80 (35%), Positives = 46/80 (57%), Gaps = 5/80 (6%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +F+ NL +  T E L + F ++G V  AR++ D  +G S+G  FV + TK   +  LE+ 
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 129 N-----GVELEGRAMRVSLA 143
           +     G+ L+GR + V+LA
Sbjct: 63  DNAEDSGLSLDGRRLIVTLA 82

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

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 62.5 bits (152), Expect = 7e-14
 Identities = 26/60 (43%), Positives = 35/60 (58%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFVG LSW  T E+L + F +YG VV   ++ D  + RSRG+GFV +     + T L  
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

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

 Score = 62.2 bits (152), Expect = 9e-14
 Identities = 29/76 (38%), Positives = 49/76 (64%), Gaps = 3/76 (3%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFVG L  + T E +   F+EYGN+    ++ D ++G+S+G  FV +S++ E + A+E+
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 128 LNG-VELEG--RAMRV 140
           L+G V + G  R ++V
Sbjct: 61  LHGKVTMPGASRPLQV 76

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|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 = 61.5 bits (150), Expect = 1e-13
 Identities = 22/48 (45%), Positives = 35/48 (72%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          + ++ ++ D ETG SRGF FVT  +VED +A I +L+G+E  GR+++V
Sbjct: 28 VEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKV 75

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

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

 Score = 61.2 bits (149), Expect = 1e-13
 Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           F LFVGNL +  T E L   F+  G     R+L D ++G+S+G  FV + T   M  AL 
Sbjct: 1   FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL- 59

Query: 127 SLNGVELEGRAMRV 140
            L+   L+GR + V
Sbjct: 60  KLHHTLLKGRKINV 73

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

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

 Score = 61.1 bits (149), Expect = 2e-13
 Identities = 29/75 (38%), Positives = 39/75 (52%), Gaps = 8/75 (10%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V NL  S T E L + F EYG V   + + D        Y FV +  + +   A+E +
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 129 NGVELEGRAMRVSLA 143
           NG ELEG  + VSLA
Sbjct: 56  NGKELEGSPIEVSLA 70

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

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

 Score = 60.8 bits (148), Expect = 3e-13
 Identities = 29/76 (38%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG L   VT E   + F ++G VV A+++ D ++GRSRG+GFV + +++ +E    S
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVF-S 59

Query: 128 LNGVELEGRAMRVSLA 143
              +EL G+ + V  A
Sbjct: 60  AGMLELGGKQVEVKRA 75

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

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

 Score = 60.6 bits (148), Expect = 3e-13
 Identities = 29/68 (42%), Positives = 43/68 (63%), Gaps = 2/68 (2%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V NL  SVT E L + F  YG V G R++ + +  R RG+ FV +++  + E AL+ L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 129 NGVELEGR 136
           NG+ L+GR
Sbjct: 59  NGLVLDGR 66

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

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

 Score = 60.4 bits (147), Expect = 3e-13
 Identities = 29/79 (36%), Positives = 42/79 (53%), Gaps = 3/79 (3%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDG---ESGRSRGYGFVCYSTKAEMETA 124
           +L++GNL   +T   L + F +YG +     L+       G+ RGY FV + TK E E A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 125 LESLNGVELEGRAMRVSLA 143
           L+SLNG    G+ + V  A
Sbjct: 61  LKSLNGKTALGKKLVVRWA 79

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

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

 Score = 60.0 bits (146), Expect = 4e-13
 Identities = 24/78 (30%), Positives = 45/78 (57%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
              ++V NL +S+T   L + F +YG VV   ++ D E+ +S+G  F+ +  + +    +
Sbjct: 1   KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60

Query: 126 ESLNGVELEGRAMRVSLA 143
           ++LN  EL GR ++ S+A
Sbjct: 61  KALNNKELFGRTLKCSIA 78

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

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

 Score = 60.3 bits (147), Expect = 5e-13
 Identities = 25/78 (32%), Positives = 48/78 (61%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV  L++  T   L + F+EYG +   R++ D ++G+ RGY F+ +  + +M+ A +  
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 129 NGVELEGRAMRVSLAQGR 146
           +G +++GR + V + +GR
Sbjct: 64  DGKKIDGRRVLVDVERGR 81

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

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

 Score = 60.2 bits (146), Expect = 5e-13
 Identities = 30/79 (37%), Positives = 46/79 (58%), Gaps = 1/79 (1%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQE-YGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           ++ +FVG+LS  V    L   FQ  + +   A+++ D  +G SRGYGFV +S + + + A
Sbjct: 1   EYSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRA 60

Query: 125 LESLNGVELEGRAMRVSLA 143
           L  + GV   GR MR+S A
Sbjct: 61  LIEMQGVYCGGRPMRISTA 79

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

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

 Score = 59.6 bits (144), Expect = 1e-12
 Identities = 26/74 (35%), Positives = 46/74 (62%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V  L  ++T + L Q F +YG ++ +R+L D  +G SRG GF+ +  + E E A++ L
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 129 NGVELEGRAMRVSL 142
           NG + EG +  +++
Sbjct: 63  NGQKPEGASEPITV 76

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 59.2 bits (144), Expect = 1e-12
 Identities = 24/67 (35%), Positives = 39/67 (58%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V  L  ++T + L   F  YG ++ +R+L D  +G SRG GF+ +  + E E A+++L
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 129 NGVELEG 135
           NG    G
Sbjct: 63  NGTIPPG 69

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

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

 Score = 59.0 bits (143), Expect = 2e-12
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFV  L +SVT E L + F+++G V   R L    SG+ +G  +V Y  ++    A+  
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVR-LVTNRSGKPKGLAYVEYENESSASQAVLK 62

Query: 128 LNGVELEGRAMRVSLA 143
           ++G E++ + + V+++
Sbjct: 63  MDGTEIKEKTISVAIS 78

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 58.4 bits (142), Expect = 2e-12
 Identities = 23/73 (31%), Positives = 42/73 (57%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VG L+  V  + L  AF  +G++   ++  D E+ + RG+ FV +    +   A++++
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 129 NGVELEGRAMRVS 141
           N  EL GR +RV+
Sbjct: 61  NESELFGRTIRVN 73

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

 Score = 58.4 bits (142), Expect = 2e-12
 Identities = 26/72 (36%), Positives = 39/72 (54%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L VGNL    T E   +    +G V    ++Y   +G S+GYGFV Y++KA    A   L
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 129 NGVELEGRAMRV 140
           +G ++ GR ++V
Sbjct: 62  DGKQIGGRKLQV 73

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

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

 Score = 57.6 bits (140), Expect = 3e-12
 Identities = 20/48 (41%), Positives = 32/48 (66%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          +  + ++ D+ETG+S+GFAFV   + ED    +E L+G+E  GR L+V
Sbjct: 26 VESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 62.3 bits (151), Expect = 3e-12
 Identities = 33/121 (27%), Positives = 64/121 (52%), Gaps = 5/121 (4%)

Query: 10  DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKL 69
           D+ TG+S G+ FV     ED    + +L+G     + ++V+++ +P       +     L
Sbjct: 38  DKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA-RPSSD----SIKGANL 92

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           +V  L  ++T   L   F  +G ++ +R+L D  +G S+G GF+ +  + E + A+++LN
Sbjct: 93  YVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLN 152

Query: 130 G 130
           G
Sbjct: 153 G 153

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

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 57.4 bits (139), Expect = 5e-12
 Identities = 25/72 (34%), Positives = 40/72 (55%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V  LS +     L Q F +YG VVGA+++ +  S  +R +GFV  ++  E    ++ L
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 129 NGVELEGRAMRV 140
           +  EL GR + V
Sbjct: 62  HRTELHGRVISV 73

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

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

 Score = 57.2 bits (139), Expect = 6e-12
 Identities = 25/51 (49%), Positives = 35/51 (68%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          + K+ V+YD++TGRSRGF FV   +VED     E L+G E  GR +RV++S
Sbjct: 26 IEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRVDYS 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 56.9 bits (138), Expect = 6e-12
 Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 8/73 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFVGNL  + T+E L   F++YG V    V+        + YGFV    + + E A+++
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKA 52

Query: 128 LNGVELEGRAMRV 140
           LNG E  G+ + V
Sbjct: 53  LNGYEFMGKRINV 65

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

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

 Score = 57.0 bits (138), Expect = 9e-12
 Identities = 27/76 (35%), Positives = 48/76 (63%), Gaps = 5/76 (6%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLF+G LS+  T +SL   F ++G +    V+ D  + RSRG+GFV +++ +E++ A+ +
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 128 ----LNGVELEG-RAM 138
               ++G E+E  RA+
Sbjct: 61  RPHKVDGREVEPKRAV 76

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 56.9 bits (138), Expect = 9e-12
 Identities = 22/72 (30%), Positives = 45/72 (62%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +++G L + +T   +   F +YG +V   ++ D ++G+S+G+ F+ Y  +     A+++L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 129 NGVELEGRAMRV 140
           NG++L GR +RV
Sbjct: 72  NGIKLLGRTIRV 83

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

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

 Score = 56.5 bits (137), Expect = 1e-11
 Identities = 18/49 (36%), Positives = 30/49 (61%)

Query: 4  KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
             ++ DR+TG+ +G+ F     +E   + I NL+G E+ GR LRV+F+
Sbjct: 27 SFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRALRVDFA 75

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

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 56.8 bits (137), Expect = 1e-11
 Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 5/81 (6%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGR-----SRGYGFVCYSTKAEMET 123
           LFV NL++S T + LT AF+     V ARV    +  R     S G+GFV + TK + + 
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 124 ALESLNGVELEGRAMRVSLAQ 144
           AL++++G  L+G  + V  + 
Sbjct: 63  ALKAMDGFVLDGHTLVVKFSH 83

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 56.5 bits (137), Expect = 1e-11
 Identities = 26/72 (36%), Positives = 44/72 (61%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V NL++  T + L + F++YG V    +  D  +  SRG+ FV +  K + E A++++
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 129 NGVELEGRAMRV 140
           +G EL+GR +RV
Sbjct: 61  DGKELDGRELRV 72

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

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

 Score = 56.6 bits (137), Expect = 1e-11
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFVGNL   VT E L + F + G + G ++  D   G+ + + FV +  +  +  A++ L
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 129 NGVELEGRAMRVS 141
           NG+ L GR +R+ 
Sbjct: 63  NGIRLFGRELRIK 75

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

>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 56.3 bits (136), Expect = 1e-11
 Identities = 22/59 (37%), Positives = 34/59 (57%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +F+G LSW  T E L + F ++G +    V+ D  + RSRG+GFV +S  A ++  L  
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQ 59

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

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

 Score = 59.8 bits (145), Expect = 2e-11
 Identities = 29/76 (38%), Positives = 44/76 (57%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VG+L   VT   L   F+ +G V+  RV  D  + RS GYG+V +   A+ E ALE++
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 129 NGVELEGRAMRVSLAQ 144
           N   L G+ +R+  +Q
Sbjct: 63  NFKRLGGKPIRIMWSQ 78

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

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

 Score = 56.1 bits (136), Expect = 2e-11
 Identities = 19/77 (24%), Positives = 42/77 (54%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
            +++V ++   ++ + +   F+ +G +    +  D E+G+ +GYGF+ Y      + A+ 
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 127 SLNGVELEGRAMRVSLA 143
           S+N  +L G+ +RV  A
Sbjct: 61  SMNLFDLGGQQLRVGKA 77

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

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 56.1 bits (136), Expect = 2e-11
 Identities = 23/62 (37%), Positives = 38/62 (61%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++G+L   +    +  AF E G V   +++ + ++G+S GYGFV ++T    E AL+SL
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 129 NG 130
           NG
Sbjct: 62  NG 63

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

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

 Score = 56.0 bits (136), Expect = 2e-11
 Identities = 24/51 (47%), Positives = 33/51 (64%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          +S++ +  D+ETG+SRGFAFVT  T ED    IE L+G  Y   IL V ++
Sbjct: 26 ISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGYDNLILSVEWA 76

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

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

 Score = 55.8 bits (135), Expect = 2e-11
 Identities = 25/75 (33%), Positives = 42/75 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L   +T E L   F+  G +   +++ D  +G+S GYGFV Y  + + + A+ +L
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 129 NGVELEGRAMRVSLA 143
           NG E+  + ++VS A
Sbjct: 63  NGFEIRNKRLKVSYA 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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 55.6 bits (134), Expect = 3e-11
 Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 4/71 (5%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE- 126
           KLFVG L+   +   L + F  YG +    V+ D  + RSRG+GF+ +S+  E + A+E 
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

Query: 127 ---SLNGVELE 134
              S++G ++E
Sbjct: 64  QPHSIDGNQIE 74

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

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

 Score = 55.8 bits (134), Expect = 3e-11
 Identities = 29/79 (36%), Positives = 47/79 (59%), Gaps = 1/79 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLF+G LS+  T ESL   F+++G +    V+ D  + RSRG+GFV YS+  E++ A+ +
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

Query: 128 LNGVELEGRAMRVSLAQGR 146
               +++GR +    A  R
Sbjct: 64  -RPHKVDGRVVEPKRAVSR 81

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

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

 Score = 55.3 bits (134), Expect = 4e-11
 Identities = 21/73 (28%), Positives = 39/73 (53%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L VG L+ +V  + L + F  YG V    +  D E    RGY +V + +  + E A++ +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 129 NGVELEGRAMRVS 141
           +G +++G+ + V 
Sbjct: 61  DGGQIDGQEVTVE 73

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

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

 Score = 55.0 bits (133), Expect = 4e-11
 Identities = 23/73 (31%), Positives = 38/73 (52%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFV NL ++ T E L + F+ +G +    +  D E+ RS+G+ FV +        A   
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 128 LNGVELEGRAMRV 140
           L+G   +GR + V
Sbjct: 61  LDGSIFQGRLLHV 73

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

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

 Score = 59.3 bits (143), Expect = 4e-11
 Identities = 33/138 (23%), Positives = 68/138 (49%), Gaps = 6/138 (4%)

Query: 9   YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF-SDKPKPK-----LPLY 62
           +D  TG+ +GFAFV     E     +E ++G+   GR ++V   S+ P+ +     +   
Sbjct: 141 WDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEE 200

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A+   +++V ++   ++   +   F+ +G +V  ++         +GYGF+ Y+      
Sbjct: 201 AKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS 260

Query: 123 TALESLNGVELEGRAMRV 140
            A+ S+N  +L G+ +RV
Sbjct: 261 EAIASMNLFDLGGQYLRV 278

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

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

 Score = 55.0 bits (133), Expect = 4e-11
 Identities = 27/74 (36%), Positives = 39/74 (52%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FV NL        L Q F  +G V   +V+ D  + + +GYGFV  +   E  +A+ SL
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 129 NGVELEGRAMRVSL 142
           NG  L GR ++VS 
Sbjct: 64  NGYRLGGRVLQVSF 77

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

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

 Score = 54.7 bits (132), Expect = 5e-11
 Identities = 28/74 (37%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FV NL + V  + L + F+  G VV A +  D E G+SRG G V +    E   A+   
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 129 NGVELEGRAMRVSL 142
           NG  L  R MRV +
Sbjct: 60  NGQMLFDRPMRVKM 73

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

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

 Score = 55.3 bits (134), Expect = 5e-11
 Identities = 25/79 (31%), Positives = 41/79 (51%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFVG LS   T E+L + F  YG++   R++ D  +G S+GY FV Y  + +   A    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 129 NGVELEGRAMRVSLAQGRR 147
           + + ++G  + V   + R 
Sbjct: 66  HKLVIDGSEIFVDFERERT 84

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

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

 Score = 54.9 bits (132), Expect = 6e-11
 Identities = 24/58 (41%), Positives = 35/58 (60%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           +FVG LSW  T + L + F ++G VV   +  D  +GRSRG+GFV +   A +E  L+
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLD 58

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

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

 Score = 54.4 bits (131), Expect = 7e-11
 Identities = 24/75 (32%), Positives = 42/75 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L  ++T + +   F   G +   +++ D  +G+S GYGFV Y    + E A+ +L
Sbjct: 4   LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 129 NGVELEGRAMRVSLA 143
           NG+ L+ + ++VS A
Sbjct: 64  NGLRLQNKTIKVSYA 78

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

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 54.2 bits (131), Expect = 7e-11
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++VGNL   +T E L + F  +G +   RV  D       GY FV + T     TA+ ++
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIVAV 56

Query: 129 NGVELEGRAMRVS 141
           NG  + G+ ++ S
Sbjct: 57  NGTSINGQTVKCS 69

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

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

 Score = 54.2 bits (130), Expect = 9e-11
 Identities = 29/70 (41%), Positives = 41/70 (58%)

Query: 71  VGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNG 130
           V  LS   T   L + F  YG + G  V+YD  +GRSRG+ FV +    + + A+E  NG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 131 VELEGRAMRV 140
           +EL+GR +RV
Sbjct: 64  MELDGRRIRV 73

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

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

 Score = 53.8 bits (130), Expect = 1e-10
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FV NL +SV  + L + F + G +   R++ +   G+S+GY +V +  +  ++ AL  L
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEFENEESVQEAL-KL 59

Query: 129 NGVELEGRAMRVS 141
           +   ++GR M VS
Sbjct: 60  DRELIKGRPMFVS 72

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

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

 Score = 53.8 bits (130), Expect = 1e-10
 Identities = 24/73 (32%), Positives = 44/73 (60%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++VGNL   VT E L + F + G VV   +  D  +   +GYGFV + ++ + + A++ +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 129 NGVELEGRAMRVS 141
           N ++L G+ +RV+
Sbjct: 61  NMIKLYGKPIRVN 73

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

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 54.0 bits (129), Expect = 1e-10
 Identities = 26/70 (37%), Positives = 42/70 (60%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D  L+V  L  ++T + L Q F +YG ++ +R+L D  +G SRG GF+ +  + E E A+
Sbjct: 5   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64

Query: 126 ESLNGVELEG 135
           + LNG +  G
Sbjct: 65  KGLNGQKPPG 74

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 53.6 bits (128), Expect = 2e-10
 Identities = 26/70 (37%), Positives = 42/70 (60%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D  L+V  L  ++T + L Q F +YG ++ +R+L D  +G SRG GF+ +  + E E A+
Sbjct: 2   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61

Query: 126 ESLNGVELEG 135
           + LNG +  G
Sbjct: 62  KGLNGQKPSG 71

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 53.9 bits (129), Expect = 2e-10
 Identities = 23/78 (29%), Positives = 44/78 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LF+ +L      + L Q F  +GNVV A+V  D ++  S+ +GFV Y      + A++++
Sbjct: 10  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 129 NGVELEGRAMRVSLAQGR 146
           NG ++  + ++V L + +
Sbjct: 70  NGFQIGMKRLKVQLKRSK 87

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

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

 Score = 52.9 bits (127), Expect = 2e-10
 Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 8/75 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVGN+S + T++ L   F+E+G VV        E  + + Y FV    + E   A+E+
Sbjct: 2   KIFVGNVSATCTSDELRGLFEEFGRVV--------ECDKVKDYAFVHMEREEEALAAIEA 53

Query: 128 LNGVELEGRAMRVSL 142
           LNG E++GR + V L
Sbjct: 54  LNGKEVKGRRINVEL 68

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 53.3 bits (128), Expect = 2e-10
 Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 68  KLFVGNLSWSVTT-ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           KL + NL WS+     L + F  YG V  A +      G+  G+ FV    +   E ALE
Sbjct: 2   KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKR-GGKLCGFAFVTMKKRKNAEIALE 60

Query: 127 SLNGVELEGRAMRVSLA 143
           + NG+E++GR + V  A
Sbjct: 61  NTNGLEIDGRPVAVDWA 77

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

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

 Score = 53.0 bits (128), Expect = 2e-10
 Identities = 22/46 (47%), Positives = 29/46 (63%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFV 113
           KLFVG L   VT E L + F +YGNV    ++ D E+G+ RG+ FV
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFV 46

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

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

 Score = 53.1 bits (128), Expect = 2e-10
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           FVGN+ +  T E L + F+  G +    +L D  +G+ +G+ ++ +  K+ +E AL  LN
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LLN 61

Query: 130 GVELEGRAMRVS 141
             E  GR ++V+
Sbjct: 62  ESEFRGRQIKVT 73

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

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

 Score = 52.6 bits (127), Expect = 3e-10
 Identities = 20/41 (48%), Positives = 25/41 (60%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
          D ET + RGFAFV     ED  A I+N++  E  GR +RVN
Sbjct: 33 DYETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGRTIRVN 73

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

 Score = 53.5 bits (128), Expect = 3e-10
 Identities = 28/75 (37%), Positives = 42/75 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  LS   T   L + F +YG +    ++YD +S RSRG+ FV +    + + A E  
Sbjct: 12  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 71

Query: 129 NGVELEGRAMRVSLA 143
           NG+EL+GR +RV  +
Sbjct: 72  NGMELDGRRIRVDFS 86

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

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

 Score = 53.2 bits (127), Expect = 3e-10
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           KLF+G LS+  T +SL + F+++G +    V+ D ++ RSRG+GFV YS   E++ A+
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61

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

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

 Score = 53.0 bits (128), Expect = 3e-10
 Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KL V N+ +  T + L + F  +G V   R L     G  RG+ FV + TK E + A+E+
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVR-LPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 128 LNGVELEGR 136
           L    L GR
Sbjct: 61  LKSTHLYGR 69

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

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

 Score = 52.7 bits (126), Expect = 3e-10
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D  LFVGNL   V  E L + F + G +    +  D E G+ + +GFVC+     +  A+
Sbjct: 1   DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAI 59

Query: 126 ESLNGVELEGRAMRVS 141
             LNG+ L GR ++V 
Sbjct: 60  ALLNGIRLYGRPIKVH 75

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

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

 Score = 52.8 bits (126), Expect = 3e-10
 Identities = 24/60 (40%), Positives = 38/60 (63%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLF+G LS+  T ESL   ++++G +    V+ D  S RSRG+GFV +S   E++ A+ +
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 52.3 bits (125), Expect = 4e-10
 Identities = 22/59 (37%), Positives = 34/59 (57%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           K+FVG LSW  + + L   F ++G V    +  D  +GRSRG+GF+ +   + +E  LE
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLE 59

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 52.2 bits (125), Expect = 5e-10
 Identities = 19/47 (40%), Positives = 31/47 (65%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           +F+G L+W  T +SL + F ++G V    V+ D  +GRSRG+GF+ +
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTF 47

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

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

 Score = 51.9 bits (125), Expect = 7e-10
 Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGA-RVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           LF+GNL   V  + L   F  +G ++   +++ D ++G S+G+ F+ Y +    + A+E+
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 128 LNGVELEGRAMRVSLA 143
           +NG  L  R + VS A
Sbjct: 64  MNGQYLCNRPITVSYA 79

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

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

 Score = 52.0 bits (124), Expect = 7e-10
 Identities = 27/76 (35%), Positives = 43/76 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L  ++T + L   F   G V  A+++ D  +G S GYGFV Y    + E A+ +L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 129 NGVELEGRAMRVSLAQ 144
           NG+ L+ + ++VS A+
Sbjct: 64  NGLRLQSKTIKVSYAR 79

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

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 51.8 bits (124), Expect = 8e-10
 Identities = 21/72 (29%), Positives = 41/72 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LF+ +L        L Q F  +GNV+ A+V  D  + +S+ +GFV +   A  + A++++
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 129 NGVELEGRAMRV 140
           NG ++  + ++V
Sbjct: 67  NGFQIGMKRLKV 78

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

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

 Score = 51.9 bits (124), Expect = 8e-10
 Identities = 22/72 (30%), Positives = 41/72 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LF+ +L    T   L Q F  +GNV+ A+V  D ++  S+ +GFV Y      + A++++
Sbjct: 7   LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 129 NGVELEGRAMRV 140
           NG ++  + ++V
Sbjct: 67  NGFQIGTKRLKV 78

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 51.5 bits (123), Expect = 9e-10
 Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 1/69 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+F+G LSW  + + LT+    +G V+   +  D  +GRSRG+GFV +   A ++  LE 
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLE- 59

Query: 128 LNGVELEGR 136
           L   +L+G+
Sbjct: 60  LKEHKLDGK 68

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

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

 Score = 51.2 bits (123), Expect = 1e-09
 Identities = 24/46 (52%), Positives = 31/46 (67%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          V+ DRETGRSRGF +V   + ED    IE +DG+E  GR + V+FS
Sbjct: 31 VITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76

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

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

 Score = 54.6 bits (131), Expect = 1e-09
 Identities = 26/85 (30%), Positives = 41/85 (48%)

Query: 57  PKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYS 116
            ++       + +FV NLS       L Q F  +G V   +++ D  + + +GYGFV  +
Sbjct: 260 AQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMT 319

Query: 117 TKAEMETALESLNGVELEGRAMRVS 141
              E   A+ SLNG  L  R ++VS
Sbjct: 320 NYDEAAMAILSLNGYTLGNRVLQVS 344

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

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

 Score = 51.4 bits (123), Expect = 1e-09
 Identities = 29/75 (38%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VGNL   VT + L Q FQ  G V   +++ D ++ +   YGFV Y    + E AL++L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 129 NGVELEGRAMRVSLA 143
           NG ++E   +RV+ A
Sbjct: 60  NGRQIENNEIRVNWA 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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 52.2 bits (125), Expect = 1e-09
 Identities = 24/60 (40%), Positives = 34/60 (56%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           DF LFV NL +  T ESL   F ++G+V  A  + D  +GR++G GFVC+  +      L
Sbjct: 1   DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

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

 Score = 51.0 bits (123), Expect = 1e-09
 Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +F+ NL  S+  ++L   F  +GN++  +V  D E+G S+GYGFV + T+     A+E +
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 129 NGVELEGRAMRV 140
           NG+ L  + + V
Sbjct: 64  NGMLLNDKKVFV 75

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

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 51.0 bits (122), Expect = 2e-09
 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 4/72 (5%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV NL +++T + L + F+   + V  R+   G+ G S+G  ++ + T+AE E ALE  
Sbjct: 6   LFVKNLPYNITVDELKEVFE---DAVDIRLPS-GKDGSSKGIAYIEFKTEAEAEKALEEK 61

Query: 129 NGVELEGRAMRV 140
            G E++GR++ V
Sbjct: 62  QGAEVDGRSIVV 73

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 51.2 bits (122), Expect = 2e-09
 Identities = 23/65 (35%), Positives = 40/65 (61%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D  L+V  L  +++ + + Q F +YG ++ +R+L D  +G SRG GF+ +  + E E A+
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60

Query: 126 ESLNG 130
           + LNG
Sbjct: 61  KGLNG 65

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 50.9 bits (121), Expect = 2e-09
 Identities = 26/76 (34%), Positives = 43/76 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L  ++T E L   F   G +   +++ D  +G+S GYGFV Y    + E A+ +L
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 129 NGVELEGRAMRVSLAQ 144
           NG+ L+ + ++VS A+
Sbjct: 67  NGLRLQTKTIKVSYAR 82

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 50.4 bits (120), Expect = 2e-09
 Identities = 23/58 (39%), Positives = 35/58 (60%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           K+F+G LSW  T E L + F ++G V    V+ D  + RSRG+GFV +  +A ++  L
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 50.7 bits (121), Expect = 3e-09
 Identities = 23/51 (45%), Positives = 35/51 (68%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          L+ + V+YD+ TGRSRGFAFV    ++D    +E+ +G E  GR +RV++S
Sbjct: 26 LAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRVDYS 76

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

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 50.5 bits (120), Expect = 3e-09
 Identities = 21/58 (36%), Positives = 35/58 (60%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           K+F+G LSW  + +SL   F ++G +    V+ D  + RSRG+GFV ++  A ++  L
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVL 58

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

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

 Score = 50.1 bits (120), Expect = 3e-09
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 4/71 (5%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL-- 125
           K+FVG L  +VT   L + F ++G V    V+YD E  R RG+GF+ + ++  ++  +  
Sbjct: 4   KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE 63

Query: 126 --ESLNGVELE 134
               +NG ++E
Sbjct: 64  HFHDINGKKVE 74

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

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

 Score = 50.3 bits (121), Expect = 3e-09
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++FVG +    T E L   F  +G+V   +++ D  +G S+GYGFV + T+ + E  L  
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62

Query: 128 LNGVELEGRAMRVSLA 143
            N +   G+ + +  A
Sbjct: 63  GN-LNFRGKKLNIGPA 77

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

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

 Score = 51.6 bits (123), Expect = 4e-09
 Identities = 25/55 (45%), Positives = 33/55 (60%), Gaps = 1/55 (1%)

Query: 6   TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
            V+ DRETGRSRGF FV  +      A I  +DG+E  GR +RVN ++  +P  P
Sbjct: 65  KVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAND-RPSAP 118

Length = 144

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

 Score = 49.9 bits (120), Expect = 4e-09
 Identities = 17/46 (36%), Positives = 27/46 (58%)

Query: 5  LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
          + +  D ETGRS+G+ F+  +  ED    +E L+G E  GR ++V 
Sbjct: 28 VQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKVG 73

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

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

 Score = 49.9 bits (120), Expect = 4e-09
 Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARV-----LYDGESGRSRGYGFVCYSTKAEMET 123
           LFV NL++  T E+L + F++ G V    +             S GYGFV + +K   + 
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 124 ALESLNGVELEGRAMRVSL 142
           AL+ L G  L+G A+ + L
Sbjct: 63  ALKRLQGTVLDGHALELKL 81

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

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

 Score = 49.6 bits (119), Expect = 4e-09
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 3/75 (4%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VGNL  +VT + L + F + G +   +++ +        Y FV Y        AL+++
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE-HGNDP--YAFVEYYDHRSAAAALQTM 57

Query: 129 NGVELEGRAMRVSLA 143
           NG  + G+ ++V+ A
Sbjct: 58  NGRLILGQEIKVNWA 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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 49.8 bits (119), Expect = 4e-09
 Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 8/76 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVGN+    + E L   F+ YG V+   V+        R + FV    +A  + A+E 
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEE 53

Query: 128 LNGVELEGRAMRVSLA 143
           LNG EL GR + V  +
Sbjct: 54  LNGRELHGRKLVVEHS 69

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|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 50.1 bits (120), Expect = 4e-09
 Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D KLFVG LS   T + + + F+ +G +    +L  G  G S+G  FV +S+ AE + A+
Sbjct: 1   DRKLFVGMLSKQQTEDDVRRLFEPFGTIEECTIL-RGPDGNSKGCAFVKFSSHAEAQAAI 59

Query: 126 ESLNG 130
            +L+G
Sbjct: 60  NALHG 64

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 49.6 bits (118), Expect = 6e-09
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 4/66 (6%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES- 127
           +F+G LSW  T + L   F ++G VV   +  D  +GRSRG+GFV +     ++  ++  
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 128 ---LNG 130
              LNG
Sbjct: 61  EHKLNG 66

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 49.6 bits (118), Expect = 6e-09
 Identities = 21/74 (28%), Positives = 42/74 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++  L  ++T + +   F  +G ++ +RVL D  +G SRG  F+ +  ++E E A+ S 
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 129 NGVELEGRAMRVSL 142
           NG +  G +  +++
Sbjct: 63  NGHKPPGSSEPITV 76

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

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

 Score = 49.2 bits (118), Expect = 6e-09
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFVGNL   +T E   + F +YG V  + V  + E    +G+GF+   T+   E A   
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEV--SEVFLNKE----KGFGFIRLDTRTNAEKAKAE 56

Query: 128 LNGVELEGRAMRV 140
           L+G+  +GR +RV
Sbjct: 57  LDGIMRKGRQLRV 69

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

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 49.3 bits (117), Expect = 6e-09
 Identities = 28/72 (38%), Positives = 38/72 (52%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V  LS +     L   F +YG VVGA+V+ +  S  +R YGFV  ST  E    +  L
Sbjct: 4   LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63

Query: 129 NGVELEGRAMRV 140
           +  EL GR + V
Sbjct: 64  HRTELHGRMISV 75

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

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

 Score = 49.1 bits (117), Expect = 8e-09
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V NLS+S + +SL + F++       R+  +  +GR +GY FV + +  + + AL S 
Sbjct: 4   LVVNNLSYSASEDSLQEVFEK---ATSIRIPQN--NGRPKGYAFVEFESAEDAKEALNSC 58

Query: 129 NGVELEGRAMRVSL 142
           N  E+EGR++R+  
Sbjct: 59  NNTEIEGRSIRLEF 72

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 49.3 bits (118), Expect = 9e-09
 Identities = 21/60 (35%), Positives = 34/60 (56%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFVGNL   +T + L + F+E+GNV+  R+   G  GR   +GFV +     ++  L +
Sbjct: 5   QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

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

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

 Score = 48.9 bits (116), Expect = 9e-09
 Identities = 21/59 (35%), Positives = 35/59 (59%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           K+FVG LS +   E + Q F+++G V  A +++D  + R RG+GFV +  +  +E   E
Sbjct: 5   KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 49.3 bits (117), Expect = 1e-08
 Identities = 24/76 (31%), Positives = 43/76 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L  ++T E     F   G +   +++ D  +G+S GYGFV Y    + + A+ +L
Sbjct: 6   LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 129 NGVELEGRAMRVSLAQ 144
           NG++L+ + ++VS A+
Sbjct: 66  NGLKLQTKTIKVSYAR 81

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 48.9 bits (116), Expect = 1e-08
 Identities = 22/59 (37%), Positives = 37/59 (62%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           K+FVG LS + T E + Q F+++G V  A +++D  + R RG+GFV + ++  +E   E
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

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

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

 Score = 48.6 bits (116), Expect = 1e-08
 Identities = 24/76 (31%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +L V N+ +      L Q F ++G ++   ++++ E G S+G+GFV ++  A+ + A E 
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFN-ERG-SKGFGFVTFANSADADRAREK 59

Query: 128 LNGVELEGRAMRVSLA 143
           L+G  +EGR + V+ A
Sbjct: 60  LHGTVVEGRKIEVNNA 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|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 48.8 bits (117), Expect = 1e-08
 Identities = 24/75 (32%), Positives = 37/75 (49%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FV  +      E +   F E+G +    +  D  +G  +GY  + Y TK E + A+E L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 129 NGVELEGRAMRVSLA 143
           NG EL G+ + V  A
Sbjct: 69  NGKELLGQTISVDWA 83

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

>gnl|CDD|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 = 48.3 bits (115), Expect = 2e-08
 Identities = 21/53 (39%), Positives = 33/53 (62%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
          +S++ V+ DRET RSRGF FVT    +D    +  ++G+   GR +RV+ + K
Sbjct: 27 ISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQAGK 79

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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 48.1 bits (115), Expect = 2e-08
 Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           F  FVGNL ++     L   F++  +V   R++ D E+ + +G+ +V +     ++ ALE
Sbjct: 2   FTAFVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE 60

Query: 127 SLNGVELEGRAMRVSLA 143
             +G   + R++RV +A
Sbjct: 61  -YDGALFDDRSLRVDIA 76

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 48.0 bits (114), Expect = 2e-08
 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D  LFVGNL   VT E + + F + G V+  ++  D + G+ + + FV +  +  +  A+
Sbjct: 1   DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKD-GKPKQFAFVNFKHEVSVPYAM 59

Query: 126 ESLNGVELEGRAMRV 140
             LNG++L GR + +
Sbjct: 60  NLLNGIKLYGRPLNI 74

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

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 48.4 bits (115), Expect = 2e-08
 Identities = 22/62 (35%), Positives = 40/62 (64%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFVG++  ++T + +   F+E+GNV+   ++ D  +G  +G  FV YST+ E + A+ +
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 128 LN 129
           L+
Sbjct: 61  LH 62

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 48.2 bits (115), Expect = 2e-08
 Identities = 22/73 (30%), Positives = 44/73 (60%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +++VG++S+ +  +++ QAF  +G +    + +D  + + +G+ FV Y      + ALE 
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 128 LNGVELEGRAMRV 140
           +NGV L GR ++V
Sbjct: 62  MNGVMLGGRNIKV 74

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

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

 Score = 48.0 bits (115), Expect = 2e-08
 Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 4/78 (5%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSR---GYGFVCYSTKAEMETA 124
           +++V NL + +  + L   F ++G V   R+    +  + R   G+ FV +   +  E A
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 125 LESLNGVELEGRAMRVSL 142
           L+ LNG EL GR + VSL
Sbjct: 62  LQ-LNGTELGGRKISVSL 78

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 48.2 bits (115), Expect = 2e-08
 Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 7/83 (8%)

Query: 69  LFVGNLSWSVTTESLTQA----FQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           +FV +L  S + + L  A    F +YG +V  +VL D    R R Y FV ++   + + A
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDW---RQRPYAFVQFTNDDDAKNA 61

Query: 125 LESLNGVELEGRAMRVSLAQGRR 147
           L    G  L+GR +R   A+  R
Sbjct: 62  LAKGQGTILDGRHIRCERAKVNR 84

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

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

 Score = 47.9 bits (115), Expect = 2e-08
 Identities = 19/46 (41%), Positives = 29/46 (63%), Gaps = 3/46 (6%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIE---NLDGREYLGRILRVNFS 52
          D+ TG SRGFAFV   ++ED    ++   NLD     GR++RV+++
Sbjct: 39 DKLTGTSRGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVVRVSYA 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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 47.8 bits (114), Expect = 2e-08
 Identities = 18/48 (37%), Positives = 32/48 (66%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           K+FVG LS + T + + + F ++G V  A +++D ++ R RG+GFV +
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48

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

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

 Score = 47.7 bits (114), Expect = 3e-08
 Identities = 17/43 (39%), Positives = 27/43 (62%)

Query: 8  LYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
          +   + G+S+GFAFV   + ED    +E L+G+E  GR L+V+
Sbjct: 30 IVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 47.8 bits (113), Expect = 3e-08
 Identities = 26/79 (32%), Positives = 40/79 (50%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FV NLS       L Q F  +G V   +V+ D  + + +G+GFV  +   E   A+ SL
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 129 NGVELEGRAMRVSLAQGRR 147
           NG  L  R ++VS    ++
Sbjct: 64  NGYRLGDRVLQVSFKTSKQ 82

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 47.3 bits (113), Expect = 4e-08
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 6/78 (7%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++G+LS  VT E L   F+EYG +    ++        RG  +VC  T+ +   AL+ L
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRALQKL 58

Query: 129 NGVELEGRAMRVSLAQGR 146
             V+L G+ ++V+ A  +
Sbjct: 59  RNVKLAGKKIKVAWAPNK 76

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

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 47.8 bits (113), Expect = 4e-08
 Identities = 25/76 (32%), Positives = 42/76 (55%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L  ++T E     F   G +   +++ D  +G+S GYGFV Y    + E A+ +L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 129 NGVELEGRAMRVSLAQ 144
           NG+ L+ + ++VS A+
Sbjct: 65  NGLRLQTKTIKVSYAR 80

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 47.8 bits (113), Expect = 4e-08
 Identities = 26/82 (31%), Positives = 41/82 (50%)

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           T + +FV NL+       L Q F  +G V   +V+ D  + + +G+GFV  +   E   A
Sbjct: 2   TGWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMA 61

Query: 125 LESLNGVELEGRAMRVSLAQGR 146
           + SLNG  L  R ++VS    +
Sbjct: 62  IASLNGYRLGDRVLQVSFKTNK 83

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

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

 Score = 46.8 bits (112), Expect = 5e-08
 Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 4/40 (10%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIE----NLDGRE 41
           ++ D  TGRSRGF FVT +     + V+      LDGRE
Sbjct: 29 VIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLDGRE 68

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

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

 Score = 47.0 bits (112), Expect = 5e-08
 Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 3/78 (3%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARV-LYDGESGRSRGYGFVCYSTKAEMETAL 125
           +  ++GNL + VT E + + F+   NV   R+    G+ GR RG+G+  +  +  +  AL
Sbjct: 2   YTAYLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQAL 60

Query: 126 ESLNGVELEGRAMRVSLA 143
            SLN   L+ R +RV +A
Sbjct: 61  -SLNDESLKNRRIRVDIA 77

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

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

 Score = 47.1 bits (112), Expect = 5e-08
 Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 3/76 (3%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFVGNLS+  T + L   F   G +   R++   +SG+ +G+ FV +    E+E A  +L
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFE---EIEFATNAL 57

Query: 129 NGVELEGRAMRVSLAQ 144
            G  L GRA+RV   +
Sbjct: 58  KGKHLNGRALRVEYGE 73

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

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

 Score = 47.0 bits (112), Expect = 5e-08
 Identities = 23/79 (29%), Positives = 40/79 (50%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V N++ +   + L + F +YG +V   +  D  + R RG+ +V +    + E AL  L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 129 NGVELEGRAMRVSLAQGRR 147
           +     GR + +  AQG R
Sbjct: 63  DRTRFLGREIEIQFAQGDR 81

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 49.9 bits (119), Expect = 6e-08
 Identities = 27/81 (33%), Positives = 45/81 (55%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           E+   L V  L  ++T E +   F   G +   +++ D  +G+S GYGFV Y    + E 
Sbjct: 1   ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 124 ALESLNGVELEGRAMRVSLAQ 144
           A+ SLNG+ L+ + ++VS A+
Sbjct: 61  AVNSLNGLRLQNKTIKVSYAR 81

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

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

 Score = 46.9 bits (112), Expect = 6e-08
 Identities = 19/48 (39%), Positives = 28/48 (58%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          +S++ +  D+ET RS+GFAFV+    E        LDG  + GR+L V
Sbjct: 26 ISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLLHV 73

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

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

 Score = 46.8 bits (111), Expect = 6e-08
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFVGNL    T + +   F++YG V+   ++        + YGFV    K   + A+ +
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRN 53

Query: 128 LNGVELEGRAMRV 140
           L+  +L G A+ V
Sbjct: 54  LHHYKLHGVAINV 66

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

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

 Score = 46.6 bits (111), Expect = 6e-08
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L V  L W  T + L   F  +G ++  +V  D ++G+S+G+GFV +   A+ E  ++ 
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRF---ADYEDQVKV 57

Query: 128 LNGVE-LEGRAMRVSLA 143
           L+    ++GR   V + 
Sbjct: 58  LSQRHMIDGRWCDVKIP 74

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

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

 Score = 46.4 bits (111), Expect = 7e-08
 Identities = 22/60 (36%), Positives = 35/60 (58%)

Query: 71  VGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNG 130
           V NLS     + L + F+ +G +    +  D E+G+SRG+ FV + T+ + E A+E LNG
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

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

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

 Score = 50.1 bits (119), Expect = 7e-08
 Identities = 21/77 (27%), Positives = 44/77 (57%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +++VG++S+ +  +++ +AF  +G +    + +D  +G+ +G+ FV Y      + ALE 
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168

Query: 128 LNGVELEGRAMRVSLAQ 144
           +NG  L GR ++V    
Sbjct: 169 MNGQMLGGRNIKVGRPS 185

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

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

 Score = 47.0 bits (111), Expect = 7e-08
 Identities = 27/82 (32%), Positives = 41/82 (50%)

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           T + +FV NLS       L Q F  +G V   +V+ D  + + +G+GFV  +   E   A
Sbjct: 2   TGWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMA 61

Query: 125 LESLNGVELEGRAMRVSLAQGR 146
           + SLNG  L  R ++VS    +
Sbjct: 62  IASLNGYRLGDRVLQVSFKTNK 83

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

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

 Score = 46.5 bits (111), Expect = 8e-08
 Identities = 19/76 (25%), Positives = 40/76 (52%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+F+G L   ++ + + +  + +G +    ++ D  +G S+GY F  Y   +  + A+  
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 128 LNGVELEGRAMRVSLA 143
           LNG++L  + + V  A
Sbjct: 62  LNGMQLGDKKLTVQRA 77

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

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

 Score = 47.0 bits (111), Expect = 9e-08
 Identities = 21/51 (41%), Positives = 34/51 (66%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          ++ ++++YD+++ RSRGFAFV    V+D     E  +G E  GR +RV+FS
Sbjct: 36 IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 86

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

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

 Score = 46.4 bits (110), Expect = 1e-07
 Identities = 26/64 (40%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFVG L+   T + + + F  YG V    ++ D E  +SRG  FV YS+K   + A+++
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKA 59

Query: 128 LNGV 131
           LNGV
Sbjct: 60  LNGV 63

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

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

 Score = 45.6 bits (109), Expect = 1e-07
 Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 5/57 (8%)

Query: 87  FQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
           F  +GNV   ++L         G+ FV +ST+   E A++ LNGV   GR +RV  +
Sbjct: 5   FSPFGNVEKIKLLKK-----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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 45.7 bits (109), Expect = 2e-07
 Identities = 20/37 (54%), Positives = 24/37 (64%)

Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR 48
          ETGRS+GFAFV     ED    +E L+G+E  GR LR
Sbjct: 34 ETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRELR 70

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

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

 Score = 45.6 bits (109), Expect = 2e-07
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTK-AEMETALES 127
           LFVG LS SVT   L + F  +G V    ++   ++G  RG+ ++   T  A+++    +
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 128 LNGVELEGRAMRVSLAQ 144
           LNG + +G  +++  A+
Sbjct: 62  LNGTKWKGSVLKIEEAK 78

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

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

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           + +FVG LS  VT E L + F  +G ++   ++       +  + F+ +  +     A+E
Sbjct: 4   YSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVE 61

Query: 127 SLNGVELEGRAMRV 140
           S N   L+ + M V
Sbjct: 62  SENHSMLKNKTMHV 75

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

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 46.1 bits (109), Expect = 2e-07
 Identities = 26/79 (32%), Positives = 41/79 (51%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV N++    +E L + F  YG +V   V  D  + R RG+ +V +    + E AL +L
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 129 NGVELEGRAMRVSLAQGRR 147
           +   + GR + +  AQG R
Sbjct: 63  DRKWICGRQIEIQFAQGDR 81

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 45.7 bits (109), Expect = 2e-07
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 4/77 (5%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGE---SGRSRGYGFVCYSTKAEMETAL 125
           L+VGNL+W  T E L  A  E G VV  + +   E   +G+S+G+ +V ++++A      
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAG-VVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVK 59

Query: 126 ESLNGVELEGRAMRVSL 142
           E L G E  G+   V+ 
Sbjct: 60  EKLEGREFNGKKCVVTY 76

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

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

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 26/79 (32%), Positives = 41/79 (51%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV N++ +   E L + F  YG +V   V  D  + R RG+ ++ +    + E AL +L
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 129 NGVELEGRAMRVSLAQGRR 147
           N   + GR + +  AQG R
Sbjct: 63  NRKWVCGRQIEIQFAQGDR 81

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|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 45.4 bits (107), Expect = 2e-07
 Identities = 24/76 (31%), Positives = 46/76 (60%), Gaps = 3/76 (3%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV  LS   T E+L ++F      + AR++ D ++G S+G+GFV +S++ + + A E++
Sbjct: 3   LFVKGLSEDTTEETLKESFD---GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 129 NGVELEGRAMRVSLAQ 144
              E++G  + +  A+
Sbjct: 60  EDGEIDGNKVTLDFAK 75

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

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

 Score = 45.7 bits (109), Expect = 2e-07
 Identities = 23/76 (30%), Positives = 38/76 (50%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV  L+   T E L   F  +G +    V+ D ++G S  Y F+ + TK + E A   +
Sbjct: 6   LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKM 65

Query: 129 NGVELEGRAMRVSLAQ 144
           + V ++ R + V  +Q
Sbjct: 66  DNVLIDDRRIHVDFSQ 81

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

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

 Score = 45.5 bits (108), Expect = 2e-07
 Identities = 22/75 (29%), Positives = 42/75 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L +  L  ++T E     F   G V   +++ D  +G S G+GFV Y +  + + A+ +L
Sbjct: 3   LIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTL 62

Query: 129 NGVELEGRAMRVSLA 143
           NG++L+ + ++V+ A
Sbjct: 63  NGLQLQNKRIKVAYA 77

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

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

 Score = 45.0 bits (107), Expect = 3e-07
 Identities = 16/46 (34%), Positives = 29/46 (63%)

Query: 4  KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          K+T++ D+ET +S+G AF+     ED +  ++ L+ +E  GR L+ 
Sbjct: 30 KVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLKC 75

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

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

 Score = 45.3 bits (107), Expect = 3e-07
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA--- 124
           KLFVG L   V    LT+ F ++G V  A V+ D ++G+ RG+GFV +      + A   
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 125 -LESLNGVELE 134
               +NG  +E
Sbjct: 61  KFHPINGHRVE 71

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

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

 Score = 44.9 bits (107), Expect = 3e-07
 Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 11/81 (13%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYG---NVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           K++VGNL    T   L   F++YG   +V  AR           G+ FV +    + E A
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR--------NPPGFAFVEFEDPRDAEDA 52

Query: 125 LESLNGVELEGRAMRVSLAQG 145
           + +L+G  + G  +RV L++G
Sbjct: 53  VRALDGRRICGNRVRVELSRG 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|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 44.7 bits (106), Expect = 3e-07
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           ++L V NLS  V+ + L    ++ G V      Y     +    G V ++T ++M+ A+E
Sbjct: 1   YRLIVENLSSRVSWQDLKDFMRKAGEVT-----YADAHKQRPNEGVVEFATYSDMKRAIE 55

Query: 127 SLNGVELEGRAMRVS 141
            L+G EL GR +++ 
Sbjct: 56  KLDGTELNGRKIKLI 70

This subfamily corresponds to the RRM2 of 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 is 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 = 72

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

 Score = 44.6 bits (105), Expect = 4e-07
 Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 8/73 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KL VGN+S S T + L   F+EYG V+   ++ D        Y FV      +   A+  
Sbjct: 2   KLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRG 53

Query: 128 LNGVELEGRAMRV 140
           L+  E +G+ M V
Sbjct: 54  LDNTEFQGKRMHV 66

This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

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

 Score = 44.6 bits (105), Expect = 4e-07
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 8/76 (10%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV NL+ +VT E L +AF ++G +   + L D        Y F+ +  +     A+E +
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 55

Query: 129 NGVELEGRAMRVSLAQ 144
           NG ELEG  + +  A+
Sbjct: 56  NGKELEGENIEIVFAK 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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 44.7 bits (106), Expect = 4e-07
 Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++GNLS  V    L Q F+E+   V + ++      +  GY FV    ++  + A+E L
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLV------KKGGYAFVDCPDQSWADKAIEKL 54

Query: 129 NGVELEGRAMRVSLAQGRR 147
           NG  L+G+ + V  +  ++
Sbjct: 55  NGKILQGKVIEVEHSVPKK 73

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

>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2)

 Score = 44.6 bits (105), Expect = 4e-07
 Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 7/74 (9%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KL++GNLS +VT E L Q F +    +  +VL         GY FV Y  +     A+E+
Sbjct: 3   KLYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLL------KSGYAFVDYPDQNWAIRAIET 56

Query: 128 LNG-VELEGRAMRV 140
           L+G VEL G+ M V
Sbjct: 57  LSGKVELHGKVMEV 70

This subgroup corresponds to the RRM1 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, which is a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

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

 Score = 43.7 bits (104), Expect = 6e-07
 Identities = 16/38 (42%), Positives = 23/38 (60%)

Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          +  GFAFV  ST E     ++ L+G  + GR LRV++S
Sbjct: 19 KKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 44.7 bits (105), Expect = 6e-07
 Identities = 23/78 (29%), Positives = 38/78 (48%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +F+ NL        L Q F  +G V   +V+ D  + + +G+GFV  +   E   A+ SL
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 129 NGVELEGRAMRVSLAQGR 146
           NG  L  + ++VS    +
Sbjct: 64  NGYRLGDKILQVSFKTSK 81

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

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 44.2 bits (105), Expect = 6e-07
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FVG L  +VT + L   F  +G +V  ++         +G GFV +  +A  E A++ L
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKI------PPGKGCGFVQFVHRAAAEAAIQQL 57

Query: 129 NGVELEGRAMRVS 141
            G  + G  +R+S
Sbjct: 58  QGTIIGGSRIRLS 70

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

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

 Score = 44.0 bits (104), Expect = 6e-07
 Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           +VGN+    T   L   FQ +G ++  R   D      RG+ FV   T  +   A+  L 
Sbjct: 4   YVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQLQ 57

Query: 130 GVELEGRAMRVSLAQGR 146
           G  + GR +R    + R
Sbjct: 58  GFPVHGRPLRCGWGKDR 74

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

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

 Score = 43.9 bits (104), Expect = 7e-07
 Identities = 21/72 (29%), Positives = 44/72 (61%), Gaps = 2/72 (2%)

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           ++GNL+W +T + + + F+    +   R+  D E+G  +G+G V ++ +  ++ AL+ L+
Sbjct: 3   YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALK-LD 60

Query: 130 GVELEGRAMRVS 141
           G  L GR +R++
Sbjct: 61  GTVLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 44.2 bits (105), Expect = 8e-07
 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 77  SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG- 135
           SVT + L +AF  +G +    V+ D ++  S+G  +V ++  +    A+E +NG  L G 
Sbjct: 13  SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72

Query: 136 -RAMRVSLA 143
            + ++V +A
Sbjct: 73  TKPLKVLIA 81

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

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

 Score = 44.0 bits (104), Expect = 8e-07
 Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+ V NL +  T + +   F  YG +   RV    +   +RG+ FV +ST  E   A+ +
Sbjct: 2   KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQS-ARGFAFVEFSTAKEALNAMNA 60

Query: 128 LNGVELEGR 136
           L    L GR
Sbjct: 61  LKDTHLLGR 69

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

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 43.9 bits (103), Expect = 9e-07
 Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 2/75 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++FV NL + +T + L + F + G+V+ A +    E+G+S+G G V + +    E A   
Sbjct: 1   QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEI--KMENGKSKGCGTVRFDSPESAEKACRL 58

Query: 128 LNGVELEGRAMRVSL 142
           +NG+++ GR + V L
Sbjct: 59  MNGIKINGREIDVRL 73

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

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

 Score = 43.4 bits (103), Expect = 1e-06
 Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 4/38 (10%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIEN----LDGR 40
          V+ DR+TG+SRG+ FVT    E      ++    +DGR
Sbjct: 32 VITDRQTGKSRGYGFVTFKDKESAERACKDPNPIIDGR 69

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

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

 Score = 43.4 bits (103), Expect = 1e-06
 Identities = 19/40 (47%), Positives = 23/40 (57%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          DR T  SRGFAFV      D    ++ +DG+E  GR LRV
Sbjct: 33 DRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELRV 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|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 21/73 (28%), Positives = 40/73 (54%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFV NL +S   + L + F ++G +    V  D +SG+S+G+ +V +    +   A + 
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 128 LNGVELEGRAMRV 140
           L+G   +GR + +
Sbjct: 64  LDGKVFQGRLIHI 76

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

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

 Score = 43.5 bits (102), Expect = 1e-06
 Identities = 27/74 (36%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FV NL + V  + L + F   G VV A +L D + G+SRG G V +    E   A+   
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILED-KDGKSRGIGTVTFEQPIEAVQAISMF 61

Query: 129 NGVELEGRAMRVSL 142
           NG  L  R M V +
Sbjct: 62  NGQLLFDRPMHVKM 75

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

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 43.1 bits (101), Expect = 1e-06
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 8/76 (10%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV NL+ +VT E L ++F E+G +   + L D        Y FV +  +     A++ +
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAMDEM 55

Query: 129 NGVELEGRAMRVSLAQ 144
           NG E+EG  + + LA+
Sbjct: 56  NGKEIEGEEIEIVLAK 71

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 42.9 bits (102), Expect = 2e-06
 Identities = 15/36 (41%), Positives = 25/36 (69%)

Query: 4  KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDG 39
          ++T++ D++TG+S+G AFV  S+ E+    IE L G
Sbjct: 28 EVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 63

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

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

 Score = 43.3 bits (103), Expect = 2e-06
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 73  NLSWSVTTESLTQAFQEYGNVV--GARVLYDGESGRSRGYGFVCYSTKAEMETALESLNG 130
            L    T E + QA     +V     R++ D  +G SRG+ FV + +  +    +++LN 
Sbjct: 9   GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68

Query: 131 V---ELEGRAMRVSLA 143
           +    ++GR +RVS A
Sbjct: 69  LDPFVIDGRVVRVSYA 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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 43.0 bits (102), Expect = 2e-06
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V NL + +++E L   F +YG +   R+   G +  +RG  FV Y    + + A + L
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRI---GNTKETRGTAFVVYEDIYDAKNACDHL 61

Query: 129 NGVELEGR 136
           +G  +  R
Sbjct: 62  SGFNVANR 69

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

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

 Score = 43.0 bits (102), Expect = 2e-06
 Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 1/71 (1%)

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           FV  LS  V    L + F + G V   R++ D  S RS+G  +V +  +  +  AL  L 
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-LT 61

Query: 130 GVELEGRAMRV 140
           G  L G+ + V
Sbjct: 62  GQRLLGQPIMV 72

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

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

 Score = 42.9 bits (101), Expect = 2e-06
 Identities = 19/72 (26%), Positives = 37/72 (51%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +++G+L      + L + F ++G V   RV    ++G S+ YGF+ +        A +S+
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 129 NGVELEGRAMRV 140
           N   L G+ ++V
Sbjct: 62  NNYLLMGKVLQV 73

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

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

 Score = 42.6 bits (101), Expect = 2e-06
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
            +L V NL  SVT + + + F   G +  AR++         G   V Y  K +  TA++
Sbjct: 1   TRLVVSNLHPSVTEDDIVELFSAIGALKRARLV-------RPGVAEVVYVRKDDALTAID 53

Query: 127 SLNGVELEGRAMRVSL 142
             N  EL+G+ M+  L
Sbjct: 54  KYNNRELDGQPMKCKL 69

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 43.0 bits (101), Expect = 2e-06
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++FVG +   V  + L   F+  G +   R++ D + G++RGY FV Y+ K E + A+  
Sbjct: 3   EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMYTQKHEAKRAVRE 61

Query: 128 LNGVELE-GRAMRV 140
           LN  E+  GR + V
Sbjct: 62  LNNYEIRPGRLLGV 75

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 23/76 (30%), Positives = 44/76 (57%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L   +T   L   F+  G +   R++ D ++G S GY FV + ++A+ + A+++L
Sbjct: 110 LIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNL 169

Query: 129 NGVELEGRAMRVSLAQ 144
           NG+ +  + ++VS A+
Sbjct: 170 NGITVRNKRLKVSYAR 185

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 42.7 bits (101), Expect = 3e-06
 Identities = 17/45 (37%), Positives = 29/45 (64%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
          V+ D  T + +G+ FVTM+  E+  + I +L+G    GR+L+V+F
Sbjct: 33 VIRDLTTNKCKGYGFVTMTNYEEAYSAIASLNGYRLGGRVLQVSF 77

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

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 42.6 bits (100), Expect = 3e-06
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++FV NL +  T + L   F E G+V+ A +    E+G+S+G G V + +    E A   
Sbjct: 1   QIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVRFESPEVAERACRM 58

Query: 128 LNGVELEGRAMRVSL 142
           +NG +L GR + V +
Sbjct: 59  MNGYKLNGREIDVRI 73

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 42.3 bits (100), Expect = 3e-06
 Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +L V NL   +  + L + F+ +G +   ++ Y  + G+ R +GFV Y T+ E + AL+ 
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYT-KDGKFRKFGFVGYKTEEEAQKALKH 60

Query: 128 LNG 130
            N 
Sbjct: 61  FNN 63

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

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 42.4 bits (100), Expect = 3e-06
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 81  ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV 140
            SLT+ F   G +    +  D E+G S+G+ ++ + +   +E ALE L+G +L G  + V
Sbjct: 18  RSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE-LDGSDLGGGNLVV 76

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 42.5 bits (100), Expect = 3e-06
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++VGN+ +  T E L   F   G+V    +L D  SG  +G+ ++ +S K  + TAL +L
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL-AL 60

Query: 129 NGVELEGRAMRVSL 142
           +     GR ++V  
Sbjct: 61  DESLFRGRQIKVMP 74

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

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

 Score = 42.1 bits (100), Expect = 3e-06
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 4/76 (5%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLY--DGESGRSRGYGFVCYSTKAEMETALE 126
           L+VGNLS+  T E + + F   G++   R++   D  +    G+ FV Y T+ + E A++
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDI--KRIIMGLDRFTKTPCGFCFVEYYTREDAENAVK 58

Query: 127 SLNGVELEGRAMRVSL 142
            LNG +L+ R +RV  
Sbjct: 59  YLNGTKLDDRIIRVDW 74

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

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

 Score = 42.3 bits (100), Expect = 3e-06
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 5/68 (7%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV N++ +V  E L   F+++G++   R LY   + + RG+  V Y        A  +L
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDI---RTLYT--ACKHRGFIMVSYYDIRAARRAKRAL 58

Query: 129 NGVELEGR 136
            G EL GR
Sbjct: 59  QGTELGGR 66

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

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

 Score = 42.2 bits (100), Expect = 4e-06
 Identities = 15/48 (31%), Positives = 26/48 (54%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
          V+ D+ + + RGF +VT +  ED    +E     ++ GR + V F+ K
Sbjct: 31 VVKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFAKK 78

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

>gnl|CDD|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1)

 Score = 41.9 bits (98), Expect = 4e-06
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 9/75 (12%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFV-CYSTKAEMETALE 126
           KL++GNL+ SVT   L + F+++      ++ Y G+     GY FV C   +  M+ A+E
Sbjct: 3   KLYIGNLNESVTPADLEKVFEDH------KISYSGQFLVKSGYAFVDCPDEQWAMK-AIE 55

Query: 127 SLNG-VELEGRAMRV 140
           + +G VEL G+ + +
Sbjct: 56  TFSGKVELHGKRLEI 70

This subgroup corresponds to the RRM1 of IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also termed coding region determinant-binding protein (CRD-BP), or VICKZ family member 1, or zipcode-binding protein 1 (ZBP-1). IGF2BP1 is a multi-functional regulator of RNA metabolism that has been implicated in the control of aspects of localization, stability, and translation for many mRNAs. It is predominantly located in cytoplasm and was initially identified as a trans-acting factor that interacts with the zipcode in the 3'- untranslated region (UTR) of the beta-actin mRNA, which is important for its localization and translational regulation. It inhibits IGF-II mRNA translation through binding to the 5'-UTR of the transcript. IGF2BP1 also acts as human immunodeficiency virus type 1 (HIV-1) Gag-binding factor that interacts with HIV-1 Gag protein and blocks the formation of infectious HIV-1 particles. IGF2BP1 promotes mRNA stabilization; it functions as a coding region determinant (CRD)-binding protein that binds to the coding region of betaTrCP1 mRNA and prevents miR-183-mediated degradation of betaTrCP1 mRNA. It also promotes c-myc mRNA stability by associating with the CRD and stabilizes CD44 mRNA via interaction with the 3'-UTR of the transcript. In addition, IGF2BP1 specifically interacts with both Hepatitis C virus (HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing HCV internal ribosome entry site (IRES)-mediated translation initiation via the 3'-UTR. IGF2BP1 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. It also contains two putative nuclear export signals (NESs) and a putative nuclear localization signal (NLS). . Length = 77

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

 Score = 42.3 bits (100), Expect = 4e-06
 Identities = 28/72 (38%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V NLS  V+ E L QAF ++G V  A V+ D + GRS G G V +S K   + A++  
Sbjct: 2   LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVD-DRGRSTGEGIVEFSRKPGAQAAIKRC 60

Query: 129 N-GVELEGRAMR 139
           + G  L   + R
Sbjct: 61  SEGCFLLTASPR 72

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

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

 Score = 41.7 bits (98), Expect = 5e-06
 Identities = 19/49 (38%), Positives = 31/49 (63%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
           V+ D ETG SRG+ FVT + +ED    +  L  ++  GRILR++ +++
Sbjct: 30 VVVTDPETGESRGYGFVTFAMLEDAQEALAKLKNKKLHGRILRLDIAER 78

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

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

 Score = 42.2 bits (100), Expect = 5e-06
 Identities = 20/74 (27%), Positives = 39/74 (52%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            +FVGN+   V+ + + +  ++ G V+  + + D  +G+ + +GF  +        AL  
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 128 LNGVELEGRAMRVS 141
           LNG+EL G+ + V 
Sbjct: 62  LNGLELGGKKLLVK 75

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 42.0 bits (98), Expect = 5e-06
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D KLF+G +S       +   F  +G +   R+L  G  G SRG  FV ++T+A  +TA+
Sbjct: 1   DRKLFIGMVSKKCNENDIRVMFSPFGQIEECRIL-RGPDGLSRGCAFVTFTTRAMAQTAI 59

Query: 126 ESLNGVE-LEG 135
           ++++  + +EG
Sbjct: 60  KAMHQAQTMEG 70

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 42.0 bits (98), Expect = 5e-06
 Identities = 18/48 (37%), Positives = 27/48 (56%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           KLFVG +        L   F+EYG +    ++ D +SG+ RG+GFV +
Sbjct: 2   KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTF 49

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 41.5 bits (98), Expect = 6e-06
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           F++ V  L    + + L    ++ G+V  A V  D E     G G V ++++ +ME AL 
Sbjct: 1   FRVVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQE-----GEGVVEFTSQEDMERALR 55

Query: 127 SLNGVELEGRAMRV 140
            L+G E  GR +RV
Sbjct: 56  KLDGTEFRGRRVRV 69

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 41.7 bits (98), Expect = 6e-06
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFVG LS       +   F  +G++    VL D  +G+SRG  FV ++++     A+++
Sbjct: 3   KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQ-NGQSRGCAFVTFASRQCALNAIKA 61

Query: 128 LN 129
           ++
Sbjct: 62  MH 63

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 44.2 bits (104), Expect = 6e-06
 Identities = 38/135 (28%), Positives = 63/135 (46%), Gaps = 14/135 (10%)

Query: 15  RSRGFAFVTMSTVEDCNAVIEN----LDGREYL-GRILRVNFSDKPKPKLPLYAETDFKL 69
           ++RGFAFV     E   A        + GR  L G ++ V++++  +            L
Sbjct: 180 KNRGFAFVEY---ESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKIL 236

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           +V NL  + T E + ++F E+      RV       + R Y FV +  + +   A++ LN
Sbjct: 237 YVRNLMTTTTEEIIEKSFSEFKPGKVERV------KKIRDYAFVHFEDREDAVKAMDELN 290

Query: 130 GVELEGRAMRVSLAQ 144
           G ELEG  + V+LA+
Sbjct: 291 GKELEGSEIEVTLAK 305

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

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

 Score = 41.6 bits (97), Expect = 6e-06
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V NL    + +++ + F ++      RV       + R Y FV ++++ +   A+ +L
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERV------KKIRDYAFVHFTSREDAVHAMNNL 57

Query: 129 NGVELEGRAMRVSLAQ 144
           NG ELEG  + V+LA+
Sbjct: 58  NGTELEGSCIEVTLAK 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|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 41.1 bits (97), Expect = 7e-06
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 9/69 (13%)

Query: 68  KLFVGNLSWSVTT-ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           ++FVGNL+    + E L + F +YG ++G  +         +GYGFV +  + +   A+ 
Sbjct: 2   RVFVGNLNTDKVSKEDLEEIFSKYGKILGISLH--------KGYGFVQFDNEEDARAAVA 53

Query: 127 SLNGVELEG 135
             NG E+ G
Sbjct: 54  GENGREIAG 62

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

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

 Score = 44.1 bits (104), Expect = 7e-06
 Identities = 29/149 (19%), Positives = 60/149 (40%), Gaps = 25/149 (16%)

Query: 19  FAFVTMSTVEDCNAVIENLDGREYLGRILRV----NFSDKPK-------PKLPLYAETDF 67
           FAF+   TVE+    +  LD   Y    L++    ++   P+             A+   
Sbjct: 225 FAFLEFRTVEEATFAMA-LDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVE 283

Query: 68  -------------KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVC 114
                        ++++GNL   +  + + +  + +G++    ++ D  +G S+GY F  
Sbjct: 284 KLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCE 343

Query: 115 YSTKAEMETALESLNGVELEGRAMRVSLA 143
           Y   +  + A+ +LNG +     + V  A
Sbjct: 344 YKDPSVTDVAIAALNGKDTGDNKLHVQRA 372

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

 Score = 41.3 bits (97), Expect = 8e-06
 Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++FVG + +      L + F +YG V   +++ D  +G S+GYGFV + T+ + +  L+ 
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQE 62

Query: 128 LNGVELEGRAMRVSLA 143
            N +    + + +  A
Sbjct: 63  ANRLCFRDKKLNIGQA 78

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 41.2 bits (97), Expect = 8e-06
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++ NL   +  + L    + YG V+  R+L D   G+SRG GF    ++ + E  +   
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRD-SKGQSRGVGFARMESREKCEDIISKF 61

Query: 129 NGVELEG 135
           NG  L+G
Sbjct: 62  NGKYLKG 68

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

>gnl|CDD|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 = 41.3 bits (97), Expect = 8e-06
 Identities = 21/72 (29%), Positives = 38/72 (52%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           + + N+ +S+  E L    ++ G  +     Y  ++G  RG  F  + +  E +T +E+L
Sbjct: 4   IVIKNIPFSLRKEQLLDIIEDLGIPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVVEAL 63

Query: 129 NGVELEGRAMRV 140
           NG E+ GR +RV
Sbjct: 64  NGYEISGRRLRV 75

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

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 41.2 bits (97), Expect = 8e-06
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
            VG +  S++ + L + F   G V   R+   G+   S  + FV ++      +AL +L+
Sbjct: 4   HVGGIDGSLSEDDLKEFFSNCGEVTRVRLC--GDRQHSARFAFVEFADAESALSAL-NLS 60

Query: 130 GVELEGRAMRVS 141
           G  L G  +RVS
Sbjct: 61  GTLLGGHPLRVS 72

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 41.2 bits (97), Expect = 9e-06
 Identities = 18/60 (30%), Positives = 36/60 (60%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG LS   T E + + F ++GN+V   +  D ++ + RG+ F+ + ++  ++  LE+
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|241087 cd12643, RRM_CFIm68, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

 Score = 41.3 bits (97), Expect = 9e-06
 Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYG--NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           L+VGNL+W  T + LT+A Q  G  +++  +   +  +G+S+G+  +   +++     ++
Sbjct: 2   LYVGNLTWWTTDQDLTEAIQSIGVNDLLEIKFFENRANGQSKGFALIVLGSESSSRKLMD 61

Query: 127 SLNGVELEGRA 137
            L   EL G+ 
Sbjct: 62  KLPKKELHGQN 72

This subgroup corresponds to the RRM of CFIm68. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm68, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF6), or cleavage and polyadenylation specificity factor 68 kDa subunit (CPSF68), or protein HPBRII-4/7. CFIm68 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm68 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping. . Length = 77

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

 Score = 41.0 bits (96), Expect = 1e-05
 Identities = 15/45 (33%), Positives = 28/45 (62%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
          V++D ++GRSRG+ FV+  + +D    I  ++G+    R +R N+
Sbjct: 31 VMWDMKSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSRPIRCNW 75

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

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

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 18/46 (39%), Positives = 28/46 (60%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          ++YDRETG+ +G+ F      E   + + NL+G E  GR LRV+ +
Sbjct: 30 LVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQLRVDNA 75

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

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 40.8 bits (96), Expect = 1e-05
 Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
          D+ET + +GF +V    VE     +E  DG  +  R LRV+
Sbjct: 35 DKETDKFKGFCYVEFEDVESLKEALE-YDGALFDDRSLRVD 74

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 41.2 bits (97), Expect = 1e-05
 Identities = 20/73 (27%), Positives = 37/73 (50%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LF+ NL+++ T E L + F +YG +    +  D  + + +G+ FV Y        A   
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 128 LNGVELEGRAMRV 140
           L+G   +GR + +
Sbjct: 64  LDGTVFQGRLLHL 76

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

>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 40.8 bits (95), Expect = 1e-05
 Identities = 23/72 (31%), Positives = 38/72 (52%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V  LS +     L   F +YG V+ A+V+ +  S  ++ YG V  S+ AE+   +  L
Sbjct: 2   LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61

Query: 129 NGVELEGRAMRV 140
           +  EL G+ + V
Sbjct: 62  HRTELHGQQISV 73

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

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

 Score = 40.7 bits (96), Expect = 1e-05
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 69  LFVGNLSWSVT-TESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           LFV  L  +      L + F + G     ++     +G+ RG+ FV Y+T  + E A ++
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAI-APNGQPRGFAFVEYATAEDAEEAQQA 63

Query: 128 LNGVELEGRAMRVS 141
           LNG  L+G  +RVS
Sbjct: 64  LNGHSLQGSPIRVS 77

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

 Score = 40.6 bits (96), Expect = 1e-05
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FVG +   +  + L   F++ G +   R++ D  SG +RGY FV Y+ K   + A++ L
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 129 NGVELE-GRAMRVS 141
           +  E+  G+ + V 
Sbjct: 63  HNYEIRPGKRLGVC 76

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

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 16/40 (40%), Positives = 26/40 (65%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          D++TG+S+GFAF+           ++NL+G + LGR +RV
Sbjct: 44 DKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRV 83

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

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

 Score = 40.4 bits (95), Expect = 2e-05
 Identities = 15/45 (33%), Positives = 24/45 (53%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
          ++ DR TG+S G+ FV      D    I  L+G E   + L+V++
Sbjct: 32 IVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKVSY 76

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|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 20/50 (40%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
          ++ DR+TG S+GF FV  S+ ED  A  E ++  E  G  + ++F+ KPK
Sbjct: 29 IVTDRDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDGNKVTLDFA-KPK 77

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

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

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFVGNL   +T E   + F++YG      +       R RG+GF+   ++   E A   
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 56

Query: 128 LNGVELEGRAMRV 140
           L+G  L+ R +R+
Sbjct: 57  LDGTILKNRPLRI 69

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

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++F+G L   +  + L    ++ G +   R++ D  +G +RGY FV +S K E + A++ 
Sbjct: 3   EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDF-NGNNRGYAFVTFSNKQEAKNAIKQ 61

Query: 128 LNGVELE-GRAMRV 140
           LN  E+  GR + V
Sbjct: 62  LNNYEIRNGRLLGV 75

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

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

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 13/63 (20%), Positives = 31/63 (49%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPL 61
          + ++ + +  +T +  G A V   +V+     +E L+    +G+I++V    K + +  L
Sbjct: 29 VEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVMGKIIKVFLDPKGEIRKRL 88

Query: 62 YAE 64
          Y +
Sbjct: 89 YED 91

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

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

 Score = 40.3 bits (95), Expect = 2e-05
 Identities = 11/28 (39%), Positives = 20/28 (71%)

Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDG 39
          ETG+++G+AFV  +T E+    ++ L+G
Sbjct: 45 ETGKTKGYAFVEFATPEEAKEAVKALNG 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|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 39.9 bits (94), Expect = 2e-05
 Identities = 13/43 (30%), Positives = 25/43 (58%)

Query: 88  QEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNG 130
           Q +G ++  + + D ++ + +GYGFV + +      A+E LNG
Sbjct: 22  QPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNG 64

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

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 40.2 bits (93), Expect = 2e-05
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 2/68 (2%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++  L    T + L +  Q YG +V  + + D  + + +GYGFV + + A  + A+ SL
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

Query: 129 --NGVELE 134
             NGV+ +
Sbjct: 67  KANGVQAQ 74

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 40.6 bits (94), Expect = 2e-05
 Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++  L  + T + L +  Q YG +V  + + D  + + +GYGFV + + A  + A+ +L
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

Query: 129 --NGVELE 134
             +GV+ +
Sbjct: 70  KASGVQAQ 77

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 40.2 bits (95), Expect = 2e-05
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 7/79 (8%)

Query: 69  LFVGNLSWSVTTESLTQA----FQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           L++ NL+  +  + L ++    F ++G V+        ++ + RG  FV +        A
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVAS---KTLKMRGQAFVVFKDVESATNA 58

Query: 125 LESLNGVELEGRAMRVSLA 143
           L +L G     + MR+  A
Sbjct: 59  LRALQGFPFYDKPMRIQYA 77

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

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 24/70 (34%), Positives = 33/70 (47%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V NL  S T E   +  + YGN+    ++Y   +G S+GYGFV Y  K     A   L
Sbjct: 2   LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLEL 61

Query: 129 NGVELEGRAM 138
            G +L    +
Sbjct: 62  LGKQLGESTL 71

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

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

 Score = 40.0 bits (93), Expect = 2e-05
 Identities = 26/58 (44%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           L V NLS  V+ E L QAF ++G V  A V+ D + GR  G GFV ++ K     ALE
Sbjct: 2   LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVD-DRGRPTGKGFVEFAAKPAARKALE 58

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

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

 Score = 39.9 bits (93), Expect = 2e-05
 Identities = 22/72 (30%), Positives = 35/72 (48%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L + NL  + T +   +  + +GN+    ++Y   +G S+GYGFV Y  K     A   L
Sbjct: 2   LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61

Query: 129 NGVELEGRAMRV 140
            G +L  R + V
Sbjct: 62  LGKQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>gnl|CDD|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 = 39.9 bits (94), Expect = 3e-05
 Identities = 15/45 (33%), Positives = 25/45 (55%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
           V  D+ TG+S+ F FV+    E   A I+ ++G +  G+ L+V 
Sbjct: 29 KVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 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|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 39.9 bits (93), Expect = 3e-05
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 1/66 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++FVG +   +  + L   F+  G +   R++ +  SG +RGY FV Y+TK E + A+  
Sbjct: 3   EVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEF-SGENRGYAFVMYTTKEEAQLAIRI 61

Query: 128 LNGVEL 133
           LN  E+
Sbjct: 62  LNNYEI 67

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 39.5 bits (92), Expect = 3e-05
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFVGNL   +T E + + F++YG      +  D      +G+GF+   T+   E A   
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAE 56

Query: 128 LNGVELEGRAMRV 140
           L+ + L G+ +RV
Sbjct: 57  LDNMPLRGKQLRV 69

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

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

 Score = 39.7 bits (93), Expect = 3e-05
 Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 4/72 (5%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++ G    S     + + F+  G V    +L    S   + + F+ +      + A+E+L
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIETL 57

Query: 129 NGVELEGRAMRV 140
           NG  ++G  ++V
Sbjct: 58  NGASVDGNCIKV 69

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

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 40.1 bits (93), Expect = 3e-05
 Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++ NL  S+  + L    + +G+V+  R+L D  +G SRG GF    +  + E  ++  
Sbjct: 4   LYISNLPVSMDEQELENMLKPFGHVISTRILRDA-NGVSRGVGFARMESTEKCEVVIQHF 62

Query: 129 NGVELE 134
           NG  L+
Sbjct: 63  NGKYLK 68

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

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

 Score = 39.7 bits (93), Expect = 3e-05
 Identities = 24/73 (32%), Positives = 41/73 (56%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++F+ N+ + +  + L   F+E    V    L+  E G+SRG G V +  K  ++ ALE+
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALET 60

Query: 128 LNGVELEGRAMRV 140
           +N  EL+GR + V
Sbjct: 61  MNRYELKGRKLVV 73

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 39.9 bits (93), Expect = 3e-05
 Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 8  LY-DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
          LY DRETG+ +G A V+        A I+  DG+E+ G  ++V+F
Sbjct: 42 LYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 86

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 39.6 bits (92), Expect = 3e-05
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQE-YGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           + F+ N+ + V  +SL    +E  G V    +L D E G+SRG   V +  +  M+ A+E
Sbjct: 1   RAFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAE-GKSRGCAVVEFKMEESMKKAVE 59

Query: 127 SLNGVELEGRAMRV 140
            LN   L GR ++V
Sbjct: 60  VLNKHVLNGRPLKV 73

This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

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

 Score = 39.3 bits (92), Expect = 4e-05
 Identities = 15/41 (36%), Positives = 26/41 (63%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
          D ++GR +GF +V  S+ E   A ++ L G + LGR +R++
Sbjct: 33 DPDSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGRPVRLD 73

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

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

 Score = 39.5 bits (93), Expect = 4e-05
 Identities = 14/38 (36%), Positives = 21/38 (55%)

Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          + G+S+GF FV     E     +E L+G+E  G+ L V
Sbjct: 37 DEGKSKGFGFVNFENHEAAQKAVEELNGKEVNGKKLYV 74

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

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

 Score = 39.5 bits (93), Expect = 4e-05
 Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
          + K+ + YDR +GRS G A V     ED    I+  +G    G+ ++V  
Sbjct: 27 VKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPMQVEL 75

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

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

 Score = 39.3 bits (92), Expect = 4e-05
 Identities = 14/35 (40%), Positives = 18/35 (51%)

Query: 16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
          S+GF FVT +   D +   E L G    GR + VN
Sbjct: 39 SKGFGFVTFANSADADRAREKLHGTVVEGRKIEVN 73

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

 Score = 39.6 bits (93), Expect = 4e-05
 Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFV  +S SVT E L + F     +    +  D  +G+S+G+ +V YS  A    A E 
Sbjct: 2   RLFV-VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEK 60

Query: 128 LNGVEL 133
           LNG E 
Sbjct: 61  LNGFEY 66

This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

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

 Score = 39.6 bits (92), Expect = 4e-05
 Identities = 19/66 (28%), Positives = 36/66 (54%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++FVG +   +  + L   F++ G +   R++ D  +G +RGY FV + TK   + A++ 
Sbjct: 3   EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62

Query: 128 LNGVEL 133
            N  E+
Sbjct: 63  YNNHEI 68

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

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

 Score = 39.2 bits (92), Expect = 5e-05
 Identities = 16/47 (34%), Positives = 29/47 (61%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
          D +TG S+GFAF++  + E  +A IE ++G+    R + V+++ K  
Sbjct: 37 DPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPITVSYAFKKD 83

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

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

 Score = 39.1 bits (92), Expect = 5e-05
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++ V NL   VT + L + F+  G V   +V+   + G+SR +GFV + ++ + + A++ 
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQAVKY 60

Query: 128 LNGVELEGRAMRVSLA 143
            N   ++   + V LA
Sbjct: 61  FNKTFIDTSKISVELA 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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 39.3 bits (91), Expect = 5e-05
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++ NL  S+  + L    + +G V+  R+L D  SG SRG GF    +  + E  +   
Sbjct: 3   LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVISHF 61

Query: 129 NG 130
           NG
Sbjct: 62  NG 63

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

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

 Score = 39.1 bits (92), Expect = 6e-05
 Identities = 16/43 (37%), Positives = 27/43 (62%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
           DR TG  +G+A +   T ++  A IE L+G+E LG+ + V++
Sbjct: 40 LDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTISVDW 82

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

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

 Score = 39.0 bits (90), Expect = 6e-05
 Identities = 18/68 (26%), Positives = 37/68 (54%), Gaps = 2/68 (2%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++  L    T + L +  Q YG +V  + + D  + + +GYGFV + + +  + A+ +L
Sbjct: 4   LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63

Query: 129 --NGVELE 134
             +GV+ +
Sbjct: 64  KASGVQAQ 71

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 38.8 bits (91), Expect = 6e-05
 Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 6/78 (7%)

Query: 69  LFVGNLSWS-VTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           L V NL+   VT ++L   F  YG+VV  ++L+       +    +  +   + +TAL  
Sbjct: 2   LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILF-----NKKDTALIQMADPQQAQTALTH 56

Query: 128 LNGVELEGRAMRVSLAQG 145
           LNG+ L G+ +RV+L++ 
Sbjct: 57  LNGIRLHGKKLRVTLSKH 74

This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. 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. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian 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 may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 38.9 bits (91), Expect = 6e-05
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFVG +  ++  + L   F+++G +    VL D  +G  +G  F+ Y  +     A  +
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66

Query: 128 LNGVE-LEG--RAMRVSLA 143
           L+  + L G  R ++V  A
Sbjct: 67  LHEQKTLPGMNRPIQVKPA 85

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

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

 Score = 38.7 bits (90), Expect = 7e-05
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 10/75 (13%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGES--GRSRGYGFVCYSTKAEMETAL 125
           +LFVGNL   +T +   + F +YG          GE    + +G+GF+   ++A  E A 
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGE--------PGEVFINKGKGFGFIKLESRALAEIAK 54

Query: 126 ESLNGVELEGRAMRV 140
             L+   + GR +RV
Sbjct: 55  AELDDTPMRGRQLRV 69

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

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

 Score = 38.8 bits (91), Expect = 7e-05
 Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 6/67 (8%)

Query: 77  SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR 136
            +T E L +AF  +GN++   +  + E    +  GFV +      + A+  LNG  ++G 
Sbjct: 13  GLTEEILKKAFSPFGNII--NISMEKE----KNCGFVTFEKMESADRAIAELNGTTVQGV 66

Query: 137 AMRVSLA 143
            ++VSLA
Sbjct: 67  QLKVSLA 73

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

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 38.5 bits (89), Expect = 8e-05
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG LS   T E + + F  +G +    +  D ++   RG+ FV Y+ +  ++  LES
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 17/50 (34%), Positives = 27/50 (54%)

Query: 10  DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL 59
           D ETGRS+GF F+     E+    +E ++G E  GR ++V ++      L
Sbjct: 221 DPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLL 270

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

 Score = 38.0 bits (89), Expect = 1e-04
 Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG 44
            K  V+ D+ TG+S+G+ FV+ S   D    ++ ++G+ Y+G
Sbjct: 33 FQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEMNGK-YVG 74

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

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

 Score = 37.9 bits (89), Expect = 1e-04
 Identities = 18/42 (42%), Positives = 23/42 (54%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR 48
          V   R   R RGFAFV  ++ ED  A ++ L+G    GR LR
Sbjct: 28 VRLVRNKDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRTLR 69

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

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

 Score = 38.0 bits (89), Expect = 1e-04
 Identities = 14/36 (38%), Positives = 23/36 (63%)

Query: 14 GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          G+ RG+ FVT  T E+    +++L+G+  LG+ L V
Sbjct: 41 GQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVV 76

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

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 38.1 bits (89), Expect = 1e-04
 Identities = 14/44 (31%), Positives = 26/44 (59%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
           ++ +  +  +R F FVTM++VE+    I++L   E  GR++ V
Sbjct: 30 KIVTNARSPGARCFGFVTMASVEEAAKCIQHLHRTELHGRVISV 73

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|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 = 38.2 bits (89), Expect = 1e-04
 Identities = 17/43 (39%), Positives = 23/43 (53%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
          Y  + G  RG AF    + E+   V+E L+G E  GR LRV +
Sbjct: 35 YHFDNGVFRGLAFANFRSPEEAQTVVEALNGYEISGRRLRVEY 77

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|241088 cd12644, RRM_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYG--NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           ++VGN SW  T + L Q  +  G  +VV  +   +  +G+S+GY  V  +++  +   LE
Sbjct: 4   VYVGNFSWWTTDQQLIQVIRSVGVKDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 63

Query: 127 SLNGVELEGRAMRVSLA 143
            L G  L G  + V  A
Sbjct: 64  LLPGKVLNGEKVDVRPA 80

This subgroup corresponds to the RRM of CFIm59. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. The two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59). CFIm59 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm59 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping. . Length = 90

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 38.3 bits (90), Expect = 1e-04
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 7/74 (9%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LF+ NL    T E L   F ++      R++        RG  FV + T+ +   AL++L
Sbjct: 5   LFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFETEEQATVALQAL 58

Query: 129 NGVEL-EGRAMRVS 141
            G ++  G AM++S
Sbjct: 59  QGFKITPGHAMKIS 72

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

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

 Score = 38.3 bits (90), Expect = 1e-04
 Identities = 17/73 (23%), Positives = 36/73 (49%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +++G+L        L + F ++G V   R+    ++G+S+GY FV + +    +   E++
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 129 NGVELEGRAMRVS 141
           N   L  R ++  
Sbjct: 62  NNYLLFERLLKCK 74

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

>gnl|CDD|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 = 37.8 bits (88), Expect = 1e-04
 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 9/76 (11%)

Query: 69  LFVGNLS-WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           LFV      +   E + + F+ +G +V   +         + + FV +    +   ALE+
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKALEA 53

Query: 128 LNGVELEGRAMRVSLA 143
           L+G  ++G  + V   
Sbjct: 54  LHGSRIDGSVLTVEFV 69

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

 Score = 38.1 bits (88), Expect = 1e-04
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FV NL + V  + L + F   G V  A +  D + G+SRG G V +    E   A+   
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKED-KDGKSRGMGTVTFEQPIEAVQAISMF 61

Query: 129 NGVELEGRAMRVSL 142
           NG  L  R M V +
Sbjct: 62  NGQFLFDRPMHVKM 75

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

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++ NL  S+  + L    + +G V+  R+L D  SG SRG GF    +  + E  +   
Sbjct: 3   LYISNLPLSMDEQELESMLKPFGQVISTRILRDA-SGTSRGVGFARMESTEKCEAIITHF 61

Query: 129 NG 130
           NG
Sbjct: 62  NG 63

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 38.1 bits (89), Expect = 1e-04
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYD-GESGRSRGYGFVCYSTKAEMETALE 126
           K+ V N+ +  T + L + F  +G +   R+      +G  RG+GFV + TK + + A +
Sbjct: 2   KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61

Query: 127 SL 128
           +L
Sbjct: 62  AL 63

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 37.7 bits (87), Expect = 1e-04
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 68  KLFVGNLSWSVTTESLTQA-FQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           ++F+GNL+  V  +S  +A F +YG +VG  V         +G+ FV Y  +     A+ 
Sbjct: 3   RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVA 54

Query: 127 SLNGVELEGRAMRVSLA 143
             +G  + G+ + ++LA
Sbjct: 55  GEDGRMIAGQVLDINLA 71

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, 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 hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

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

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FV  L+       L + F + G V   + + D  S RS+G  +V +     +  AL +L
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-AL 150

Query: 129 NGVELEGRAMRVSLAQGRR 147
            G  L GR + V  +Q  +
Sbjct: 151 TGQMLLGRPIIVQSSQAEK 169

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

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 12/40 (30%), Positives = 25/40 (62%)

Query: 13 TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
           G+ +GFAFV  ++  D    I+ ++G++  GR + V+++
Sbjct: 36 DGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRPVAVDWA 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 37.2 bits (87), Expect = 2e-04
 Identities = 11/31 (35%), Positives = 18/31 (58%)

Query: 19 FAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          + FV M   ED    I+ L+G E++G+ + V
Sbjct: 35 YGFVHMEEEEDAEDAIKALNGYEFMGKRINV 65

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

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 15/39 (38%), Positives = 24/39 (61%)

Query: 14 GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          G+  GFAFVTM   ++    +EN +G E  GR + V+++
Sbjct: 39 GKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDWA 77

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

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

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++FVG +   +  + L   F++ G +   R++ D  SG++RGY FV +  K E + A++ 
Sbjct: 60  EVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKL 118

Query: 128 LNGVELE-GRAMRV 140
           LN  E+  GR + V
Sbjct: 119 LNNYEIRPGRLLGV 132

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

>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 18/48 (37%), Positives = 26/48 (54%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           +LFVGNL   +    L + F  +GNVV  R+   G  G+   +GFV +
Sbjct: 7   QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVF 54

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

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

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGAR-------VLYDGESGRSRGYGFVCYSTKAEM 121
           +++  L   VT +SL + F   G +   +        +Y  +    +G   V Y   +  
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 122 ETALESLNGVELEGRAMRVSL 142
           + A+E  NG E  G  ++VSL
Sbjct: 61  QAAIEWFNGYEFRGNKIKVSL 81

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

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

 Score = 37.3 bits (86), Expect = 2e-04
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 9/77 (11%)

Query: 68  KLFVGNLSWSVTTESLTQA-FQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           ++F+GNL+ +V  +S  +  F +YG VVG  V         +GY FV YS +     A+ 
Sbjct: 3   RVFIGNLNTAVVKKSDVETIFSKYGRVVGCSV--------HKGYAFVQYSNERHARGAVI 54

Query: 127 SLNGVELEGRAMRVSLA 143
             NG  L G+ + +++A
Sbjct: 55  GENGRVLAGQTLDINMA 71

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

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

 Score = 37.5 bits (88), Expect = 2e-04
 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 68  KLFVGNLSWSVTTESLTQ---AFQEYGNVVGARVLYD-GESGRSRGYGFVCYSTKAEMET 123
           +L+V NLS  VT E L      F +  +             GR +G  FV + ++     
Sbjct: 3   RLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATK 62

Query: 124 ALESLNGVELEGRAMRVSLA 143
           AL  +NG  L+G+ M +   
Sbjct: 63  ALNLVNGYVLKGKPMVIQFG 82

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

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

 Score = 37.3 bits (86), Expect = 2e-04
 Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 6/71 (8%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++ G ++  +T + + Q F  +G ++  RV  D      +GY FV +++      A+ S+
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSV 56

Query: 129 NGVELEGRAMR 139
           NG  +EG  ++
Sbjct: 57  NGTTIEGHVVK 67

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

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 3/48 (6%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           +LFVGNL   V    L + FQ+YGNVV  R+      G+   +GFV +
Sbjct: 5   QLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVF 49

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

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

 Score = 37.1 bits (86), Expect = 3e-04
 Identities = 13/34 (38%), Positives = 22/34 (64%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIE 35
          L++  V+ D  T RSRGF F+T S+ ++ +  +E
Sbjct: 29 LTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

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

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

 Score = 36.8 bits (85), Expect = 3e-04
 Identities = 13/38 (34%), Positives = 21/38 (55%)

Query: 14 GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
          GR +G+AFV   + ED    + + +  E  GR +R+ F
Sbjct: 35 GRPKGYAFVEFESAEDAKEALNSCNNTEIEGRSIRLEF 72

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

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

 Score = 37.0 bits (85), Expect = 3e-04
 Identities = 17/50 (34%), Positives = 30/50 (60%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
          ++ + V+ D  T + +GF FVTM+  E+    I +L+G     +IL+V+F
Sbjct: 28 VTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSF 77

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

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

 Score = 36.8 bits (86), Expect = 3e-04
 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 14 GRSRGFAFVTMSTVEDCNAVIENLDGREY-LGRILRVNFS 52
          G +RG+AFVT +  E     ++ L   E   G+ L V  S
Sbjct: 39 GLNRGYAFVTYTNKEAAQRAVKQLHNYEIRPGKRLGVCIS 78

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

>gnl|CDD|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 = 3e-04
 Identities = 19/53 (35%), Positives = 34/53 (64%), Gaps = 3/53 (5%)

Query: 83  LTQAFQE--YGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL 133
           L + F +   G +VG  +  D E+G+++GY FV ++T  E + A+++LNG +L
Sbjct: 24  LRKIFSKFGVGKIVGIYMPVD-ETGKTKGYAFVEFATPEEAKEAVKALNGYKL 75

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

>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +FVG +   +    +   F +YG+V   +++ D  +G S+GYGFV +    +++  +ES
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDVQKIVES 65

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 37.2 bits (86), Expect = 3e-04
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++VGN+ +  T E L   F   G +    +L D  SG  +GY ++ ++T+  +E A+  L
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVA-L 60

Query: 129 NGVELEGRAMRV 140
           +     GR ++V
Sbjct: 61  DESSFRGRVIKV 72

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

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

 Score = 36.9 bits (86), Expect = 3e-04
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAF-QEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           +L V NL  S+T   L + F +  G +   ++L   E G+SR   F+ Y T+ E + A +
Sbjct: 2   RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRT-EDGKSRRIAFIGYKTEEEAQKAKD 60

Query: 127 SLNGVELEGRAMRVSLA 143
             N   +    + V  A
Sbjct: 61  YFNNTYINTSKISVEFA 77

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

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

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 14/51 (27%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF-SDKPK 56
           ++ D  T + +G+ FV+M+  ++    I +L+G     R+L+V+F ++K  
Sbjct: 301 IIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAY 351

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

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

 Score = 37.0 bits (86), Expect = 4e-04
 Identities = 16/43 (37%), Positives = 22/43 (51%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          D  T R RGFA+V    V D    +  LD   +LGR + + F+
Sbjct: 35 DFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEIQFA 77

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

 Score = 36.4 bits (85), Expect = 4e-04
 Identities = 14/35 (40%), Positives = 16/35 (45%)

Query: 18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          GFAFV      D    +  LDGR   G  +RV  S
Sbjct: 37 GFAFVEFEDPRDAEDAVRALDGRRICGNRVRVELS 71

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

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

 Score = 36.9 bits (86), Expect = 4e-04
 Identities = 15/33 (45%), Positives = 19/33 (57%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREY 42
          D  TG+S+GFA+VT S         E L+G EY
Sbjct: 34 DPYTGKSKGFAYVTYSNPASAIYAKEKLNGFEY 66

This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

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

 Score = 37.0 bits (85), Expect = 4e-04
 Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           L V NLS  V+ E L +AF ++G V  A V+ D + GRS G G V +++K     A E
Sbjct: 2   LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVD-DRGRSTGKGIVEFASKPAARKAFE 58

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

>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 36.7 bits (85), Expect = 4e-04
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           F LFVGNL+ +   + L  A  E+ +     V  D   G S+ +G+V + +  ++E ALE
Sbjct: 1   FSLFVGNLNPNKDFDELKTAISEFFSKKNLAVQ-DVRIGSSKKFGYVDFESAEDLEKALE 59

Query: 127 SLNGVELEGRAMRVSLA 143
            L G +L G  +++  A
Sbjct: 60  -LTGKKLLGNEIKLEKA 75

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 36.9 bits (86), Expect = 4e-04
 Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 18/89 (20%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGAR---VLYDGESGRSRGY--------------G 111
           +FVGNL  +   + L + F+++G +   R   V    +    +                 
Sbjct: 3   VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRV 140
           +V +  +   E AL+ LNG E EG  +RV
Sbjct: 63  YVVFKEEESAEKALK-LNGTEFEGHHIRV 90

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

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

 Score = 36.9 bits (86), Expect = 5e-04
 Identities = 18/52 (34%), Positives = 26/52 (50%)

Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYA 63
            G+ RGFAFV  +T ED     + L+G    G  +RV+F +  +P   L  
Sbjct: 39 PNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRVSFGNPGRPGASLLN 90

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

 Score = 36.2 bits (84), Expect = 6e-04
 Identities = 17/48 (35%), Positives = 31/48 (64%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          LS++ V  D+++G+S+GFA+V     ED     + LDG+ + GR++ +
Sbjct: 29 LSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVFQGRLIHI 76

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

>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 36.1 bits (84), Expect = 6e-04
 Identities = 13/31 (41%), Positives = 19/31 (61%)

Query: 19 FAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          FAFVT  + E+    +E LDG ++ GR+L  
Sbjct: 44 FAFVTFRSEEERQKALEILDGFKWKGRVLSA 74

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 36.4 bits (85), Expect = 6e-04
 Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 3/47 (6%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD 53
          V++DR      G A V     E+ +  IE L+GR + GR L     D
Sbjct: 43 VVFDRH---PDGVASVKFKEPEEADRCIEALNGRWFAGRQLEAERWD 86

This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 91

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

 Score = 36.2 bits (83), Expect = 6e-04
 Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 6/71 (8%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++ G ++  +T + + Q F  +G ++  RV  +      +GY F+ +ST      A+ S+
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE------KGYSFIRFSTHESAAHAIVSV 56

Query: 129 NGVELEGRAMR 139
           NG  +EG  ++
Sbjct: 57  NGTTIEGHVVK 67

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

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

 Score = 36.2 bits (83), Expect = 7e-04
 Identities = 16/50 (32%), Positives = 30/50 (60%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
          ++ + V+ D  T + +GF FVTM+  ++    I +L+G     R+L+V+F
Sbjct: 30 VTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSF 79

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

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

 Score = 36.1 bits (83), Expect = 7e-04
 Identities = 17/66 (25%), Positives = 36/66 (54%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++FVG +   +  + L   F++ G +   R++ D  SG++RGY F+ +  K   + A++ 
Sbjct: 3   EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKL 62

Query: 128 LNGVEL 133
            +  E+
Sbjct: 63  CDNYEI 68

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma Protein (EWS)

 Score = 36.4 bits (84), Expect = 7e-04
 Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 8/82 (9%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNV-VGAR-------VLYDGESGRSRGYGFVCYSTKAE 120
           ++V  L+ +VT E L   F+  G V +  R       +  D E+G+ +G   V Y     
Sbjct: 3   IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPS 62

Query: 121 METALESLNGVELEGRAMRVSL 142
            + A+E  +G + +G  ++VSL
Sbjct: 63  AKAAVEWFDGKDFQGSKLKVSL 84

This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene. . Length = 84

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

 Score = 35.8 bits (82), Expect = 8e-04
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VGNLS  VT   + Q F + G     +++ D  +  +  Y FV +        +L ++
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59

Query: 129 NGVELEGRAMRVSLA 143
           NG ++ G+ ++V+ A
Sbjct: 60  NGRKIMGKEVKVNWA 74

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 35.4 bits (82), Expect = 0.001
 Identities = 16/44 (36%), Positives = 28/44 (63%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
          V+ D +TG+S+G+ FV+    ED    I++++G+   GR +R N
Sbjct: 31 VVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAIRTN 74

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

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

 Score = 35.4 bits (82), Expect = 0.001
 Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 3/28 (10%)

Query: 6  TVLYDRETGRSRGFAFVTM---STVEDC 30
           ++ D +TGRSRGF FVT    S VE  
Sbjct: 30 QLMQDHDTGRSRGFGFVTFDSESAVERV 57

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

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 35.3 bits (82), Expect = 0.001
 Identities = 10/34 (29%), Positives = 23/34 (67%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGR 40
          ++ +++TG+S G+ FV  +T E     +++L+G+
Sbjct: 31 IIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGK 64

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

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

 Score = 35.3 bits (82), Expect = 0.001
 Identities = 13/40 (32%), Positives = 19/40 (47%)

Query: 13 TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
           G  RGFAFV   T ++    +E L      GR L + ++
Sbjct: 37 DGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLVLEYA 76

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

>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 35.8 bits (82), Expect = 0.001
 Identities = 17/57 (29%), Positives = 32/57 (56%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          ++ + V+ D  T + +GF FVTM+  ++    I +L+G     R+L+V+F    + K
Sbjct: 28 VTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTSKQHK 84

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

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

 Score = 35.8 bits (82), Expect = 0.001
 Identities = 16/50 (32%), Positives = 30/50 (60%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
          ++ + V+ D  T + +GF FVTM+  ++    I +L+G     R+L+V+F
Sbjct: 30 VNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSF 79

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

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 35.4 bits (82), Expect = 0.001
 Identities = 17/50 (34%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 1  MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
           ++++++  DRETG S+GFA++   +V+     +E LDG +  G  L V+
Sbjct: 29 EITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE-LDGSDLGGGNLVVD 77

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 35.6 bits (83), Expect = 0.001
 Identities = 11/42 (26%), Positives = 20/42 (47%)

Query: 11 RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
           +T + RG AFV    VE     +  L G  +  + +R+ ++
Sbjct: 36 SKTLKMRGQAFVVFKDVESATNALRALQGFPFYDKPMRIQYA 77

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

>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 12/36 (33%), Positives = 22/36 (61%)

Query: 110 YGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG 145
           + FV + ++ E + ALE L+G + +GR +   LA+ 
Sbjct: 44  FAFVTFRSEEERQKALEILDGFKWKGRVLSARLAKP 79

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGR--SRGYGFVCYSTKAEMETAL 125
           K+FVG +  S + + L + F++YG V    VL D       S+G  FV + T+   + AL
Sbjct: 3   KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTR---KAAL 59

Query: 126 ESLN 129
           E+ N
Sbjct: 60  EAQN 63

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 4/79 (5%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FVGNL +    E L + F + G +   R++ D ++   +G+ +V +  +  +E AL  L
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL-LL 60

Query: 129 NGVE---LEGRAMRVSLAQ 144
           N  +   +  R +RVS  +
Sbjct: 61  NEKKFPPMLPRELRVSRCK 79

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241208 cd12764, RRM2_SRSF4, RNA recognition motif 2 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 35.5 bits (81), Expect = 0.001
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 5/74 (6%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           ++L V NLS   + + L    ++ G V  A    D   GR +  G + + + ++M+ ALE
Sbjct: 1   YRLIVENLSSRCSWQDLKDYMRQAGEVTYA----DAHKGR-KNEGVIEFRSYSDMKRALE 55

Query: 127 SLNGVELEGRAMRV 140
            L+G E+ GR +R+
Sbjct: 56  KLDGTEVNGRKIRL 69

This subgroup corresponds to the RRM2 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4), 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. SFRS4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, SRSF4 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 RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|241071 cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3)

 Score = 35.3 bits (81), Expect = 0.001
 Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 9/82 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFV-CYSTKAEMETALE 126
           KL++GNLS + +   L   F++      +++ + G      GY FV C      M+ A++
Sbjct: 3   KLYIGNLSENASPLDLESIFKD------SKIPFSGPFLVKSGYAFVDCPDESWAMK-AID 55

Query: 127 SLNG-VELEGRAMRVSLAQGRR 147
           +L+G VEL G+ + V  +  +R
Sbjct: 56  TLSGKVELHGKVIEVEHSVPKR 77

This subgroup corresponds to the RRM1 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 35.3 bits (81), Expect = 0.001
 Identities = 15/48 (31%), Positives = 25/48 (52%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           K+FVG +        L   F++YG +    ++ D  SG+ RG+ FV +
Sbjct: 2   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 49

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

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

 Score = 35.3 bits (82), Expect = 0.001
 Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 9/79 (11%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE-S 127
           L+VG L   VT + L   F ++G +    V+        +   FV ++T+   E A E  
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREAAEKAAERL 57

Query: 128 LNGVELEGRAMRVSLAQGR 146
            N + + GR  R+ L  GR
Sbjct: 58  FNKLIINGR--RLKLKWGR 74

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 15/77 (19%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGN---------VVGARVLYDGES------GRSRGYGF 112
           +L + NL  SV  + L + F +  +         +   +++ D +       G+S+GYGF
Sbjct: 2   RLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGF 61

Query: 113 VCYSTKAEMETALESLN 129
           V ++       AL +LN
Sbjct: 62  VEFTNHEHALKALRALN 78

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

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

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V NL  S T E++ + F         RV       + R Y FV +S + +   A+ +L
Sbjct: 11  LYVRNLMLSTTEETIEKEFNSIKPGAVERV------KKIRDYAFVHFSNREDAVDAMNAL 64

Query: 129 NGVELEGRAMRVSLAQ 144
           NG  ++G  + V+LA+
Sbjct: 65  NGKVIDGSPIEVTLAK 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|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 35.3 bits (82), Expect = 0.001
 Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 8/68 (11%)

Query: 69  LFVGN--LSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           L V N  L   V+ E L + F++YG V    +         + Y FV YS+  +   A +
Sbjct: 4   LVVANGGLGNGVSREELLRVFEKYGTVEDLVMP------PGKPYCFVSYSSIEDAAAAYD 57

Query: 127 SLNGVELE 134
           +LNG ELE
Sbjct: 58  ALNGKELE 65

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

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

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 4/39 (10%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIEN----LDGRE 41
          V+ D  T RSRGF FVT ++  + +A +      +DGRE
Sbjct: 31 VMKDPNTKRSRGFGFVTFASASEVDAAMNARPHKVDGRE 69

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

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

 Score = 34.8 bits (81), Expect = 0.002
 Identities = 14/40 (35%), Positives = 23/40 (57%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          DRE    RG+A+V   + ED    I+++DG +  G+ + V
Sbjct: 33 DREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTV 72

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

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

 Score = 35.5 bits (81), Expect = 0.002
 Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 4/43 (9%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVI----ENLDGR 40
          L+   V+ D +T RSRGF FVT S VE+ +A +      +DGR
Sbjct: 29 LTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSARPHKVDGR 71

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

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

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 15/45 (33%), Positives = 25/45 (55%)

Query: 5  LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          +     +  G+S+GFA+V  ++     AV E L+GRE+ G+   V
Sbjct: 30 IKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNGKKCVV 74

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

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           +VGNL  + T + L + F + G V   R+   G+  +   Y FV ++ +  +  AL+ LN
Sbjct: 8   YVGNLDPTTTADQLLEFFSQAGEVKYVRMA--GDETQPTRYAFVEFAEQTSVINALK-LN 64

Query: 130 GVELEGRAMRV 140
           G    GR ++V
Sbjct: 65  GAMFGGRPLKV 75

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

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

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V NL  SV+ + L Q F  YG +   R     E+   R + F+ +      E AL++L
Sbjct: 4   LVVFNLDPSVSNDDLHQIFGAYGEIKEIR-----ETPNKRHHKFIEFYDVRSAEAALKAL 58

Query: 129 NGVELEGRAMRV 140
           N  E+ G+ +++
Sbjct: 59  NRSEIAGKRIKL 70

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

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

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 8/78 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++++G L +      + + F+ YG +         E     G+GFV +    + + A+  
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRI--------REINLKNGFGFVEFEDPRDADDAVYE 52

Query: 128 LNGVELEGRAMRVSLAQG 145
           LNG EL G  + V  A+G
Sbjct: 53  LNGKELCGERVIVEHARG 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|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 18/61 (29%), Positives = 30/61 (49%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++V  L  + T E L   F +YG VV   +     +G  +G+ F+ + T  E + A + L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 129 N 129
           N
Sbjct: 62  N 62

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

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

 Score = 34.5 bits (79), Expect = 0.002
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 8/78 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++++G LS+ V  + + + F  YG ++        E     GYGFV +    + + A+  
Sbjct: 1   RVYIGRLSYHVREKDIQRFFGGYGKLL--------EIDLKNGYGFVEFEDSRDADDAVYE 52

Query: 128 LNGVELEGRAMRVSLAQG 145
           LNG +L G  + V  A+G
Sbjct: 53  LNGKDLCGERVIVEHARG 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|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 35.1 bits (81), Expect = 0.002
 Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 11/83 (13%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSR--------GYGFVCYSTKA 119
           ++++ NLS+S + E L +  +++  V    VL   ++ R          G  +  +S+  
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDFEPV---SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPE 57

Query: 120 EMETALESLNGVELEGRAMRVSL 142
           + E  ++ LNG   + R + V L
Sbjct: 58  QAEKVVKDLNGKVFKNRKLFVKL 80

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

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

 Score = 34.2 bits (79), Expect = 0.003
 Identities = 15/36 (41%), Positives = 19/36 (52%)

Query: 14 GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          GRS+GF  V   + ED    IE  +G +  GR L V
Sbjct: 36 GRSKGFGTVLFESPEDAQRAIEMFNGYDLEGRELEV 71

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

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

 Score = 34.5 bits (80), Expect = 0.003
 Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 5/51 (9%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL-----GRILRVNFS 52
          ++ D+ TG S+G AFV   T E     +E  D  E       GR L V  +
Sbjct: 32 IVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDGRRLIVTLA 82

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

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

 Score = 34.2 bits (79), Expect = 0.003
 Identities = 11/17 (64%), Positives = 15/17 (88%)

Query: 7  VLYDRETGRSRGFAFVT 23
          ++ D+ETG+ RGFAFVT
Sbjct: 31 IVTDKETGKKRGFAFVT 47

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

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

 Score = 34.5 bits (80), Expect = 0.003
 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 16/54 (29%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDC--------NAVIENLDGREYLGRILRVNFS 52
          V+ D++TG S  +AF+   T EDC        N +I++        R + V+FS
Sbjct: 35 VIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDD--------RRIHVDFS 80

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

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

 Score = 34.4 bits (79), Expect = 0.003
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L + NL  +V++E+L   FQ YG+V   R     E+   R   FV +    +   AL ++
Sbjct: 4   LVIFNLDPTVSSETLRSIFQVYGDVKELR-----ETPCKREQRFVEFFDVRDAAKALRAM 58

Query: 129 NGVELEGRAMRV 140
           NG E+ G+ + +
Sbjct: 59  NGKEISGKPVVI 70

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

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

 Score = 34.7 bits (79), Expect = 0.003
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VGNLS  VT   + Q F + G     +++   E   +  Y FV +    +   AL ++
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMI--TEHTSNDPYCFVEFYEHRDAAAALAAM 59

Query: 129 NGVELEGRAMRVSLA 143
           NG ++ G+ ++V+ A
Sbjct: 60  NGRKILGKEVKVNWA 74

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

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

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 8/80 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++++G LS+      + + F+ YG ++        E     GYGFV +    + + A+  
Sbjct: 1   RVYIGRLSYQARERDVERFFKGYGKIL--------EVDLKNGYGFVEFDDLRDADDAVYE 52

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           LNG +L G  + V  A+G R
Sbjct: 53  LNGKDLCGERVIVEHARGPR 72

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

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

 Score = 34.4 bits (79), Expect = 0.003
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++VGNL   +    +   F +YG +V   +       R  GY F+ +    + E A+   
Sbjct: 2   VYVGNLPGDIREREVEDLFYKYGPIVDIDLKL---PPRPPGYAFIEFEDARDAEDAIRGR 58

Query: 129 NGVELEGRAMRVSL 142
           +G + +G+ +RV L
Sbjct: 59  DGYDFDGQRLRVEL 72

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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 16/48 (33%), Positives = 26/48 (54%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           K+FVG +        L   F++YG +    V+ D +SG+ RG+ FV +
Sbjct: 2   KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF 49

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|241139 cd12695, RRM3_PTBP1, RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 1 (PTB)

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 69  LFVGNLS-WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           L V NL+   VT + L   F  YG+V   ++L++ +         V  +   + + A+  
Sbjct: 2   LLVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAMSH 56

Query: 128 LNGVELEGRAMRVSLAQ 144
           LNG +L G+ +R++L++
Sbjct: 57  LNGQKLHGKPLRITLSK 73

This subgroup corresponds to the RRM3 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence show that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution. . Length = 93

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 34.4 bits (79), Expect = 0.004
 Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 4/38 (10%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIEN----LDGR 40
          ++ D+ T RSRGF FV          V+      LDGR
Sbjct: 31 IMKDKTTNRSRGFGFVKFKDPNCVGTVLAGGPHTLDGR 68

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

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

 Score = 33.9 bits (78), Expect = 0.004
 Identities = 14/46 (30%), Positives = 25/46 (54%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          ++ D+ TG S GF FV   + ED    I  L+G +   + ++V ++
Sbjct: 32 IVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYA 77

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

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

 Score = 34.1 bits (79), Expect = 0.004
 Identities = 12/39 (30%), Positives = 22/39 (56%)

Query: 11 RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          ++TG+S+G+AFV   + E    V E ++      R+L+ 
Sbjct: 35 KKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKC 73

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

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

 Score = 34.2 bits (78), Expect = 0.004
 Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           L V NL   V+ E L +AF  +G V  A V+ D + GR  G G V ++ K     AL+
Sbjct: 2   LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVD-DRGRPTGKGIVEFAGKPSARKALD 58

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

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

 Score = 33.9 bits (78), Expect = 0.004
 Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 8  LY-DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          LY D++TG  +G A VT       +A IE  + ++++G  ++V
Sbjct: 38 LYKDKDTGEPKGEATVTYDDPHAASAAIEWFNNKDFMGNTIKV 80

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

>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 33.8 bits (77), Expect = 0.004
 Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQE-YGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           ++F+ N+ + +  +++    +E  G V    +  D E G+SRG G V +  +  ++ ALE
Sbjct: 1   RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAE-GKSRGCGVVEFKDEEFVKKALE 59

Query: 127 SLNGVELEGRAMRV 140
            +N  +L GR + +
Sbjct: 60  VMNKYDLNGRPLNI 73

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	148
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.97
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.96
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.96
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.95
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.95
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.94
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.93
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.93
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.92
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.92
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.92
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.91
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.9
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.89
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.89
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.88
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.88
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.88
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.88
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.87
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.81
KOG0122	270	consensus Translation initiation factor 3, subunit	99.81
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.81
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.81
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.8
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.79
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.78
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.78
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.77
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.77
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.76
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.74
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.74
PLN03120	260	nucleic acid binding protein; Provisional	99.72
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.72
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.71
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.7
smart00362	72	RRM_2 RNA recognition motif.	99.69
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.69
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.67
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.66
smart00360	71	RRM RNA recognition motif.	99.66
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.66
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.66
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.65
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.64
PLN03213	759	repressor of silencing 3; Provisional	99.64
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.63
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.62
PLN03121	243	nucleic acid binding protein; Provisional	99.62
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.61
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.61
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.59
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.58
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.56
smart00361	70	RRM_1 RNA recognition motif.	99.56
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.56
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.56
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.53
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.53
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.52
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.51
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.49
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.49
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.44
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.44
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.43
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.43
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.43
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.37
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.33
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.32
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.32
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.31
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.3
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.28
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.27
smart00361	70	RRM_1 RNA recognition motif.	99.26
KOG0226	290	consensus RNA-binding proteins [General function p	99.23
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.23
KOG0122	270	consensus Translation initiation factor 3, subunit	99.22
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.2
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.16
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.16
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.15
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.12
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	99.11
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.09
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.08
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.06
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.01
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.0
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.0
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.0
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.99
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.97
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.96
smart00360	71	RRM RNA recognition motif.	98.94
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.94
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.94
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.94
KOG4210	285	consensus Nuclear localization sequence binding pr	98.9
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.88
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.88
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.87
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.82
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.81
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	98.78
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.74
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.74
smart00362	72	RRM_2 RNA recognition motif.	98.73
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.72
KOG0151	877	consensus Predicted splicing regulator, contains R	98.7
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.69
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.66
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.64
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.63
PLN03121	243	nucleic acid binding protein; Provisional	98.59
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.59
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.59
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.59
PLN03120	260	nucleic acid binding protein; Provisional	98.58
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	98.58
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.56
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	98.53
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.4
PLN03213	759	repressor of silencing 3; Provisional	98.38
KOG0226	290	consensus RNA-binding proteins [General function p	98.32
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.31
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.23
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.16
KOG3152	278	consensus TBP-binding protein, activator of basal	98.12
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	98.11
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	98.07
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	98.04
KOG1996	378	consensus mRNA splicing factor [RNA processing and	98.03
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.99
KOG2314	698	consensus Translation initiation factor 3, subunit	97.98
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	97.97
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.95
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.82
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.81
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.77
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.63
KOG2591	684	consensus c-Mpl binding protein, contains La domai	97.6
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.58
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.56
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.51
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.48
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.47
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.45
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	97.39
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.38
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	97.35
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	97.23
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.1
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.96
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.94
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	96.86
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	96.84
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	96.82
KOG2314	698	consensus Translation initiation factor 3, subunit	96.7
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	96.52
KOG0533	243	consensus RRM motif-containing protein [RNA proces	96.52
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.31
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.22
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.2
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.91
KOG0151	877	consensus Predicted splicing regulator, contains R	95.88
KOG2135	526	consensus Proteins containing the RNA recognition	95.82
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.81
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.58
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	95.55
KOG4660	549	consensus Protein Mei2, essential for commitment t	95.52
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.96
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.79
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.69
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	94.67
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	94.47
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	94.4
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.3
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.14
COG5175	480	MOT2 Transcriptional repressor [Transcription]	93.99
KOG1996	378	consensus mRNA splicing factor [RNA processing and	93.41
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	93.26
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	91.04
KOG4210	285	consensus Nuclear localization sequence binding pr	90.89
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	89.45
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	88.54
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	87.36
PF07530	68	PRE_C2HC: Associated with zinc fingers; InterPro:	85.47
smart00596	69	PRE_C2HC PRE_C2HC domain.	85.04
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	82.37
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	81.25
KOG2318	650	consensus Uncharacterized conserved protein [Funct	81.12
PF02714	325	DUF221: Domain of unknown function DUF221; InterPr	80.63

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=6.1e-32  Score=188.13  Aligned_cols=141  Identities=30%  Similarity=0.521  Sum_probs=128.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      .|++|+|++|+.+++++|||||+|.++++|++|+..|++..+.+++|.|.++.+....     ....+|||.|||.++++
T Consensus       133 ~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~~~-----~~~~~lfV~nLp~~vte  207 (346)
T TIGR01659       133 PINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGES-----IKDTNLYVTNLPRTITD  207 (346)
T ss_pred             CEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccccccc-----cccceeEEeCCCCcccH
Confidence            4789999999999999999999999999999999999999999999999988653321     23568999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEeccCC
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG--RAMRVSLAQGR  146 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g--~~l~v~~~~~~  146 (148)
                      ++|+++|++||.|..+.++.+..++.++++|||+|.+.++|++|++.||+..+.|  +.|.|.++..+
T Consensus       208 e~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       208 DQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             HHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcc
Confidence            9999999999999999999998889999999999999999999999999998866  78999988654

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).

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

Probab=100.00  E-value=3.8e-31  Score=193.27  Aligned_cols=146  Identities=21%  Similarity=0.404  Sum_probs=129.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC------CCCCCCcceEEEcCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL------PLYAETDFKLFVGNL   74 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~------~~~~~~~~~l~i~nl   74 (148)
                      .|.+|++++|+.+|+++|||||+|.+.++|+.|+..++|..+.|+.|.|.+........      .......++|||+||
T Consensus       133 ~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnL  212 (612)
T TIGR01645       133 PIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASV  212 (612)
T ss_pred             CEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccccccccccccccccccccccceEEeecC
Confidence            37899999999999999999999999999999999999999999999998654322111      111234578999999


Q ss_pred             CCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           75 SWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        75 p~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      |+++++++|+++|+.||.|.++.+.+++.++.++|||||+|.+.++|.+|+..||+..++|+.|+|.++.++
T Consensus       213 p~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       213 HPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             CCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCC
Confidence            999999999999999999999999999888899999999999999999999999999999999999998653

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.

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

Probab=99.97  E-value=4.1e-30  Score=167.63  Aligned_cols=139  Identities=27%  Similarity=0.536  Sum_probs=126.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC-----------CCCCCCcceE
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL-----------PLYAETDFKL   69 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~-----------~~~~~~~~~l   69 (148)
                      .|.+.+|++|..|++++||+||.|...++|+.||..++|..++++.|+-.|+.++....           ......+++|
T Consensus        88 evS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsV  167 (321)
T KOG0148|consen   88 EVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSV  167 (321)
T ss_pred             ccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCCccHHHHhccCCCCCceE
Confidence            37789999999999999999999999999999999999999999999999997765322           1234578999


Q ss_pred             EEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           70 FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        70 ~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      |++|++..+++++|++.|.+||+|..+++.++      +||+||.|++.|.|..|+-.+|+.+|.|..++..|-+.
T Consensus       168 Y~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe  237 (321)
T KOG0148|consen  168 YVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKE  237 (321)
T ss_pred             EeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEecccc
Confidence            99999999999999999999999999999977      67999999999999999999999999999999988543

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=3.2e-29  Score=176.69  Aligned_cols=146  Identities=27%  Similarity=0.465  Sum_probs=125.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecC--cEEEEeecCCCCCCC-------------------
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG--RILRVNFSDKPKPKL-------------------   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~--~~i~v~~~~~~~~~~-------------------   59 (148)
                      +|..++++.+..++.++|||||+|.+.++|+.|+..|++..+.+  .++.+.++..+....                   
T Consensus       115 ~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (352)
T TIGR01661       115 QIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRV  194 (352)
T ss_pred             CEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCC
Confidence            36788899998899999999999999999999999999998876  567777764332000                   


Q ss_pred             --------------------------------------------------CC------------------CCCCcceEEE
Q 032044           60 --------------------------------------------------PL------------------YAETDFKLFV   71 (148)
Q Consensus        60 --------------------------------------------------~~------------------~~~~~~~l~i   71 (148)
                                                                        ..                  ......+|||
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV  274 (352)
T TIGR01661       195 PLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFV  274 (352)
T ss_pred             CccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEE
Confidence                                                              00                  0011236999


Q ss_pred             cCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           72 GNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        72 ~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      +|||+.+++++|+++|++||.|.+++++.++.++.++|||||+|.+.++|..|+..|||..++|+.|+|.|...+
T Consensus       275 ~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       275 YNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNK  349 (352)
T ss_pred             eCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCC
Confidence            999999999999999999999999999999889999999999999999999999999999999999999998765

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=5.3e-29  Score=175.56  Aligned_cols=141  Identities=25%  Similarity=0.518  Sum_probs=127.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      .|.+|+|++++.+|+++|||||+|.+.++|.+|+..|++..+.|++|.|.++.+....     ...++|||.|||..+++
T Consensus        29 ~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~~-----~~~~~l~v~~l~~~~~~  103 (352)
T TIGR01661        29 EIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSDS-----IKGANLYVSGLPKTMTQ  103 (352)
T ss_pred             CEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecccccc-----cccceEEECCccccCCH
Confidence            4789999999999999999999999999999999999999999999999998654322     23568999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEeccCC
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG--RAMRVSLAQGR  146 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g--~~l~v~~~~~~  146 (148)
                      ++|+++|.+||.+..+.++.+..++.++|+|||+|.+.++|+.|+..|||..+.|  .+|.+.++..+
T Consensus       104 ~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~  171 (352)
T TIGR01661       104 HELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNP  171 (352)
T ss_pred             HHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCC
Confidence            9999999999999999999887778899999999999999999999999998877  67888887654

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

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

Probab=99.97  E-value=1.5e-28  Score=178.44  Aligned_cols=143  Identities=35%  Similarity=0.608  Sum_probs=127.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC-------CCCCCCcceEEEcC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL-------PLYAETDFKLFVGN   73 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~-------~~~~~~~~~l~i~n   73 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|.+|+. +++..+.|++|.|.++.......       ........+|||+|
T Consensus       115 ~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~n  193 (457)
T TIGR01622       115 KVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGN  193 (457)
T ss_pred             CeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcC
Confidence            47899999999999999999999999999999997 99999999999998765432211       11112368999999


Q ss_pred             CCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           74 LSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        74 lp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ||..+++++|+++|++||.|..+.+..+..++.++|+|||+|.+.++|..|+..|+|..|.|+.|.|.++.
T Consensus       194 l~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       194 LHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            99999999999999999999999999998888899999999999999999999999999999999999965

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.

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

Probab=99.96  E-value=1.6e-28  Score=159.74  Aligned_cols=140  Identities=28%  Similarity=0.533  Sum_probs=127.9

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHH
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTE   81 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~   81 (148)
                      |++|+++||+.+|++.||+||-|.+++||++|+..|||..+..++|+|.|+.+....     .....|||++||...+..
T Consensus        68 iEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~~-----Ik~aNLYvSGlPktMtqk  142 (360)
T KOG0145|consen   68 IESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSDS-----IKDANLYVSGLPKTMTQK  142 (360)
T ss_pred             eeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChhh-----hcccceEEecCCccchHH
Confidence            899999999999999999999999999999999999999999999999999765443     244579999999999999


Q ss_pred             HHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCe--EEEEEeccCC
Q 032044           82 SLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR--AMRVSLAQGR  146 (148)
Q Consensus        82 ~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~--~l~v~~~~~~  146 (148)
                      +|+++|++||.|.-.+|..+.-++.++|.+||.|+....|++|+..|||..-.|.  +|.|+++..+
T Consensus       143 elE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannP  209 (360)
T KOG0145|consen  143 ELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNP  209 (360)
T ss_pred             HHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCc
Confidence            9999999999988888888888899999999999999999999999999887764  6999988644

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

Probab=99.96  E-value=3.9e-27  Score=174.75  Aligned_cols=141  Identities=27%  Similarity=0.469  Sum_probs=125.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      .|.+|+|.+|+.|++++|||||+|.+.++|++|+..+++..+.|++|.|.|+......   ......+|||+|||.++++
T Consensus        26 ~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~~---~~~~~~~vfV~nLp~~~~~  102 (562)
T TIGR01628        26 PVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPSL---RRSGVGNIFVKNLDKSVDN  102 (562)
T ss_pred             CEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccccc---cccCCCceEEcCCCccCCH
Confidence            3789999999999999999999999999999999999999999999999997543221   2224557999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      ++|+++|+.||.|..+.+..+ .++.++|+|||+|.+.++|++|+..+||..++|+.|.+....+
T Consensus       103 ~~L~~~F~~~G~i~~~~i~~~-~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~  166 (562)
T TIGR01628       103 KALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIK  166 (562)
T ss_pred             HHHHHHHHhcCCcceeEeeec-CCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEecccc
Confidence            999999999999999999887 4677899999999999999999999999999999999876543

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

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

Probab=99.95  E-value=3e-27  Score=163.39  Aligned_cols=138  Identities=31%  Similarity=0.452  Sum_probs=116.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCee-cCcEEEEeecCCCC---------C-------------
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREY-LGRILRVNFSDKPK---------P-------------   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~-~~~~i~v~~~~~~~---------~-------------   57 (148)
                      +|.++++|+|+.+|.++|||||.|.+++.|+.|++.||+..| .|+.|.|..+....         .             
T Consensus       109 ~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan~RLFiG~IPK~k~keeIlee~~kV  188 (506)
T KOG0117|consen  109 KIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKV  188 (506)
T ss_pred             ceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeecceeEeccCCccccHHHHHHHHHhh
Confidence            578999999999999999999999999999999999999987 47777775432210         0             


Q ss_pred             --------------------------------------------------------------CCCCCCCCcceEEEcCCC
Q 032044           58 --------------------------------------------------------------KLPLYAETDFKLFVGNLS   75 (148)
Q Consensus        58 --------------------------------------------------------------~~~~~~~~~~~l~i~nlp   75 (148)
                                                                                    ..+.....-..|||+||+
T Consensus       189 teGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~  268 (506)
T KOG0117|consen  189 TEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLM  268 (506)
T ss_pred             CCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccc
Confidence                                                                          000011123579999999


Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           76 WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        76 ~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      .++|++.|++.|++||.|.++..+++        ||||.|.+.++|-+|++.+||++|+|..|.|.+++|.
T Consensus       269 ~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~  331 (506)
T KOG0117|consen  269 ESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPV  331 (506)
T ss_pred             hhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCCh
Confidence            99999999999999999999877644        9999999999999999999999999999999999875

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

Probab=99.95  E-value=1.9e-26  Score=171.11  Aligned_cols=144  Identities=36%  Similarity=0.617  Sum_probs=127.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeec----CcEEEEeecCCCCCCC-------------CCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL----GRILRVNFSDKPKPKL-------------PLYA   63 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~----~~~i~v~~~~~~~~~~-------------~~~~   63 (148)
                      .|.++.++++. +|.++|||||+|.+.++|.+|++.+++..+.    |+.+.+.++.......             ....
T Consensus       204 ~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~  282 (562)
T TIGR01628       204 EITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMK  282 (562)
T ss_pred             CEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcc
Confidence            37789999985 7899999999999999999999999999999    9999998775443220             1113


Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ....+|||+||+.++++++|+++|++||.|.++.++.+ .++.++|+|||+|.+.++|.+|+..+||..++|+.|.|.++
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            35668999999999999999999999999999999988 67889999999999999999999999999999999999998


Q ss_pred             cCC
Q 032044          144 QGR  146 (148)
Q Consensus       144 ~~~  146 (148)
                      .++
T Consensus       362 ~~k  364 (562)
T TIGR01628       362 QRK  364 (562)
T ss_pred             cCc
Confidence            765

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

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

Probab=99.95  E-value=2.1e-27  Score=163.61  Aligned_cols=143  Identities=29%  Similarity=0.530  Sum_probs=126.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCee---cCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREY---LGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWS   77 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~---~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~   77 (148)
                      .|.+|.|++|+.|+.++|||||.|.+.++|.+|+..|++...   ...++.|+|+....++.    ...++|||+-|+..
T Consensus        60 ~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er~----~~e~KLFvg~lsK~  135 (510)
T KOG0144|consen   60 NVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERERI----VEERKLFVGMLSKQ  135 (510)
T ss_pred             ceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhcc----ccchhhhhhhcccc
Confidence            378999999999999999999999999999999999988753   35778999887665543    34568999999999


Q ss_pred             CCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCc-eeCC--eEEEEEeccCCCC
Q 032044           78 VTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV-ELEG--RAMRVSLAQGRRS  148 (148)
Q Consensus        78 ~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~-~i~g--~~l~v~~~~~~~~  148 (148)
                      ++|.+++++|.+||.|+.+.|.++ ..+.+||+|||.|.+.+.|..|++.|||. .+.|  .+|.|+|++++++
T Consensus       136 ~te~evr~iFs~fG~Ied~~ilrd-~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkd  208 (510)
T KOG0144|consen  136 CTENEVREIFSRFGHIEDCYILRD-PDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKD  208 (510)
T ss_pred             ccHHHHHHHHHhhCccchhhheec-ccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCC
Confidence            999999999999999999999999 45889999999999999999999999995 5655  6899999988764

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

Probab=99.94  E-value=1.3e-25  Score=165.10  Aligned_cols=137  Identities=20%  Similarity=0.395  Sum_probs=115.8

Q ss_pred             eecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC------------------------CCCC
Q 032044            8 LYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL------------------------PLYA   63 (148)
Q Consensus         8 ~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~------------------------~~~~   63 (148)
                      +.+...+.++|||||+|.+.++|..||. |+|..+.|.+|.|..........                        ....
T Consensus       214 v~~~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  292 (509)
T TIGR01642       214 VSSVNINKEKNFAFLEFRTVEEATFAMA-LDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVL  292 (509)
T ss_pred             eEEEEECCCCCEEEEEeCCHHHHhhhhc-CCCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCC
Confidence            3333445678999999999999999995 99999999999997543221000                        0012


Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ....+|||+|||..+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|+.|+..|+|..++|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            34578999999999999999999999999999999999888999999999999999999999999999999999999997


Q ss_pred             cC
Q 032044          144 QG  145 (148)
Q Consensus       144 ~~  145 (148)
                      ..
T Consensus       373 ~~  374 (509)
T TIGR01642       373 CV  374 (509)
T ss_pred             cc
Confidence            54

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

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

Probab=99.94  E-value=2.3e-26  Score=142.22  Aligned_cols=141  Identities=30%  Similarity=0.527  Sum_probs=126.5

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHH
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTE   81 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~   81 (148)
                      |.++.+.+|+.+...+||||++|.++++|+.|+.-|+...++|++|++..++..+...    .....++|+||.+.+++.
T Consensus        36 Vv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~~~~nl----~vganlfvgNLd~~vDe~  111 (203)
T KOG0131|consen   36 VVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASAHQKNL----DVGANLFVGNLDPEVDEK  111 (203)
T ss_pred             eeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecccccccc----cccccccccccCcchhHH
Confidence            5688999999999999999999999999999999999999999999999887333332    233689999999999999


Q ss_pred             HHHHHHhhcCCeeE-EEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           82 SLTQAFQEYGNVVG-ARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        82 ~l~~~f~~~g~v~~-~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      .|.+.|+.||.+.. -.+++++.++.+++++|+.|.+.+.+..|+..+||..++++++.|.++..+
T Consensus       112 ~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~  177 (203)
T KOG0131|consen  112 LLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKK  177 (203)
T ss_pred             HHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEec
Confidence            99999999998654 477888899999999999999999999999999999999999999998654

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

Probab=99.94  E-value=6.3e-25  Score=160.54  Aligned_cols=127  Identities=27%  Similarity=0.450  Sum_probs=111.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCC--CeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhh
Q 032044           12 ETGRSRGFAFVTMSTVEDCNAVIENLDG--REYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQE   89 (148)
Q Consensus        12 ~~~~~~g~afv~f~~~~~a~~a~~~l~~--~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~   89 (148)
                      ..++++|||||+|.+.++|..|++.|..  ..+.++.|.|.|+.+.....+.......+|||+|||.++++++|+++|++
T Consensus       177 ~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~  256 (578)
T TIGR01648       177 DKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSE  256 (578)
T ss_pred             ccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHh
Confidence            3568899999999999999999988764  46789999999987765444444455678999999999999999999999


Q ss_pred             c--CCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           90 Y--GNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        90 ~--g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      |  |.|..+.++        +++|||+|.+.++|++|+..||+..|+|+.|+|.++.++
T Consensus       257 f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~  307 (578)
T TIGR01648       257 FKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPV  307 (578)
T ss_pred             cCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCC
Confidence            9  999988765        448999999999999999999999999999999999774

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.

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

Probab=99.93  E-value=1.7e-24  Score=157.78  Aligned_cols=140  Identities=21%  Similarity=0.329  Sum_probs=115.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC--------------------
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP--------------------   60 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~--------------------   60 (148)
                      .|.+|++++++     +|+|||+|.+.++|..|+..|++..+.|++|.|.++.......+                    
T Consensus       302 ~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~  376 (481)
T TIGR01649       302 NVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRN  376 (481)
T ss_pred             CeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCcc
Confidence            47889999874     58999999999999999999999999999999998754311000                    


Q ss_pred             ------------CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCC--eeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHH
Q 032044           61 ------------LYAETDFKLFVGNLSWSVTTESLTQAFQEYGN--VVGARVLYDGESGRSRGYGFVCYSTKAEMETALE  126 (148)
Q Consensus        61 ------------~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~--v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~  126 (148)
                                  ....++.+|||.|||..+++++|+++|++||.  +..+.+....  +..+++|||+|.+.++|.+|+.
T Consensus       377 ~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~--~~~~~~gfVeF~~~e~A~~Al~  454 (481)
T TIGR01649       377 HRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD--NERSKMGLLEWESVEDAVEALI  454 (481)
T ss_pred             ccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC--CCcceeEEEEcCCHHHHHHHHH
Confidence                        00124568999999999999999999999998  7777775432  2357899999999999999999


Q ss_pred             HhCCceeCCeE------EEEEeccCCC
Q 032044          127 SLNGVELEGRA------MRVSLAQGRR  147 (148)
Q Consensus       127 ~l~~~~i~g~~------l~v~~~~~~~  147 (148)
                      .|||..|.|+.      |+|.+++++.
T Consensus       455 ~ln~~~l~~~~~~~~~~lkv~fs~~~~  481 (481)
T TIGR01649       455 ALNHHQLNEPNGSAPYHLKVSFSTSRI  481 (481)
T ss_pred             HhcCCccCCCCCCccceEEEEeccCCC
Confidence            99999999884      9999998763

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=99.93  E-value=9.9e-25  Score=154.35  Aligned_cols=144  Identities=26%  Similarity=0.493  Sum_probs=125.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC---------------------
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP---------------------   60 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~---------------------   60 (148)
                      |.-+.++.++.+++++|||||.|.-.+|++.|+....+..++|+.|.+.++.+......                     
T Consensus        32 ik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~  111 (678)
T KOG0127|consen   32 IKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRARSEEVEKGENKAVEKPIEQKRPTKA  111 (678)
T ss_pred             cceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccccccchhcccccchhhhcccccCCcchh
Confidence            56678899998999999999999999999999999999999999999998765432220                     


Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ....+..+|+|+|||+.+...+|..+|+.||.|..+.|++.++ ++.+|||||.|....+|..|+..+|+..|+|++|.|
T Consensus       112 ~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAV  190 (678)
T KOG0127|consen  112 KVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAV  190 (678)
T ss_pred             hccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecCceeEE
Confidence            0112356899999999999999999999999999999998765 445599999999999999999999999999999999


Q ss_pred             EeccCC
Q 032044          141 SLAQGR  146 (148)
Q Consensus       141 ~~~~~~  146 (148)
                      .|+-++
T Consensus       191 DWAV~K  196 (678)
T KOG0127|consen  191 DWAVDK  196 (678)
T ss_pred             eeeccc
Confidence            999765

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

Probab=99.92  E-value=1e-23  Score=155.03  Aligned_cols=144  Identities=20%  Similarity=0.283  Sum_probs=118.2

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC---------------------
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP---------------------   60 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~---------------------   60 (148)
                      |+.+.+++++.+|.++|||||+|.+.++|..|+..|++..++|+.|.|.++........                     
T Consensus       322 i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  401 (509)
T TIGR01642       322 LKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSI  401 (509)
T ss_pred             eeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhh
Confidence            67889999999999999999999999999999999999999999999998753221100                     


Q ss_pred             --CCCCCcceEEEcCCCCCC----------CHHHHHHHHhhcCCeeEEEEEEcC---CCCCceeEEEEEecCHHHHHHHH
Q 032044           61 --LYAETDFKLFVGNLSWSV----------TTESLTQAFQEYGNVVGARVLYDG---ESGRSRGYGFVCYSTKAEMETAL  125 (148)
Q Consensus        61 --~~~~~~~~l~i~nlp~~~----------~~~~l~~~f~~~g~v~~~~~~~~~---~~~~~~~~~fv~f~~~~~a~~a~  125 (148)
                        ....+..+|+|.|+....          ..++|++.|.+||.|..+.|++..   .++...|++||+|.+.++|++|+
T Consensus       402 ~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~  481 (509)
T TIGR01642       402 LQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAM  481 (509)
T ss_pred             ccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHH
Confidence              011245678999996431          236799999999999999998652   23445789999999999999999


Q ss_pred             HHhCCceeCCeEEEEEeccC
Q 032044          126 ESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus       126 ~~l~~~~i~g~~l~v~~~~~  145 (148)
                      ..|||..++|+.|.+.|...
T Consensus       482 ~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       482 EGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             HHcCCCEECCeEEEEEEeCH
Confidence            99999999999999998653

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

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

Probab=99.92  E-value=1.3e-23  Score=153.19  Aligned_cols=136  Identities=18%  Similarity=0.209  Sum_probs=111.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHh--CCCeecCcEEEEeecCCCCCCCCC-------CCCCcceEEE
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENL--DGREYLGRILRVNFSDKPKPKLPL-------YAETDFKLFV   71 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l--~~~~~~~~~i~v~~~~~~~~~~~~-------~~~~~~~l~i   71 (148)
                      +|.+|+++++      +|||||+|.+.++|+.|+..+  ++..+.|++|.|.|+.........       ......+|+|
T Consensus        28 ~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v  101 (481)
T TIGR01649        28 PVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIV  101 (481)
T ss_pred             CeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcccccCCCCcccCCCCCceEEEEE
Confidence            4778888854      479999999999999999864  678999999999998654322211       1122347899


Q ss_pred             cCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEeccCC
Q 032044           72 GNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG--RAMRVSLAQGR  146 (148)
Q Consensus        72 ~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g--~~l~v~~~~~~  146 (148)
                      .||++++++++|+++|++||.|.++.+.++..    .++|||+|.+.++|.+|+..|||..|.|  +.|+|.|++++
T Consensus       102 ~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       102 ENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             cCCCCCCCHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCC
Confidence            99999999999999999999999998876532    4689999999999999999999999965  58999998753

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=99.92  E-value=1.3e-23  Score=153.80  Aligned_cols=134  Identities=28%  Similarity=0.460  Sum_probs=112.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeec-CcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL-GRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVT   79 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~-~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~   79 (148)
                      .|.+++|++| .+|+++|||||+|.+.++|++|++.|++..+. ++.+.+..+.           ..++|||.|||.+++
T Consensus        84 ~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~-----------~~~rLFVgNLP~~~T  151 (578)
T TIGR01648        84 PIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV-----------DNCRLFVGGIPKNKK  151 (578)
T ss_pred             CEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc-----------cCceeEeecCCcchh
Confidence            4789999999 79999999999999999999999999999885 6766665442           356899999999999


Q ss_pred             HHHHHHHHhhcCC-eeEEEE-EEcCCCCCceeEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEEEeccCC
Q 032044           80 TESLTQAFQEYGN-VVGARV-LYDGESGRSRGYGFVCYSTKAEMETALESLNG--VELEGRAMRVSLAQGR  146 (148)
Q Consensus        80 ~~~l~~~f~~~g~-v~~~~~-~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~--~~i~g~~l~v~~~~~~  146 (148)
                      +++|.+.|.+++. +..+.+ ......+++++||||+|.+.++|..|+..|+.  ..+.|+.|.|.|+.++
T Consensus       152 eeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~  222 (578)
T TIGR01648       152 REEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPE  222 (578)
T ss_pred             hHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccc
Confidence            9999999999864 444333 33334567899999999999999999998864  4688999999998764

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.

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

Probab=99.91  E-value=6.1e-24  Score=144.44  Aligned_cols=143  Identities=22%  Similarity=0.441  Sum_probs=126.7

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC------CCCCCcceEEEcCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP------LYAETDFKLFVGNLS   75 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~------~~~~~~~~l~i~nlp   75 (148)
                      |++|++.-|+.|++++|||||+|+-++.|+.|++.+|+..++|+.|+|.....-....+      .....-++|||..+.
T Consensus       140 IKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvH  219 (544)
T KOG0124|consen  140 IKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVH  219 (544)
T ss_pred             cceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCCcccchHHHHHHHHHHhhheEEeeecC
Confidence            78999999999999999999999999999999999999999999999985433211111      112245689999999


Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           76 WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        76 ~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ++++++||+..|+-||.|.+|.+.+.+-.+..+||+|++|.+......|+..+|-..++|..|+|-.+-
T Consensus       220 pDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  220 PDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             CCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            999999999999999999999999998888899999999999999999999999999999999997763

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

Probab=99.90  E-value=3.6e-22  Score=140.13  Aligned_cols=130  Identities=29%  Similarity=0.550  Sum_probs=118.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      .|.++++-+|. |  +.|||||.|.++.+|.+|+..+|...+.|+++++-|+..-...          ++|.||+++++.
T Consensus        24 ~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~~----------~~i~nl~~~~~~   90 (369)
T KOG0123|consen   24 PVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPSL----------VFIKNLDESIDN   90 (369)
T ss_pred             CceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCce----------eeecCCCcccCc
Confidence            36799999997 6  9999999999999999999999999999999999998644332          999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      .+|.++|+.||.|.++.+..+.. | .+|+ ||+|.+++.|++|+..+||..+.|+.|.+-...++
T Consensus        91 ~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~  153 (369)
T KOG0123|consen   91 KSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERK  153 (369)
T ss_pred             HHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccch
Confidence            99999999999999999998844 4 8899 99999999999999999999999999999776543

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

Probab=99.89  E-value=5.5e-22  Score=140.59  Aligned_cols=145  Identities=28%  Similarity=0.484  Sum_probs=122.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC--------------------
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP--------------------   60 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~--------------------   60 (148)
                      +|.+|.|.+.+ .|+..|||||+|....+|..|+..+|+..|.|++|.|.|+..+.....                    
T Consensus       143 ~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e  221 (678)
T KOG0127|consen  143 KVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKE  221 (678)
T ss_pred             eEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcc
Confidence            46788999775 566669999999999999999999999999999999999754311000                    


Q ss_pred             -------------------------------------------------C----------------CCCCcceEEEcCCC
Q 032044           61 -------------------------------------------------L----------------YAETDFKLFVGNLS   75 (148)
Q Consensus        61 -------------------------------------------------~----------------~~~~~~~l~i~nlp   75 (148)
                                                                       +                ......+|||+|||
T Consensus       222 ~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~  301 (678)
T KOG0127|consen  222 ADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLP  301 (678)
T ss_pred             cccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCC
Confidence                                                             0                00012689999999


Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHh-----CC-ceeCCeEEEEEeccCC
Q 032044           76 WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL-----NG-VELEGRAMRVSLAQGR  146 (148)
Q Consensus        76 ~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l-----~~-~~i~g~~l~v~~~~~~  146 (148)
                      +++++++|.++|.+||.|.+..++.++.++.+.|.|||.|.++..|+.||...     .| ..++|+.|.|..+-.|
T Consensus       302 fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~R  378 (678)
T KOG0127|consen  302 FDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTR  378 (678)
T ss_pred             ccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccch
Confidence            99999999999999999999999999999999999999999999999999866     23 7789999999987654

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

Probab=99.89  E-value=6.9e-23  Score=148.61  Aligned_cols=147  Identities=22%  Similarity=0.397  Sum_probs=122.5

Q ss_pred             CcceeEeeecCCC---CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC----CCCCCCcceEEEcC
Q 032044            1 MLSKLTVLYDRET---GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL----PLYAETDFKLFVGN   73 (148)
Q Consensus         1 ~i~~i~~~~~~~~---~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~----~~~~~~~~~l~i~n   73 (148)
                      +|.++.|..-+..   -.|.|||||+|.++++|+.|++.|+|..+.|..+.+.++.......    .......+.|+|+|
T Consensus       541 ~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRN  620 (725)
T KOG0110|consen  541 TVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVRN  620 (725)
T ss_pred             eEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccccceeeeec
Confidence            3556666665421   1356999999999999999999999999999999999987221111    11222346899999


Q ss_pred             CCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           74 LSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        74 lp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      +|+..+..+++.+|..||.+..++++.-...+..+|+|||+|-++.+|..|+..|.+..+.|++|.++|+....
T Consensus       621 ipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  621 IPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             cchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            99999999999999999999999998776667789999999999999999999999999999999999997653

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

Probab=99.88  E-value=1.7e-21  Score=127.17  Aligned_cols=143  Identities=29%  Similarity=0.471  Sum_probs=122.3

Q ss_pred             eeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecC--cEEEEeecCCCCCCCC---------------------
Q 032044            4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG--RILRVNFSDKPKPKLP---------------------   60 (148)
Q Consensus         4 ~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~--~~i~v~~~~~~~~~~~---------------------   60 (148)
                      --+|+-|..||.++|.+||.|+...+|+.|+..|||..=.|  .+|.|+++..+.....                     
T Consensus       156 tSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh  235 (360)
T KOG0145|consen  156 TSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHH  235 (360)
T ss_pred             hhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccc
Confidence            34677788899999999999999999999999999986554  4588887755422100                     


Q ss_pred             -------------------------------------CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCC
Q 032044           61 -------------------------------------LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGE  103 (148)
Q Consensus        61 -------------------------------------~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~  103 (148)
                                                           .......+|||-||.++.++.-|.++|.+||.|..+.++++..
T Consensus       236 ~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~t  315 (360)
T KOG0145|consen  236 QAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFT  315 (360)
T ss_pred             hhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCC
Confidence                                                 0112356899999999999999999999999999999999998


Q ss_pred             CCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044          104 SGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus       104 ~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      +++.+||+||.+.+.+.|..|+..|||+.++++.|.|.+...+
T Consensus       316 tnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  316 TNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             cccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            8999999999999999999999999999999999999996544

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

Probab=99.88  E-value=1.8e-22  Score=133.32  Aligned_cols=123  Identities=27%  Similarity=0.497  Sum_probs=113.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      ||.+|.|+++        ||||-.+++..|+.|++.|++..++|..|.|+-++.+       ...+.+|+|+|+.+.++.
T Consensus        28 kVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK-------sk~stkl~vgNis~tctn   92 (346)
T KOG0109|consen   28 KVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK-------SKASTKLHVGNISPTCTN   92 (346)
T ss_pred             ceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc-------CCCccccccCCCCccccC
Confidence            5788888877        7999999999999999999999999999999988655       234568999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ++++..|++||+|..+.|.++        |+||.|+..++|..|++.|++.++.|++++|+++.+|
T Consensus        93 ~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen   93 QELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             HHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence            999999999999999999855        8999999999999999999999999999999998876

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

Probab=99.88  E-value=5.3e-21  Score=139.13  Aligned_cols=140  Identities=24%  Similarity=0.388  Sum_probs=114.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC----------------------
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK----------------------   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~----------------------   58 (148)
                      .|.+|.+++++.+|.++|||||+|.+.++|..|+..|+|..+.|++|.|.|+......                      
T Consensus       212 ~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  291 (457)
T TIGR01622       212 DIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNT  291 (457)
T ss_pred             CeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCc
Confidence            3788999999989999999999999999999999999999999999999994321000                      


Q ss_pred             -------------C------------------------------C----------------C----CCCCcceEEEcCCC
Q 032044           59 -------------L------------------------------P----------------L----YAETDFKLFVGNLS   75 (148)
Q Consensus        59 -------------~------------------------------~----------------~----~~~~~~~l~i~nlp   75 (148)
                                   .                              +                .    ......+|+|.|+.
T Consensus       292 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~  371 (457)
T TIGR01622       292 EEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMF  371 (457)
T ss_pred             cchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCC
Confidence                         0                              0                0    01234678888985


Q ss_pred             CCCC----------HHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           76 WSVT----------TESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        76 ~~~~----------~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ....          .++|++.|.+||.|..+.+...    ...|++||+|.+.++|..|++.|||..++|+.|.+.+..
T Consensus       372 ~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~----~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~  446 (457)
T TIGR01622       372 DPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK----NSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVV  446 (457)
T ss_pred             CCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC----CCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEc
Confidence            5544          3689999999999999988633    357899999999999999999999999999999999864

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.

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

Probab=99.88  E-value=1.6e-22  Score=143.21  Aligned_cols=143  Identities=31%  Similarity=0.604  Sum_probs=125.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC---------CCCCCcceEEE
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP---------LYAETDFKLFV   71 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~---------~~~~~~~~l~i   71 (148)
                      ||.+|.++.|+.+++++|.|||+|.+.+.+..|+. |.|..+.|.+|.|..+...+....         ....+...+|+
T Consensus       205 kVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~v  283 (549)
T KOG0147|consen  205 KVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSEAEKNRAANASPALQGKGFTGPMRRLYV  283 (549)
T ss_pred             CcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecccHHHHHHHHhccccccccccccchhhhhh
Confidence            68899999999999999999999999999999996 999999999999997754432211         01112233999


Q ss_pred             cCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           72 GNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        72 ~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      +||..++++++++.+|++||.|..+.+.++..+|..+||+||+|.+.++|..|+..|||.++.|+.++|....
T Consensus       284 gnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  284 GNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             cccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            9999999999999999999999999999998899999999999999999999999999999999999987643

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

Probab=99.87  E-value=2.9e-21  Score=119.65  Aligned_cols=85  Identities=42%  Similarity=0.780  Sum_probs=79.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ...+++|||.|||+++++++|+++|++||.|..+.++.++.++.+++||||+|.+.++|+.|+..||+..|+|+.|+|++
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34567899999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +.++.
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            87653

>PF00076 RRM_1: RNA recognition motif

Probab=99.81  E-value=8e-19  Score=96.27  Aligned_cols=70  Identities=41%  Similarity=0.785  Sum_probs=66.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        69 l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      |||+|||+++++++|+++|++||.+..+.+..+ .++..+++|||+|.+.++|+.|+..++|..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999887 6688899999999999999999999999999999886

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

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

Probab=99.81  E-value=2.8e-19  Score=115.69  Aligned_cols=82  Identities=24%  Similarity=0.469  Sum_probs=79.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|.|.||+.+.++++|+++|.+||.|.++.+.++..+|.++|||||.|.+.++|.+|+..|||+-+++-.|+|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            86

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.81  E-value=1.4e-19  Score=123.59  Aligned_cols=144  Identities=27%  Similarity=0.451  Sum_probs=126.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC-CCCCCcceEEEcCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP-LYAETDFKLFVGNLSWSVT   79 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~-~~~~~~~~l~i~nlp~~~~   79 (148)
                      .|.++.+++|+.+++++||+||+|++.+.+..++. .....+.++.+....+.+...... .......+++|++||.+++
T Consensus        32 ev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~  110 (311)
T KOG4205|consen   32 EVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAVSREDQTKVGRHLRTKKIFVGGLPPDTT  110 (311)
T ss_pred             ceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceeccCcccccccccccceeEEEecCcCCCCc
Confidence            36789999999999999999999999999999997 456778999999988766554432 2223567899999999999


Q ss_pred             HHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           80 TESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        80 ~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      +.++++.|.+||.|..+.++.+..+..+++++||.|.+++..++++. ..-+.++|+.+.|..+.++
T Consensus       111 e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk  176 (311)
T KOG4205|consen  111 EEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPK  176 (311)
T ss_pred             hHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccch
Confidence            99999999999999999999999999999999999999999999987 7788999999999998876

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

Probab=99.81  E-value=8.7e-19  Score=123.20  Aligned_cols=141  Identities=28%  Similarity=0.495  Sum_probs=122.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCC---CCCCcceEEEcCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPL---YAETDFKLFVGNLSWS   77 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~---~~~~~~~l~i~nlp~~   77 (148)
                      +|.||++.++. .| ++|| ||+|.+++.|++|+..+||..+.+++|+|............   ....-..+++.+++.+
T Consensus       102 ~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~  178 (369)
T KOG0123|consen  102 NILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEED  178 (369)
T ss_pred             CeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhcccccchhhhhhhhheeccccc
Confidence            47899999996 56 9999 99999999999999999999999999999877654432211   3345567999999999


Q ss_pred             CCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           78 VTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        78 ~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      .+++.|.++|..+|.+.++.++.+ ..+.+++++||.|.++++|..|+..+++..+.+..+.|..+..
T Consensus       179 ~~~~~l~~~f~~~g~i~s~~v~~~-~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqk  245 (369)
T KOG0123|consen  179 STDEELKDLFSAYGSITSVAVMRD-SIGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQK  245 (369)
T ss_pred             cchHHHHHhhcccCcceEEEEeec-CCCCCCCccceeecChhHHHHHHHhccCCcCCccceeeccccc
Confidence            999999999999999999999988 4466899999999999999999999999999998888877654

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.80  E-value=5.3e-19  Score=116.06  Aligned_cols=83  Identities=25%  Similarity=0.532  Sum_probs=79.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..|.|||-.||....+.+|-.+|-+||.|.+.++..++.++-+++++||.|+++.+|+.|++.+||..|+-++|+|++.+
T Consensus       284 eGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKR  363 (371)
T KOG0146|consen  284 EGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKR  363 (371)
T ss_pred             CcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcC
Confidence            35889999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      ++.
T Consensus       364 Pkd  366 (371)
T KOG0146|consen  364 PKD  366 (371)
T ss_pred             ccc
Confidence            874

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

Probab=99.79  E-value=6.3e-19  Score=103.58  Aligned_cols=80  Identities=26%  Similarity=0.475  Sum_probs=76.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ..+++|||+||+..++|++|.++|+.+|.|..+.+-.++.+..|.|+|||+|.+.++|..|++.++|..++.++|++.|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999885

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.78  E-value=2.8e-18  Score=119.97  Aligned_cols=85  Identities=27%  Similarity=0.475  Sum_probs=79.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||.|||+++++++|+++|..||.|..+.++.+..++.+++||||+|.++++|++|+..|++..+.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            34467899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++++.
T Consensus       183 ~a~p~  187 (346)
T TIGR01659       183 YARPG  187 (346)
T ss_pred             ccccc
Confidence            98653

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).

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

Probab=99.78  E-value=4.5e-18  Score=117.94  Aligned_cols=82  Identities=27%  Similarity=0.552  Sum_probs=77.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ..++|-+||.+.-+.+|-..|.+||.|.+.++.-++.++.++.|+||.|++...|+.|+..+||..|++++++|+..+++
T Consensus       425 anlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~  504 (510)
T KOG0144|consen  425 ANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDR  504 (510)
T ss_pred             cceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeecc
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999998877


Q ss_pred             CC
Q 032044          147 RS  148 (148)
Q Consensus       147 ~~  148 (148)
                      .+
T Consensus       505 ~n  506 (510)
T KOG0144|consen  505 NN  506 (510)
T ss_pred             CC
Confidence            53

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.77  E-value=9.2e-18  Score=92.12  Aligned_cols=70  Identities=39%  Similarity=0.715  Sum_probs=64.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        69 l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      |+|+|||+++++++|+++|..+|.|..+.+..++. +.++++|||+|.+.++|..|+..+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            78999999999999999999999999999999866 88999999999999999999999999999999885

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 ....

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

Probab=99.77  E-value=3e-18  Score=112.50  Aligned_cols=102  Identities=34%  Similarity=0.626  Sum_probs=87.4

Q ss_pred             EEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHH
Q 032044           46 ILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL  125 (148)
Q Consensus        46 ~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~  125 (148)
                      .++|.|+..+..........-.+++++.|...++.++|++.|.+||.|...++++|..+++++||+||.|.+.++|+.|+
T Consensus        42 e~~v~wa~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI  121 (321)
T KOG0148|consen   42 ELKVNWATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAI  121 (321)
T ss_pred             hhccccccCcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHH
Confidence            45566665553332223333457899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhCCceeCCeEEEEEeccCCC
Q 032044          126 ESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus       126 ~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      ..|||.+|+++.|+..|+.++.
T Consensus       122 ~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen  122 QQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             HHhCCeeeccceeeccccccCc
Confidence            9999999999999999997763

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

Probab=99.76  E-value=2.6e-17  Score=114.64  Aligned_cols=126  Identities=22%  Similarity=0.362  Sum_probs=101.3

Q ss_pred             EEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEE
Q 032044           21 FVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLY  100 (148)
Q Consensus        21 fv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~  100 (148)
                      .-...+.++|.++|..-.+..+.-..-.-++..++...........+-|||+.||.++.|++|.-+|++.|.|..+++++
T Consensus        38 ~~~~~~~eaal~al~E~tgy~l~ve~gqrk~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMm  117 (506)
T KOG0117|consen   38 VAGVQSEEAALKALLERTGYTLVVENGQRKYGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMM  117 (506)
T ss_pred             ccccccHHHHHHHHHHhcCceEEEeccccccCCCCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEee
Confidence            33444578889998876666653322222344444444444456778999999999999999999999999999999999


Q ss_pred             cCCCCCceeEEEEEecCHHHHHHHHHHhCCcee-CCeEEEEEeccCC
Q 032044          101 DGESGRSRGYGFVCYSTKAEMETALESLNGVEL-EGRAMRVSLAQGR  146 (148)
Q Consensus       101 ~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i-~g~~l~v~~~~~~  146 (148)
                      ++.+|.++|||||+|++.+.|++|++.||+++| .|+.|.|..+..+
T Consensus       118 D~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan  164 (506)
T KOG0117|consen  118 DPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVAN  164 (506)
T ss_pred             cccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeec
Confidence            999999999999999999999999999999998 5899998876543

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

Probab=99.74  E-value=1.7e-17  Score=111.58  Aligned_cols=84  Identities=27%  Similarity=0.546  Sum_probs=76.6

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      .....+++|||+|+|+..-+.||+.+|++||.|.+|.|+.+.  ..++|||||+|++.++|++|-..|||..+.|++|.|
T Consensus        91 ~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEV  168 (376)
T KOG0125|consen   91 SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEV  168 (376)
T ss_pred             CCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEE
Confidence            345567899999999999999999999999999999999873  347999999999999999999999999999999999


Q ss_pred             EeccCC
Q 032044          141 SLAQGR  146 (148)
Q Consensus       141 ~~~~~~  146 (148)
                      .-+..+
T Consensus       169 n~ATar  174 (376)
T KOG0125|consen  169 NNATAR  174 (376)
T ss_pred             eccchh
Confidence            988765

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

Probab=99.74  E-value=1.4e-17  Score=102.87  Aligned_cols=77  Identities=32%  Similarity=0.590  Sum_probs=71.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+||+..+++.+|...|..||.+..+.+..+     |.|||||+|+++.+|+.|+..|+|..|+|..++|+++.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            3678999999999999999999999999999988765     58899999999999999999999999999999999986


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      -+
T Consensus        84 G~   85 (195)
T KOG0107|consen   84 GR   85 (195)
T ss_pred             CC
Confidence            43

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.72  E-value=1.2e-16  Score=106.00  Aligned_cols=75  Identities=20%  Similarity=0.285  Sum_probs=69.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      .++|||+|||+.+++++|+++|+.||.|..+.++.++.   ++|+|||+|.++++|+.|+. |+|..|.|+.|.|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEecc
Confidence            46899999999999999999999999999999987753   47899999999999999996 99999999999999986

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

Probab=99.72  E-value=6.7e-17  Score=119.13  Aligned_cols=81  Identities=26%  Similarity=0.596  Sum_probs=76.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||+|||+++++++|+++|.+||.|.++.+++++.++.++|||||+|.+.++|+.|+..|||..++|+.|+|...
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999864


Q ss_pred             c
Q 032044          144 Q  144 (148)
Q Consensus       144 ~  144 (148)
                      .
T Consensus       185 ~  185 (612)
T TIGR01645       185 S  185 (612)
T ss_pred             c
Confidence            3

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.

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.71  E-value=2.6e-16  Score=110.85  Aligned_cols=138  Identities=22%  Similarity=0.268  Sum_probs=107.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC------CCCCCcceEEEcCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP------LYAETDFKLFVGNL   74 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~------~~~~~~~~l~i~nl   74 (148)
                      +|+++  +..+.+|+..|=|||+|.+++++++|++ .+...+..+.|.|-.+........      ........|.+++|
T Consensus        35 ~I~~~--~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~e~d~~~~~~g~~s~~~d~vVRLRGL  111 (510)
T KOG4211|consen   35 GIENL--EIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGAEADWVMRPGGPNSSANDGVVRLRGL  111 (510)
T ss_pred             ceeEE--EEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCccccccccCCCCCCCCCCceEEecCC
Confidence            46664  4444589999999999999999999998 688899999999987654432211      11235668999999


Q ss_pred             CCCCCHHHHHHHHhhcCCeeE-EEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           75 SWSVTTESLTQAFQEYGNVVG-ARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        75 p~~~~~~~l~~~f~~~g~v~~-~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      |+.|+++||.++|+..-.+.. +.++.+ ..+++.|.|||.|.+.+.|+.|++ -|...|+-+-|.|-.+
T Consensus       112 Pfscte~dI~~FFaGL~Iv~~gi~l~~d-~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  112 PFSCTEEDIVEFFAGLEIVPDGILLPMD-QRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRS  179 (510)
T ss_pred             CccCcHHHHHHHhcCCcccccceeeecc-CCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehh
Confidence            999999999999998866555 334444 456789999999999999999998 5666777777776554

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

Probab=99.70  E-value=3e-16  Score=111.79  Aligned_cols=138  Identities=26%  Similarity=0.356  Sum_probs=108.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC-----------------------
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP-----------------------   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~-----------------------   57 (148)
                      +|+.|.+.+|..||+++|||||+|...++|..|+..|||..+.|+.|.|........                       
T Consensus       304 ~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~  383 (549)
T KOG0147|consen  304 KIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGS  383 (549)
T ss_pred             cceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhcccccccc
Confidence            478899999988999999999999999999999999999999999999864221100                       


Q ss_pred             --------------------------------------------CCCCCC-------CCcceEEEcCCCCCCCH------
Q 032044           58 --------------------------------------------KLPLYA-------ETDFKLFVGNLSWSVTT------   80 (148)
Q Consensus        58 --------------------------------------------~~~~~~-------~~~~~l~i~nlp~~~~~------   80 (148)
                                                                  ....+.       .++.++.++|+-...++      
T Consensus       384 ~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d  463 (549)
T KOG0147|consen  384 GGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWD  463 (549)
T ss_pred             ccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchh
Confidence                                                        000011       23345667777433222      


Q ss_pred             ----HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           81 ----ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        81 ----~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                          +|+.+.|.+||.|..|.+.++     +.|+.||.|.+.+.|..|+..|||.|+.|+.|.+.|-
T Consensus       464 ~eI~edV~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~  525 (549)
T KOG0147|consen  464 QEIREDVIEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYL  525 (549)
T ss_pred             hHHHHHHHHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEe
Confidence                578889999999988877544     2378999999999999999999999999999998874

>smart00362 RRM_2 RNA recognition motif

Probab=99.69  E-value=5.6e-16  Score=84.83  Aligned_cols=72  Identities=40%  Similarity=0.760  Sum_probs=66.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        68 ~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      +|+|+|||..++.++|+++|.+||.+..+.+..++  +.++++|||+|.+.+.|+.|+..+++..+.|+.+.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            48999999999999999999999999999888665  6678999999999999999999999999999998874

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

Probab=99.69  E-value=5.5e-16  Score=103.18  Aligned_cols=85  Identities=28%  Similarity=0.649  Sum_probs=80.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ...+-+||||.-|++++++..|+..|+.||.|..+.++.+..+++++|||||+|+++-+...|.+..+|..|+|+.|.|.
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            34677899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      +-+.+
T Consensus       177 vERgR  181 (335)
T KOG0113|consen  177 VERGR  181 (335)
T ss_pred             ecccc
Confidence            86543

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

Probab=99.67  E-value=1.6e-15  Score=86.22  Aligned_cols=83  Identities=27%  Similarity=0.442  Sum_probs=73.6

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           60 PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        60 ~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      ..++.....|||.|||+.++.+++.++|.+||.|..+++--.+   .-+|-|||.|++..+|.+|+.+|+|..++++.+.
T Consensus        12 rlppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~   88 (124)
T KOG0114|consen   12 RLPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLV   88 (124)
T ss_pred             CCChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEE
Confidence            3455567789999999999999999999999999999996443   3578999999999999999999999999999999


Q ss_pred             EEeccC
Q 032044          140 VSLAQG  145 (148)
Q Consensus       140 v~~~~~  145 (148)
                      |-+-++
T Consensus        89 vlyyq~   94 (124)
T KOG0114|consen   89 VLYYQP   94 (124)
T ss_pred             EEecCH
Confidence            988654

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

Probab=99.66  E-value=2.9e-16  Score=99.62  Aligned_cols=81  Identities=33%  Similarity=0.603  Sum_probs=77.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .....|.|.||.+.++.++|+.+|++||.|-.|.|++++.+..++|||||.|....+|+.|+..|+|..++|+.|+|++|
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence            45568999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             c
Q 032044          144 Q  144 (148)
Q Consensus       144 ~  144 (148)
                      +
T Consensus        91 r   91 (256)
T KOG4207|consen   91 R   91 (256)
T ss_pred             h
Confidence            4

>smart00360 RRM RNA recognition motif

Probab=99.66  E-value=1.4e-15  Score=82.91  Aligned_cols=71  Identities=41%  Similarity=0.783  Sum_probs=66.0

Q ss_pred             EcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           71 VGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        71 i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      |+|||..+++++|+++|.+||.+..+.+..++.++.++++|||+|.+.+.|..|+..+++..++|+.+.|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57899999999999999999999999998887778889999999999999999999999999999998874

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

Probab=99.66  E-value=4.6e-16  Score=100.44  Aligned_cols=78  Identities=36%  Similarity=0.674  Sum_probs=69.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .-++|||+||++.+..+.|++.|++||.|....++.++.+++++||+||+|.+.+.|.+|++. -+-.|+|++.-+.++
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA   88 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLA   88 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchh
Confidence            345899999999999999999999999999999999999999999999999999999999983 344678887666664

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.66  E-value=5.9e-15  Score=102.11  Aligned_cols=136  Identities=26%  Similarity=0.418  Sum_probs=111.9

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCC--------------------
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPL--------------------   61 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~--------------------   61 (148)
                      |..|+|++++.+.     |+|+|.+...|+-|++.|+|..++|++|+|.+++......+.                    
T Consensus       325 VqRVkil~nkkd~-----ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq~d~glT~dy~~spLhrf  399 (492)
T KOG1190|consen  325 VQRVKILYNKKDN-----ALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQEDQGLTKDYGNSPLHRF  399 (492)
T ss_pred             eEEEEeeecCCcc-----eeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCCCccccccccCCCCchhhc
Confidence            6789999998754     999999999999999999999999999999998764321110                    


Q ss_pred             ----------CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCc
Q 032044           62 ----------YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV  131 (148)
Q Consensus        62 ----------~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~  131 (148)
                                ...++.++++.|+|.++++++++..|..-|...+......    +.+.++++.+.+.+.|..|+-.+|++
T Consensus       400 kkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~----kd~kmal~q~~sveeA~~ali~~hnh  475 (492)
T KOG1190|consen  400 KKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ----KDRKMALPQLESVEEAIQALIDLHNH  475 (492)
T ss_pred             cCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC----CCcceeecccCChhHhhhhccccccc
Confidence                      1134578999999999999999999999887655443322    23568999999999999999999999


Q ss_pred             eeCCe-EEEEEeccCC
Q 032044          132 ELEGR-AMRVSLAQGR  146 (148)
Q Consensus       132 ~i~g~-~l~v~~~~~~  146 (148)
                      .+++. .++|+++++.
T Consensus       476 ~lgen~hlRvSFSks~  491 (492)
T KOG1190|consen  476 YLGENHHLRVSFSKST  491 (492)
T ss_pred             cCCCCceEEEEeeccc
Confidence            99765 9999998763

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

Probab=99.65  E-value=7.1e-16  Score=96.39  Aligned_cols=80  Identities=20%  Similarity=0.440  Sum_probs=71.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ..+++||++|||.++-+.+|+++|.+||.|..|.+...   ..+..||||+|+++.+|+.|+..-+|+.++|.+|+|+++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            45679999999999999999999999999999887532   235679999999999999999999999999999999998


Q ss_pred             cCC
Q 032044          144 QGR  146 (148)
Q Consensus       144 ~~~  146 (148)
                      +.-
T Consensus        81 rgg   83 (241)
T KOG0105|consen   81 RGG   83 (241)
T ss_pred             cCC
Confidence            754

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

Probab=99.64  E-value=9.7e-15  Score=93.98  Aligned_cols=127  Identities=22%  Similarity=0.433  Sum_probs=106.8

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC---------------------------------
Q 032044           13 TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL---------------------------------   59 (148)
Q Consensus        13 ~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~---------------------------------   59 (148)
                      +.+.+|.|||.|.+.+.|..|+..|+|..+.|+++.+.|+.......                                 
T Consensus        48 t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~  127 (221)
T KOG4206|consen   48 TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFY  127 (221)
T ss_pred             CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCccchhhccCceeccccCccccccccccCCccccccccc
Confidence            66899999999999999999999999999999999999875421100                                 


Q ss_pred             ------------CCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHH
Q 032044           60 ------------PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES  127 (148)
Q Consensus        60 ------------~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~  127 (148)
                                  .....+...+++.|+|...+.+.+..+|.+|.....++++..     -.+.|||+|.+...|..|.+.
T Consensus       128 ~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~-----~~~iAfve~~~d~~a~~a~~~  202 (221)
T KOG4206|consen  128 NMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPP-----RSGIAFVEFLSDRQASAAQQA  202 (221)
T ss_pred             ccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccC-----CCceeEEecchhhhhHHHhhh
Confidence                        011345678999999999999999999999999999988754     256899999999999999999


Q ss_pred             hCCceeC-CeEEEEEecc
Q 032044          128 LNGVELE-GRAMRVSLAQ  144 (148)
Q Consensus       128 l~~~~i~-g~~l~v~~~~  144 (148)
                      +.+..|- ...+.+.+++
T Consensus       203 lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  203 LQGFKITKKNTMQITFAK  220 (221)
T ss_pred             hccceeccCceEEecccC
Confidence            9998886 7778877764

>PLN03213 repressor of silencing 3; Provisional

Probab=99.64  E-value=2.6e-15  Score=106.42  Aligned_cols=78  Identities=23%  Similarity=0.436  Sum_probs=71.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCH--HHHHHHHHHhCCceeCCeEEEEE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTK--AEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~--~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ....+|||+||++.+++++|+..|..||.|..+.|+  +.+|  +|||||+|.+.  ..+.+|+..|||..+.|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            345689999999999999999999999999999998  4455  99999999977  78999999999999999999999


Q ss_pred             eccC
Q 032044          142 LAQG  145 (148)
Q Consensus       142 ~~~~  145 (148)
                      .+++
T Consensus        84 KAKP   87 (759)
T PLN03213         84 KAKE   87 (759)
T ss_pred             eccH
Confidence            9876

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.63  E-value=9.9e-15  Score=80.22  Aligned_cols=74  Identities=43%  Similarity=0.776  Sum_probs=67.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        68 ~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      +|+|+|||..+++++|.++|..+|.+..+.+...+.+ .++++|||+|.+.++|+.|+..+++..++|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4889999999999999999999999999998877544 6789999999999999999999999999999998864

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).

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

Probab=99.62  E-value=1.8e-15  Score=107.68  Aligned_cols=80  Identities=36%  Similarity=0.723  Sum_probs=77.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      +.++|+|+|+++++++|.++|+..|.|.++++..|+.+|+++||||++|.+.++|..|++.|||.++.|++|+|.|+..+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999997654

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.62  E-value=9.3e-15  Score=95.70  Aligned_cols=76  Identities=18%  Similarity=0.265  Sum_probs=68.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ...+|+|+||++.+++++|+++|+.||.|..+.++.+.   ...++|||+|.++++++.|+. |+|..|.|++|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            34689999999999999999999999999999999774   345799999999999999996 99999999999988743

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

Probab=99.61  E-value=1.8e-15  Score=94.22  Aligned_cols=81  Identities=36%  Similarity=0.545  Sum_probs=77.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ....+||++||+..++++.|.++|-+.|+|..+.+++++.++.++||||++|.++++|+-|++-||...+.|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             c
Q 032044          144 Q  144 (148)
Q Consensus       144 ~  144 (148)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            6

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

Probab=99.61  E-value=2.9e-15  Score=89.06  Aligned_cols=81  Identities=28%  Similarity=0.518  Sum_probs=77.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .....|+|.++....++++|.+.|..||.|..+.+-.++.+|-.+|||+|+|.+.+.|+.|+..+||..+.|..|.|.||
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            35568999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             c
Q 032044          144 Q  144 (148)
Q Consensus       144 ~  144 (148)
                      -
T Consensus       150 F  150 (170)
T KOG0130|consen  150 F  150 (170)
T ss_pred             E
Confidence            4

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

Probab=99.59  E-value=2.2e-16  Score=98.26  Aligned_cols=79  Identities=28%  Similarity=0.693  Sum_probs=75.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .+.-|||+|||+.+|+-||--.|++||.|..+.++++..+|+++||||+.|++..+...|+.-|||..|.|+.|+|...
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            3457999999999999999999999999999999999999999999999999999999999999999999999999875

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

Probab=99.58  E-value=2.2e-14  Score=97.70  Aligned_cols=79  Identities=47%  Similarity=0.799  Sum_probs=75.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..+|||+|||..+++++|.++|.+||.+..+.+..++.++.++|+|||+|.+.++|..|+..++|..+.|+.|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            5899999999999999999999999999999999998889999999999999999999999999999999999999954

>PF13893 RRM_5: RNA recognition motif

Probab=99.56  E-value=3.6e-14  Score=74.34  Aligned_cols=56  Identities=32%  Similarity=0.676  Sum_probs=49.8

Q ss_pred             HHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           83 LTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        83 l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      |.++|++||.|..+.+....     +++|||+|.+.++|+.|++.|||..++|++|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999886442     578999999999999999999999999999999986

(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=99.56  E-value=5.4e-14  Score=76.95  Aligned_cols=62  Identities=21%  Similarity=0.464  Sum_probs=54.0

Q ss_pred             HHHHHHHHh----hcCCeeEEE-EEEcCCC--CCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           80 TESLTQAFQ----EYGNVVGAR-VLYDGES--GRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        80 ~~~l~~~f~----~~g~v~~~~-~~~~~~~--~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      +++|+++|.    +||.+.++. +..++.+  +.++|+|||+|.+.++|+.|+..|||..++|+.|.++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            467788887    999999985 6666555  7789999999999999999999999999999999763

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

Probab=99.56  E-value=3.4e-15  Score=95.77  Aligned_cols=84  Identities=33%  Similarity=0.585  Sum_probs=80.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||++|...+++.-|...|=+||.|..+.++.+..+++.||++||+|...++|..|+.-+|+.++.|+.|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 032044          144 QGRR  147 (148)
Q Consensus       144 ~~~~  147 (148)
                      +|.+
T Consensus        88 kP~k   91 (298)
T KOG0111|consen   88 KPEK   91 (298)
T ss_pred             CCcc
Confidence            8864

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

Probab=99.56  E-value=2.1e-13  Score=85.46  Aligned_cols=112  Identities=29%  Similarity=0.415  Sum_probs=94.6

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC---------------------CCCCCCCcceEEEcC
Q 032044           15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK---------------------LPLYAETDFKLFVGN   73 (148)
Q Consensus        15 ~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~---------------------~~~~~~~~~~l~i~n   73 (148)
                      ....||||+|++..+|+.|+-.-++..+.|+.|.|+++......                     -++.......+.|++
T Consensus        43 g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsG  122 (241)
T KOG0105|consen   43 GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSG  122 (241)
T ss_pred             CCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEec
Confidence            45789999999999999999999999999999999987543221                     122233556899999


Q ss_pred             CCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 032044           74 LSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL  133 (148)
Q Consensus        74 lp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i  133 (148)
                      ||++-+++||++++.+-|.|....+.++.       .+.|+|-..++.+-|+..|+...+
T Consensus       123 Lp~SgSWQDLKDHmReaGdvCfadv~rDg-------~GvV~~~r~eDMkYAvr~ld~~~~  175 (241)
T KOG0105|consen  123 LPPSGSWQDLKDHMREAGDVCFADVQRDG-------VGVVEYLRKEDMKYAVRKLDDQKF  175 (241)
T ss_pred             CCCCCchHHHHHHHHhhCCeeeeeeeccc-------ceeeeeeehhhHHHHHHhhccccc
Confidence            99999999999999999999888887662       689999999999999999987554

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

Probab=99.53  E-value=1.2e-14  Score=94.25  Aligned_cols=120  Identities=31%  Similarity=0.524  Sum_probs=99.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC---------------CCCCCCCCcceEEEcCCCCCCCHH
Q 032044           17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP---------------KLPLYAETDFKLFVGNLSWSVTTE   81 (148)
Q Consensus        17 ~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~---------------~~~~~~~~~~~l~i~nlp~~~~~~   81 (148)
                      .||+||+|.+..+|..|+..+++..+.+-.+.++++....-               ....+....+.+.+.+++..+.++
T Consensus        35 ~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~q  114 (216)
T KOG0106|consen   35 NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQ  114 (216)
T ss_pred             cccceeccCchhhhhcccchhcCceecceeeeeecccccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHH
Confidence            47899999999999999999999999998888888764211               011223456789999999999999


Q ss_pred             HHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           82 SLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        82 ~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      +|.++|.++|.+....+        ..+.+||+|...++|..|+..|++..+.|++|.+....
T Consensus       115 dl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~~  169 (216)
T KOG0106|consen  115 DLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKNS  169 (216)
T ss_pred             HHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecccC
Confidence            99999999999854433        34579999999999999999999999999999985543

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

Probab=99.53  E-value=7.2e-13  Score=90.11  Aligned_cols=138  Identities=23%  Similarity=0.344  Sum_probs=110.5

Q ss_pred             eeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC--------------------------
Q 032044            4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP--------------------------   57 (148)
Q Consensus         4 ~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~--------------------------   57 (148)
                      .|++.++. .|..+|-|.+.|-..+++..|+.-|++..+.|+.|+|+.+.-...                          
T Consensus       171 k~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~  249 (382)
T KOG1548|consen  171 KVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKL  249 (382)
T ss_pred             eEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhh
Confidence            47888885 699999999999999999999999999999999999985432100                          


Q ss_pred             -------CCCCCCCCcceEEEcCCCCC----CC-------HHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHH
Q 032044           58 -------KLPLYAETDFKLFVGNLSWS----VT-------TESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKA  119 (148)
Q Consensus        58 -------~~~~~~~~~~~l~i~nlp~~----~~-------~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~  119 (148)
                             ..+......++|.+.|+...    .+       .++|.+-+.+||+|.++.+.-.    .|.|.+-|.|.+.+
T Consensus       250 ~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~e  325 (382)
T KOG1548|consen  250 LDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNE  325 (382)
T ss_pred             cccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChH
Confidence                   01223345678999998432    12       3577788999999999877522    36788999999999


Q ss_pred             HHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044          120 EMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus       120 ~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      .|+.|++.|+|.+++|+.|..++...+
T Consensus       326 eA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  326 EADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            999999999999999999999886543

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

Probab=99.52  E-value=1.4e-13  Score=100.97  Aligned_cols=126  Identities=23%  Similarity=0.355  Sum_probs=102.7

Q ss_pred             EEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC-------------CC-------------------CC----
Q 032044           19 FAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK-------------LP-------------------LY----   62 (148)
Q Consensus        19 ~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~-------------~~-------------------~~----   62 (148)
                      -|+|+|.++.+|+.|.+.+....+...++++.|+....-.             ..                   ..    
T Consensus       423 ~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~  502 (725)
T KOG0110|consen  423 GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEE  502 (725)
T ss_pred             eeeeeecCccchHHHHHHhchhhhccCccccccChhhhccCCccccccccccccccccCcceecccccccccccCCcccc
Confidence            3999999999999999999999999999988875321000             00                   00    


Q ss_pred             ---------CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCC---CCceeEEEEEecCHHHHHHHHHHhCC
Q 032044           63 ---------AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGES---GRSRGYGFVCYSTKAEMETALESLNG  130 (148)
Q Consensus        63 ---------~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~~~~~fv~f~~~~~a~~a~~~l~~  130 (148)
                               ....++||+.||+++.+.+++...|...|.|.++.|.+.++.   -.+.|||||+|.++++|+.|++.|+|
T Consensus       503 ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqg  582 (725)
T KOG0110|consen  503 SSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQG  582 (725)
T ss_pred             ccchhhhhccccchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcC
Confidence                     012234999999999999999999999999999988765432   12349999999999999999999999


Q ss_pred             ceeCCeEEEEEecc
Q 032044          131 VELEGRAMRVSLAQ  144 (148)
Q Consensus       131 ~~i~g~~l~v~~~~  144 (148)
                      ..++|..|.++++.
T Consensus       583 tvldGH~l~lk~S~  596 (725)
T KOG0110|consen  583 TVLDGHKLELKISE  596 (725)
T ss_pred             ceecCceEEEEecc
Confidence            99999999999987

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

Probab=99.51  E-value=1.8e-13  Score=98.45  Aligned_cols=143  Identities=20%  Similarity=0.264  Sum_probs=106.1

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCC-------------------C
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPL-------------------Y   62 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~-------------------~   62 (148)
                      +...+++.|..+|-++||||.+|-+......|+..|||+.++++++.+..+-........                   .
T Consensus       316 lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~  395 (500)
T KOG0120|consen  316 LKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMA  395 (500)
T ss_pred             chhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccC
Confidence            345678888888999999999999999999999999999999999999866443221111                   1


Q ss_pred             CCCcceEEEcCC--CCCC-C-------HHHHHHHHhhcCCeeEEEEEEc-CCC--CCceeEEEEEecCHHHHHHHHHHhC
Q 032044           63 AETDFKLFVGNL--SWSV-T-------TESLTQAFQEYGNVVGARVLYD-GES--GRSRGYGFVCYSTKAEMETALESLN  129 (148)
Q Consensus        63 ~~~~~~l~i~nl--p~~~-~-------~~~l~~~f~~~g~v~~~~~~~~-~~~--~~~~~~~fv~f~~~~~a~~a~~~l~  129 (148)
                      ..+...|.+.|+  |..+ .       .++++.-|.+||.|..|.+++. ...  ....|-.||+|.+.+++++|+..|+
T Consensus       396 g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~  475 (500)
T KOG0120|consen  396 GIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELT  475 (500)
T ss_pred             CCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHcc
Confidence            112223333333  1111 1       1456677789999999998776 222  2335667999999999999999999


Q ss_pred             CceeCCeEEEEEecc
Q 032044          130 GVELEGRAMRVSLAQ  144 (148)
Q Consensus       130 ~~~i~g~~l~v~~~~  144 (148)
                      |.+++|+.|...|..
T Consensus       476 GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  476 GRKFANRTVVASYYD  490 (500)
T ss_pred             CceeCCcEEEEEecC
Confidence            999999999999864

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

Probab=99.49  E-value=2.2e-13  Score=87.76  Aligned_cols=80  Identities=23%  Similarity=0.519  Sum_probs=72.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHH----HHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           65 TDFKLFVGNLSWSVTTESLTQ----AFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~----~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ++.+|||.||+..+..++|+.    +|++||.|..|...   .+.+.+|.|||.|.+.+.|-.|+..|+|..+.|+.+++
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            444999999999999999988    99999999998776   44668999999999999999999999999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      +||+.+.
T Consensus        85 qyA~s~s   91 (221)
T KOG4206|consen   85 QYAKSDS   91 (221)
T ss_pred             ecccCcc
Confidence            9998764

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

Probab=99.49  E-value=2.5e-12  Score=88.55  Aligned_cols=140  Identities=19%  Similarity=0.212  Sum_probs=109.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC-----------------------
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP-----------------------   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~-----------------------   57 (148)
                      +|+.|++|+.+.     |.|.||+.+..++++|+..||+..+.|.+|.+.++.....                       
T Consensus       314 NV~rvkFmkTk~-----gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkN  388 (494)
T KOG1456|consen  314 NVERVKFMKTKP-----GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKN  388 (494)
T ss_pred             ceeeEEEeeccc-----ceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccccccCCceecCCCCcchhhcccccc
Confidence            478999999863     6799999999999999999999999999999987653211                       


Q ss_pred             ---------CCCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHH
Q 032044           58 ---------KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGN-VVGARVLYDGESGRSRGYGFVCYSTKAEMETALES  127 (148)
Q Consensus        58 ---------~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~-v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~  127 (148)
                               .......+++.|+.-|.|..++|+.|-++|...+. ..++++...+ +. ....+.++|++.++|.+|+..
T Consensus       389 nRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~k-se-rSssGllEfe~~s~Aveal~~  466 (494)
T KOG1456|consen  389 NRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLK-SE-RSSSGLLEFENKSDAVEALMK  466 (494)
T ss_pred             cccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeeccc-cc-ccccceeeeehHHHHHHHHHH
Confidence                     11122347789999999999999999999997764 3455554332 22 234589999999999999999


Q ss_pred             hCCceeCC------eEEEEEeccCCC
Q 032044          128 LNGVELEG------RAMRVSLAQGRR  147 (148)
Q Consensus       128 l~~~~i~g------~~l~v~~~~~~~  147 (148)
                      +|.+.|.+      ..+++.++.+++
T Consensus       467 ~NH~pi~~p~gs~PfilKlcfsts~~  492 (494)
T KOG1456|consen  467 LNHYPIEGPNGSFPFILKLCFSTSKH  492 (494)
T ss_pred             hccccccCCCCCCCeeeeeeeccccc
Confidence            99999865      357777776653

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

Probab=99.44  E-value=2.7e-12  Score=82.75  Aligned_cols=115  Identities=21%  Similarity=0.292  Sum_probs=88.0

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCCeec---CcEEEEeecCCCCCCC-------CC-----------------------
Q 032044           15 RSRGFAFVTMSTVEDCNAVIENLDGREYL---GRILRVNFSDKPKPKL-------PL-----------------------   61 (148)
Q Consensus        15 ~~~g~afv~f~~~~~a~~a~~~l~~~~~~---~~~i~v~~~~~~~~~~-------~~-----------------------   61 (148)
                      -.+.+||+.|.+.+.|..|+..|||+.|+   +.++++++++......       +.                       
T Consensus        75 ~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd  154 (284)
T KOG1457|consen   75 VCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHD  154 (284)
T ss_pred             cccceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhcc
Confidence            34579999999999999999999999986   7788998754311000       00                       


Q ss_pred             ---------------------------------------------------CCCCcceEEEcCCCCCCCHHHHHHHHhhc
Q 032044           62 ---------------------------------------------------YAETDFKLFVGNLSWSVTTESLTQAFQEY   90 (148)
Q Consensus        62 ---------------------------------------------------~~~~~~~l~i~nlp~~~~~~~l~~~f~~~   90 (148)
                                                                         ....-.+|||.||.+++++++|+.+|+.|
T Consensus       155 ~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~  234 (284)
T KOG1457|consen  155 EGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRY  234 (284)
T ss_pred             ccccCccccCCccccccCCCccccchhhhhhhhhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhC
Confidence                                                               00012479999999999999999999999


Q ss_pred             CCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 032044           91 GNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL  133 (148)
Q Consensus        91 g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i  133 (148)
                      ......++.-   .+ .-..||++|++.+.|..|+..|.|..|
T Consensus       235 ~gf~~l~~~~---~~-g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  235 PGFHILKIRA---RG-GMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             CCceEEEEec---CC-CcceEeecHHHHHHHHHHHHHhhccee
Confidence            8776665531   12 234799999999999999999999766

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

Probab=99.44  E-value=1.1e-13  Score=94.95  Aligned_cols=77  Identities=27%  Similarity=0.627  Sum_probs=74.3

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      .|++||+.+.+.+.++.|+..|.+||+|.++.+.+++-+++.+|||||+|+-++.|+.|+..+||..++|+.|+|..
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999864

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

Probab=99.43  E-value=3.3e-13  Score=97.05  Aligned_cols=132  Identities=23%  Similarity=0.470  Sum_probs=111.9

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC------------------CCCCCCCCcceEEEcCCC
Q 032044           14 GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP------------------KLPLYAETDFKLFVGNLS   75 (148)
Q Consensus        14 ~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~------------------~~~~~~~~~~~l~i~nlp   75 (148)
                      ...+++||++|.+.+.|..++. +++..+.|.++++.-......                  .........+.+++++||
T Consensus       220 n~~~nfa~ie~~s~~~at~~~~-~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp  298 (500)
T KOG0120|consen  220 NLEKNFAFIEFRSISEATEAMA-LDGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLP  298 (500)
T ss_pred             cccccceeEEecCCCchhhhhc-ccchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCc
Confidence            4567899999999999999997 788888898888863322111                  111123356789999999


Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           76 WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        76 ~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ..++++++.+.+..||.+....++.+..++.++||||.+|.++.....|+..|||..++++.|.|+.+-..
T Consensus       299 ~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g  369 (500)
T KOG0120|consen  299 LYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVG  369 (500)
T ss_pred             CccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhcc
Confidence            99999999999999999999999999888999999999999999999999999999999999999987543

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.43  E-value=1.5e-13  Score=94.64  Aligned_cols=139  Identities=15%  Similarity=0.212  Sum_probs=104.3

Q ss_pred             ceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC-------------------CC-------
Q 032044            3 SKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK-------------------PK-------   56 (148)
Q Consensus         3 ~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~-------------------~~-------   56 (148)
                      +.|-++..+ +|+.+|-|||.|..+++|+.|+.+ +...++.+.|.+..+..                   ..       
T Consensus       193 egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p  270 (508)
T KOG1365|consen  193 EGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGP  270 (508)
T ss_pred             cceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCc
Confidence            345556654 899999999999999999999984 44455555444422110                   00       


Q ss_pred             CCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCC-eeE--EEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 032044           57 PKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGN-VVG--ARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL  133 (148)
Q Consensus        57 ~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~-v~~--~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i  133 (148)
                      ...........+|.+++||+..+.++|.++|..|.. +..  +.+..+ ..|.+.|-|||+|.+.++|..|.+..|....
T Consensus       271 ~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~m  349 (508)
T KOG1365|consen  271 ARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLM  349 (508)
T ss_pred             cccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhc
Confidence            001122334678999999999999999999999864 333  677777 5688999999999999999999999998888


Q ss_pred             CCeEEEEEecc
Q 032044          134 EGRAMRVSLAQ  144 (148)
Q Consensus       134 ~g~~l~v~~~~  144 (148)
                      .++.|.|-.+.
T Consensus       350 k~RYiEvfp~S  360 (508)
T KOG1365|consen  350 KSRYIEVFPCS  360 (508)
T ss_pred             ccceEEEeecc
Confidence            88888887764

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

Probab=99.43  E-value=3.8e-13  Score=89.63  Aligned_cols=72  Identities=33%  Similarity=0.647  Sum_probs=68.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      .+|||+|||...++.+|+.+|++||.|..+.|+++        ||||..++...|+.|++-|||+.|+|..|.|+-++++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            47999999999999999999999999999999976        8999999999999999999999999999999998776

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

Probab=99.37  E-value=5e-12  Score=78.48  Aligned_cols=56  Identities=41%  Similarity=0.648  Sum_probs=52.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|++++++.++.+++++|||||+|.+.++|+.|+..+++..+.+++|.|.++....
T Consensus        60 ~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~  115 (144)
T PLN03134         60 DVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRP  115 (144)
T ss_pred             CeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCC
Confidence            47899999999999999999999999999999999999999999999999986544

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

Probab=99.33  E-value=9.3e-12  Score=87.38  Aligned_cols=78  Identities=29%  Similarity=0.516  Sum_probs=72.0

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHh-hcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQ-EYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~-~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      .+.+||.|+|++..+++|++++. +-|.|.++.+..+ ..++++|+|.|+|+++|.+++|+..||.+.++|+.|.|+-..
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            44599999999999999999998 5789999999988 669999999999999999999999999999999999998654

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

Probab=99.32  E-value=1.1e-10  Score=82.11  Aligned_cols=139  Identities=30%  Similarity=0.456  Sum_probs=110.6

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC------------------------
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP------------------------   57 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~------------------------   57 (148)
                      |+=|.++.|. +|+++|+|.|||.+++.+++|++.|+...+.|++|.++-....+.                        
T Consensus        72 v~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~  150 (608)
T KOG4212|consen   72 VEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGN  150 (608)
T ss_pred             eEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCchhhhhhhheeeccCcccccCcceeccc
Confidence            5567888894 899999999999999999999999999999999999964322100                        


Q ss_pred             -----------------------CCC---------------------------------CCCCCcceEEEcCCCCCCCHH
Q 032044           58 -----------------------KLP---------------------------------LYAETDFKLFVGNLSWSVTTE   81 (148)
Q Consensus        58 -----------------------~~~---------------------------------~~~~~~~~l~i~nlp~~~~~~   81 (148)
                                             ...                                 -.+.--.+++|.||.+.+...
T Consensus       151 ~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~  230 (608)
T KOG4212|consen  151 GGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNK  230 (608)
T ss_pred             ccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhhhhhccCCCCCccceeeeeccccccchH
Confidence                                   000                                 001123468999999999999


Q ss_pred             HHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           82 SLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        82 ~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      .|.+.|.-.|.+..+.+--++. +..+|+|.++|..+-.|-.|+..+++.-+.+++..++.
T Consensus       231 kL~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  231 KLKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             HHHHHhccceeeeeeceeeccc-cccCCeeEEEecchHHHHHHHHhhccCCCccccceeec
Confidence            9999999999999888776643 57889999999999999999999987665666655554

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

Probab=99.32  E-value=1.5e-11  Score=78.34  Aligned_cols=81  Identities=20%  Similarity=0.385  Sum_probs=73.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhc-CCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEY-GNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~-g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ......+++..+|..+.+.++...|.++ |.+...++.++..||.++|||||+|++.+.|..|...||++-+.|+-|.+.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3355679999999999999999999998 678888888999999999999999999999999999999999999988887


Q ss_pred             ec
Q 032044          142 LA  143 (148)
Q Consensus       142 ~~  143 (148)
                      +-
T Consensus       126 vm  127 (214)
T KOG4208|consen  126 VM  127 (214)
T ss_pred             Ee
Confidence            64

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

Probab=99.31  E-value=7.4e-12  Score=85.73  Aligned_cols=82  Identities=28%  Similarity=0.473  Sum_probs=77.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .+.+.|||=.|.+-++.++|.-+|+.||.|.++.++++..+|.+..||||+|++.+++++|.-.|++.-|++++|+|.++
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            46678999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             cC
Q 032044          144 QG  145 (148)
Q Consensus       144 ~~  145 (148)
                      .+
T Consensus       317 QS  318 (479)
T KOG0415|consen  317 QS  318 (479)
T ss_pred             hh
Confidence            64

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

Probab=99.30  E-value=2.3e-11  Score=82.98  Aligned_cols=78  Identities=23%  Similarity=0.465  Sum_probs=68.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHh-CCceeCCeEEEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL-NGVELEGRAMRVS  141 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l-~~~~i~g~~l~v~  141 (148)
                      .....+|||++|-..+++.+|+++|.+||.+.++.+...      ++.|||+|.+.+.|+.|...+ +...|+|.+|.|.
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~  298 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK  298 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEE
Confidence            345678999999999999999999999999999988744      448999999999999998755 5567899999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      |.++.
T Consensus       299 Wg~~~  303 (377)
T KOG0153|consen  299 WGRPK  303 (377)
T ss_pred             eCCCc
Confidence            98873

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

Probab=99.28  E-value=1.4e-11  Score=91.60  Aligned_cols=76  Identities=25%  Similarity=0.531  Sum_probs=70.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      .++||||++|+..+++.||.++|+.||.|.++.++-      ++++|||.+.+..+|.+|++.|+++.+.++.|++.|+.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            478999999999999999999999999999998763      47899999999999999999999999999999999986


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      .+
T Consensus       494 g~  495 (894)
T KOG0132|consen  494 GK  495 (894)
T ss_pred             cC
Confidence            54

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.27  E-value=1.6e-10  Score=80.60  Aligned_cols=124  Identities=28%  Similarity=0.432  Sum_probs=98.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCCeec--CcEEEEeecCCCCC---------------CCCC-------------------
Q 032044           18 GFAFVTMSTVEDCNAVIENLDGREYL--GRILRVNFSDKPKP---------------KLPL-------------------   61 (148)
Q Consensus        18 g~afv~f~~~~~a~~a~~~l~~~~~~--~~~i~v~~~~~~~~---------------~~~~-------------------   61 (148)
                      -.|+|+|.+.+.|+.|...|+|..|.  .+++++.|+.....               ..+.                   
T Consensus       189 FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~  268 (492)
T KOG1190|consen  189 FQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVP  268 (492)
T ss_pred             hhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccccccchhhhccccccc
Confidence            45999999999999999999998874  47788876532100               0000                   


Q ss_pred             ------------------------CCCCcceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEec
Q 032044           62 ------------------------YAETDFKLFVGNLSW-SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYS  116 (148)
Q Consensus        62 ------------------------~~~~~~~l~i~nlp~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~  116 (148)
                                              ....++.|.+.||.. .+|.+.|..+|.-||.|.++.|..+..     ..|+|.|.
T Consensus       269 ~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQms  343 (492)
T KOG1190|consen  269 AVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMS  343 (492)
T ss_pred             cccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeec
Confidence                                    000136677777755 589999999999999999999987742     46999999


Q ss_pred             CHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044          117 TKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus       117 ~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      +...|+.|+..|+|..+.|++|+|.+++-.
T Consensus       344 d~~qAqLA~~hL~g~~l~gk~lrvt~SKH~  373 (492)
T KOG1190|consen  344 DGQQAQLAMEHLEGHKLYGKKLRVTLSKHT  373 (492)
T ss_pred             chhHHHHHHHHhhcceecCceEEEeeccCc
Confidence            999999999999999999999999998643

>smart00361 RRM_1 RNA recognition motif

Probab=99.26  E-value=4e-11  Score=65.54  Aligned_cols=49  Identities=27%  Similarity=0.513  Sum_probs=43.5

Q ss_pred             CcceeE-eeecCCC--CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEE
Q 032044            1 MLSKLT-VLYDRET--GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV   49 (148)
Q Consensus         1 ~i~~i~-~~~~~~~--~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v   49 (148)
                      +|.+|. ++.++.+  +.++|||||+|.+.++|.+|+..|+|..+.|+.|.+
T Consensus        18 ~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361       18 EVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             CeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            356774 7777777  899999999999999999999999999999999876

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

Probab=99.23  E-value=2e-11  Score=80.06  Aligned_cols=139  Identities=24%  Similarity=0.446  Sum_probs=114.4

Q ss_pred             eeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC-CCCCCCCCCCCcceEEEcCCCCCCCHHH
Q 032044            4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK-PKPKLPLYAETDFKLFVGNLSWSVTTES   82 (148)
Q Consensus         4 ~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~-~~~~~~~~~~~~~~l~i~nlp~~~~~~~   82 (148)
                      ..+++++. -+.-++.+|+.|....+-.++-..-++..+...+++..-... ..+....+.....+||++.|.-.++.+-
T Consensus       128 ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedPsl~ew~~~DfRIfcgdlgNevnd~v  206 (290)
T KOG0226|consen  128 KTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDV  206 (290)
T ss_pred             hhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCcccccCccccceeecccccccccHHH
Confidence            34455554 467788999999988888888776677777777655543322 2344456677788999999999999999


Q ss_pred             HHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           83 LTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        83 l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      |...|.+|-......++++..+++.+||+||.|.+..++..|++.++|..++.+.|+++.+
T Consensus       207 l~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  207 LARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             HHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            9999999988888889999999999999999999999999999999999999999887764

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

Probab=99.23  E-value=6.9e-11  Score=78.44  Aligned_cols=82  Identities=32%  Similarity=0.570  Sum_probs=73.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ..+.+|+|.|||+.+.++||+++|..||.+..+.+.++ ..+.+.|.|-|.|...++|..|++.++|..++|+.+.+...
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~-~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            34578999999999999999999999998888888888 45888899999999999999999999999999999998886


Q ss_pred             cCC
Q 032044          144 QGR  146 (148)
Q Consensus       144 ~~~  146 (148)
                      .++
T Consensus       160 ~~~  162 (243)
T KOG0533|consen  160 SSP  162 (243)
T ss_pred             cCc
Confidence            554

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

Probab=99.22  E-value=3.7e-11  Score=78.42  Aligned_cols=54  Identities=39%  Similarity=0.663  Sum_probs=51.2

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      |..|.+.+|+.||.++|||||.|.+.++|.+|+..|+|.-++.--|.|+|+.++
T Consensus       216 i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  216 ITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSKPS  269 (270)
T ss_pred             cceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecCCC
Confidence            678999999999999999999999999999999999999999999999999764

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

Probab=99.20  E-value=3.4e-10  Score=77.04  Aligned_cols=126  Identities=30%  Similarity=0.467  Sum_probs=92.3

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC----CCCCC---------------CCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK----PKPKL---------------PLY   62 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~----~~~~~---------------~~~   62 (148)
                      |..+.+..++.+|.++|||||+|.+.++|..|+..+++..+.|+++.|.+...    .....               ...
T Consensus       142 ~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (306)
T COG0724         142 VKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALL  221 (306)
T ss_pred             eeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccccccccccccccccchhhhcccccccccc
Confidence            46789999988999999999999999999999999999999999999998532    11111               112


Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHH
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES  127 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~  127 (148)
                      ......+++.+++...+..++...|..+|.+....+........+....++.+.....+......
T Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  286 (306)
T COG0724         222 LEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSR  286 (306)
T ss_pred             ccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccchhHHHhhhhhhcc
Confidence            23456799999999999999999999999886665554433232333333444444444444443

>PF13893 RRM_5: RNA recognition motif

Probab=99.16  E-value=2e-10  Score=59.98  Aligned_cols=47  Identities=40%  Similarity=0.819  Sum_probs=40.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      +|++|.+..++     +++|||+|.+.++|+.|++.|++..+.|++|.|.|+
T Consensus        10 ~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen   10 EVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             -EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             cEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            36677776654     689999999999999999999999999999999885

(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 ....

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

Probab=99.16  E-value=5.6e-09  Score=72.38  Aligned_cols=135  Identities=19%  Similarity=0.281  Sum_probs=105.3

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeec--CcEEEEeecCCCCCC---------------------
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL--GRILRVNFSDKPKPK---------------------   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~--~~~i~v~~~~~~~~~---------------------   58 (148)
                      |..|-|++.  +|   =.|+|||++.+.|++|...|||..|+  -++++|+|+.+.+..                     
T Consensus       149 VlRIvIfkk--ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~  223 (494)
T KOG1456|consen  149 VLRIVIFKK--NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYD  223 (494)
T ss_pred             eEEEEEEec--cc---eeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCC
Confidence            445555554  33   36999999999999999999999874  588999987653110                     


Q ss_pred             --CC------------------------------------------------------CCCCCcceEEEcCCCCC-CCHH
Q 032044           59 --LP------------------------------------------------------LYAETDFKLFVGNLSWS-VTTE   81 (148)
Q Consensus        59 --~~------------------------------------------------------~~~~~~~~l~i~nlp~~-~~~~   81 (148)
                        ..                                                      ....+.+.+.|-+|... .+.+
T Consensus       224 ~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~d  303 (494)
T KOG1456|consen  224 PGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCD  303 (494)
T ss_pred             CCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchh
Confidence              00                                                      00113456888888765 6778


Q ss_pred             HHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           82 SLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        82 ~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      .|..+|=.||.|.++.+++..     .|-|.|++.+....++|+..||+..+-|.+|.+..+++.
T Consensus       304 rlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~  363 (494)
T KOG1456|consen  304 RLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQN  363 (494)
T ss_pred             hhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEeecccc
Confidence            899999999999999998763     457999999999999999999999999999999987653

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.15  E-value=1.4e-10  Score=76.90  Aligned_cols=83  Identities=33%  Similarity=0.558  Sum_probs=73.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCc-eeCC--eEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV-ELEG--RAMR  139 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~-~i~g--~~l~  139 (148)
                      ....++|||+.|...-.|+|++.+|.+||.+.++.+.+.+ .+.++|++||.|.+.-+|+.|+..|||- .+-|  ..|.
T Consensus        16 g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLV   94 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLV   94 (371)
T ss_pred             CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceE
Confidence            3367799999999999999999999999999999998884 4788999999999999999999999984 4555  5799


Q ss_pred             EEeccCC
Q 032044          140 VSLAQGR  146 (148)
Q Consensus       140 v~~~~~~  146 (148)
                      |++++..
T Consensus        95 VK~ADTd  101 (371)
T KOG0146|consen   95 VKFADTD  101 (371)
T ss_pred             EEeccch
Confidence            9998654

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.12  E-value=7.6e-11  Score=81.10  Aligned_cols=82  Identities=38%  Similarity=0.686  Sum_probs=75.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++++|++|++.++++.|++.|.+||.+..+.+++++.++.+++++||+|.+++....++. ...+.|+|+.|.+..+-
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            67899999999999999999999999999999999999999999999999999999998887 66778999999988887


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      ++.
T Consensus        84 ~r~   86 (311)
T KOG4205|consen   84 SRE   86 (311)
T ss_pred             Ccc
Confidence            764

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

Probab=99.11  E-value=2.3e-09  Score=61.59  Aligned_cols=80  Identities=20%  Similarity=0.232  Sum_probs=68.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhc--CCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC----CeEEEE
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEY--GNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELE----GRAMRV  140 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~--g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~----g~~l~v  140 (148)
                      +||.|+|+|...+.++|.+++...  |....+.++.+..++.+.|||||.|.+++.|....+.++|..+.    .+.+.+
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            589999999999999999999753  45667777888788889999999999999999999999998774    577888


Q ss_pred             EeccCC
Q 032044          141 SLAQGR  146 (148)
Q Consensus       141 ~~~~~~  146 (148)
                      .+|+-+
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            887643

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

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

Probab=99.09  E-value=2e-10  Score=74.10  Aligned_cols=58  Identities=34%  Similarity=0.618  Sum_probs=53.9

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~   59 (148)
                      |.+|.+..|..+++++|||||+|...++|..|+..+|+..+.|++|+|.++.+.+...
T Consensus        37 I~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~kike   94 (298)
T KOG0111|consen   37 IKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEKIKE   94 (298)
T ss_pred             hhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCccccC
Confidence            6789999999999999999999999999999999999999999999999998776543

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

Probab=99.08  E-value=5.7e-10  Score=81.08  Aligned_cols=79  Identities=39%  Similarity=0.598  Sum_probs=73.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      .+.|||.+|...+-..+|+.+|++||.|....++.+-.+...++|+||++.+...|.+||..||-.++.|+.|.|..+.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            4679999999999999999999999999999999887777789999999999999999999999999999999998864

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

Probab=99.06  E-value=3.6e-10  Score=72.19  Aligned_cols=55  Identities=18%  Similarity=0.388  Sum_probs=50.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      +|..+++.|++.||.|+|||||+|.+++.|.-|-+.||++.|+++-+.|.+-.+.
T Consensus        76 ~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   76 TVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             eeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            3567888899999999999999999999999999999999999999999987655

>PF00076 RRM_1: RNA recognition motif

Probab=99.01  E-value=1.5e-09  Score=58.98  Aligned_cols=47  Identities=32%  Similarity=0.704  Sum_probs=42.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEE
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR   48 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~   48 (148)
                      .|..+.++.+ .++.++|||||+|.+.++|+.|++.+++..+.|++|+
T Consensus        24 ~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   24 KIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             TEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             hccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            3678888998 6889999999999999999999999999999999875

(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 ....

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

Probab=99.00  E-value=2.1e-09  Score=76.81  Aligned_cols=80  Identities=24%  Similarity=0.470  Sum_probs=67.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      ..+|||.|||.+++..+|.++|.+||.|....|..-...++..+||||+|.+.+.++.|+. .+-..++|++|.|+-.++
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~-Asp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIE-ASPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhh-cCccccCCeeEEEEeccc
Confidence            3459999999999999999999999999998886543223334899999999999999999 558889999999987665


Q ss_pred             C
Q 032044          146 R  146 (148)
Q Consensus       146 ~  146 (148)
                      .
T Consensus       367 ~  367 (419)
T KOG0116|consen  367 G  367 (419)
T ss_pred             c
Confidence            3

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

Probab=99.00  E-value=8.9e-09  Score=66.79  Aligned_cols=83  Identities=20%  Similarity=0.382  Sum_probs=68.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEc-CCCCCceeEEEEEecCHHHHHHHHHHhCCceeC---CeEEE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYD-GESGRSRGYGFVCYSTKAEMETALESLNGVELE---GRAMR  139 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~---g~~l~  139 (148)
                      ..-++|||.+||.++-..+|..+|..|..-+...+... +.....+.+||++|.+.+.|..|+..|||..++   +..|+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            34689999999999999999999999876666555443 222334579999999999999999999999986   78899


Q ss_pred             EEeccCC
Q 032044          140 VSLAQGR  146 (148)
Q Consensus       140 v~~~~~~  146 (148)
                      +++++++
T Consensus       112 iElAKSN  118 (284)
T KOG1457|consen  112 IELAKSN  118 (284)
T ss_pred             eeehhcC
Confidence            9988654

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

Probab=99.00  E-value=5e-09  Score=71.78  Aligned_cols=80  Identities=23%  Similarity=0.523  Sum_probs=70.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCee--------EEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVV--------GARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG  135 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~--------~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g  135 (148)
                      ..+..|||+|||.++|.+++.++|+++|.|.        .+.+.++ ..|..+|-|++.|-..++...|++.|++..+.|
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd-~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRD-NQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEec-CCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            3456799999999999999999999999764        3566777 458899999999999999999999999999999


Q ss_pred             eEEEEEecc
Q 032044          136 RAMRVSLAQ  144 (148)
Q Consensus       136 ~~l~v~~~~  144 (148)
                      +.|+|+.|+
T Consensus       211 ~~~rVerAk  219 (382)
T KOG1548|consen  211 KKLRVERAK  219 (382)
T ss_pred             cEEEEehhh
Confidence            999999875

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

Probab=98.99  E-value=5.3e-10  Score=71.53  Aligned_cols=53  Identities=34%  Similarity=0.537  Sum_probs=49.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|-+|.|.+|+.|++++|||||-|....+|+.|++.|+|..++|+.|.|+.+.
T Consensus        39 ~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   39 RVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            36789999999999999999999999999999999999999999999988653

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.97  E-value=1.1e-10  Score=87.56  Aligned_cols=113  Identities=20%  Similarity=0.265  Sum_probs=96.9

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhhc
Q 032044           11 RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEY   90 (148)
Q Consensus        11 ~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~   90 (148)
                      ..+++.+|+||++|..++++.+|+....+..++                      ...++|+|.|+..|.++++.++..+
T Consensus       703 ~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g----------------------K~~v~i~g~pf~gt~e~~k~l~~~~  760 (881)
T KOG0128|consen  703 KNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG----------------------KISVAISGPPFQGTKEELKSLASKT  760 (881)
T ss_pred             hhccccccceeeEeecCCchhhhhhhhhhhhhh----------------------hhhhheeCCCCCCchHHHHhhcccc
Confidence            456789999999999999999999855555443                      1258899999999999999999999


Q ss_pred             CCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           91 GNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        91 g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      |.+.+.+++.. ..|+|+|.+++.|.++.++.+++...++..++.+.+.+..+++.
T Consensus       761 gn~~~~~~vt~-r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~  815 (881)
T KOG0128|consen  761 GNVTSLRLVTV-RAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPE  815 (881)
T ss_pred             CCccccchhhh-hccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCc
Confidence            99999888777 45889999999999999999999999998888887777776553

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

Probab=98.96  E-value=3.3e-10  Score=71.08  Aligned_cols=52  Identities=31%  Similarity=0.646  Sum_probs=48.9

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      |.+|.++||+.||+|+||||+.|.+..+-..|+..|||..+.|++|+|....
T Consensus        62 ~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   62 IVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             eEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            5789999999999999999999999999999999999999999999998543

>smart00360 RRM RNA recognition motif

Probab=98.94  E-value=5.9e-09  Score=56.27  Aligned_cols=49  Identities=39%  Similarity=0.756  Sum_probs=44.6

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEe
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN   50 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~   50 (148)
                      |..+.+..++.++.++|||||+|.+.++|..|+..+++..+.|+.+.|+
T Consensus        23 v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360       23 IESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             EeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            6788899988789999999999999999999999999999999988763

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

Probab=98.94  E-value=3.1e-09  Score=71.46  Aligned_cols=52  Identities=27%  Similarity=0.523  Sum_probs=49.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      .|+.|.+++|+.||+++|||||+|..+.+...|-...+|..|.|+.|.|.+-
T Consensus       127 ~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen  127 PIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             cceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            4889999999999999999999999999999999999999999999999753

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

Probab=98.94  E-value=1e-09  Score=79.13  Aligned_cols=72  Identities=31%  Similarity=0.436  Sum_probs=63.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      .....+|+|-|||.++++++|+.+|+.||.|..++.-     ...++.+||+|.|..+|+.|++.|++.+|.|+.+.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t-----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET-----PNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc-----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3456789999999999999999999999999986443     23578999999999999999999999999998877

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.94  E-value=4.4e-09  Score=57.32  Aligned_cols=46  Identities=43%  Similarity=0.771  Sum_probs=42.4

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEE
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR   48 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~   48 (148)
                      |..+.+..++. |+++|+|||+|.+.++|..|+..+++..+.|+.|+
T Consensus        25 v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   25 VEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            67899999976 99999999999999999999999998999999874

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 ....

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.90  E-value=3.9e-09  Score=72.38  Aligned_cols=135  Identities=23%  Similarity=0.347  Sum_probs=107.2

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC-----CCCCCCCCCcceEE-EcCCCCCCCHHHHH
Q 032044           11 RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK-----PKLPLYAETDFKLF-VGNLSWSVTTESLT   84 (148)
Q Consensus        11 ~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~-----~~~~~~~~~~~~l~-i~nlp~~~~~~~l~   84 (148)
                      .....++|++.+.|...+.+..|+.........++.+.........     .........+.+++ +.+++..+++++|.
T Consensus       124 ~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~  203 (285)
T KOG4210|consen  124 EDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLK  203 (285)
T ss_pred             ccccccccceeeccccHHHHHHHHHhhhccccccccccCcccccccccccchhcccccCccccceeecccccccchHHHh
Confidence            3456899999999999999999998544445555554443332221     11122333455666 99999999999999


Q ss_pred             HHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           85 QAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        85 ~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ..|..+|.+..++++..+.++...+++|+.|.....+..++.. .+..+.+.++.+....++
T Consensus       204 ~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  204 EHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             hhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCC
Confidence            9999999999999999999999999999999999999999987 888999999999987766

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

Probab=98.88  E-value=2.8e-09  Score=69.51  Aligned_cols=70  Identities=27%  Similarity=0.621  Sum_probs=64.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        68 ~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      .+||+++|+...+.++.++|..||.+..+.+.        .|++||+|.+..+|..|+-.+|+..++|-.+.+.++..
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            68999999999999999999999999887664        45789999999999999999999999998899999874

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

Probab=98.88  E-value=4e-09  Score=75.78  Aligned_cols=54  Identities=39%  Similarity=0.774  Sum_probs=51.0

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      |.+++++.|+.||+++||||++|.+.++|..|++.|++..+.|++++|.|....
T Consensus        45 v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   45 VLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            678999999999999999999999999999999999999999999999987543

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.87  E-value=8.6e-08  Score=68.99  Aligned_cols=109  Identities=16%  Similarity=0.231  Sum_probs=82.4

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCC----Ce-------ecCcEEEEeecCCCCC----CCCCCCCCcceEEEcCCCCCCCHHH
Q 032044           18 GFAFVTMSTVEDCNAVIENLDG----RE-------YLGRILRVNFSDKPKP----KLPLYAETDFKLFVGNLSWSVTTES   82 (148)
Q Consensus        18 g~afv~f~~~~~a~~a~~~l~~----~~-------~~~~~i~v~~~~~~~~----~~~~~~~~~~~l~i~nlp~~~~~~~   82 (148)
                      ||+|+.|.++..++.-+.....    ..       +..+.+.|.+......    ....+-++.+||||++||..++.++
T Consensus       307 ~YvflvFe~E~sV~~Ll~aC~~~~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~e  386 (520)
T KOG0129|consen  307 GYVFLVFEDERSVQSLLSACSEGEGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEE  386 (520)
T ss_pred             cEEEEEecchHHHHHHHHHHhhcccceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHH
Confidence            4999999999999887764322    11       1122233332221111    1233455778999999999999999


Q ss_pred             HHHHHh-hcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHH
Q 032044           83 LTQAFQ-EYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE  126 (148)
Q Consensus        83 l~~~f~-~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~  126 (148)
                      |..+|+ -||.|..+.|-.|+.-+.|+|.|-|+|.+.+.-.+||.
T Consensus       387 LA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  387 LAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             HHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHh
Confidence            999999 69999999999888888899999999999999999987

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.82  E-value=3.6e-08  Score=70.50  Aligned_cols=77  Identities=23%  Similarity=0.441  Sum_probs=63.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ....-|.+++||+++|++||+++|+.++ |..+.+.  +.++++.|-|||+|.+.+++++|++ .+-..+..+-|.|-.+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~--r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIP--RRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEe--ccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            3455789999999999999999999995 6665444  4568899999999999999999999 6777777788877665


Q ss_pred             c
Q 032044          144 Q  144 (148)
Q Consensus       144 ~  144 (148)
                      .
T Consensus        84 ~   84 (510)
T KOG4211|consen   84 G   84 (510)
T ss_pred             C
Confidence            3

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

Probab=98.81  E-value=1.2e-08  Score=67.95  Aligned_cols=81  Identities=27%  Similarity=0.474  Sum_probs=74.3

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ......++++|+.+.++.+++..+|+.||.+..+.+..+...+.+++++||+|.+.+..+.++. |++-.+.|..+.+.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            3456689999999999999999999999999999999998888899999999999999999999 999999999988887


Q ss_pred             cc
Q 032044          143 AQ  144 (148)
Q Consensus       143 ~~  144 (148)
                      .+
T Consensus       177 ~r  178 (231)
T KOG4209|consen  177 KR  178 (231)
T ss_pred             ee
Confidence            54

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

Probab=98.78  E-value=2.8e-08  Score=67.83  Aligned_cols=53  Identities=26%  Similarity=0.471  Sum_probs=47.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      +|.+|.|+.+. . .|||||||.|++.+||++|-++|+|..+.|++|.|..+...
T Consensus       122 ~VldVEIIfNE-R-GSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  122 KVLDVEIIFNE-R-GSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             ceeeEEEEecc-C-CCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchh
Confidence            57899999983 3 49999999999999999999999999999999999977643

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

Probab=98.74  E-value=2.7e-08  Score=64.95  Aligned_cols=52  Identities=27%  Similarity=0.455  Sum_probs=45.1

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      |.+..|+.|+.||+|+|||||.|.+.++|.+|+.. .+-.|+|++..|..+..
T Consensus        39 I~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   39 IVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLASL   90 (247)
T ss_pred             eEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhhh
Confidence            77899999999999999999999999999999983 33457999988886654

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.74  E-value=3.6e-07  Score=63.84  Aligned_cols=115  Identities=18%  Similarity=0.231  Sum_probs=84.2

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC--------CCC---CCCCCCcceEEEcCCCCCCC
Q 032044           11 RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK--------PKL---PLYAETDFKLFVGNLSWSVT   79 (148)
Q Consensus        11 ~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~--------~~~---~~~~~~~~~l~i~nlp~~~~   79 (148)
                      ...|+..|.|.|.|.+.+.-+-|+. .+...+.++.|.+-.+....        ..+   ..+...--.|.+++||++++
T Consensus        96 ~~qgrRnge~lvrf~d~e~Rdlalk-Rhkhh~g~ryievYka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat  174 (508)
T KOG1365|consen   96 NAQGRRNGEALVRFVDPEGRDLALK-RHKHHMGTRYIEVYKATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDAT  174 (508)
T ss_pred             hhhhccccceEEEecCchhhhhhhH-hhhhhccCCceeeeccCchhheEecCCccccCCCCCCcccceEEEecCCCCCcc
Confidence            3467888999999999999999997 56777777777775332211        111   11222345688999999999


Q ss_pred             HHHHHHHHhhcC----CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHH
Q 032044           80 TESLTQAFQEYG----NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES  127 (148)
Q Consensus        80 ~~~l~~~f~~~g----~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~  127 (148)
                      +.++.++|.+-.    ....+.++.. ..|++.|-|||.|..+++|+.|+..
T Consensus       175 ~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  175 ALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK  225 (508)
T ss_pred             hHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH
Confidence            999999997432    3445555544 4588999999999999999999973

>smart00362 RRM_2 RNA recognition motif

Probab=98.73  E-value=6.8e-08  Score=52.19  Aligned_cols=47  Identities=40%  Similarity=0.695  Sum_probs=41.4

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEe
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN   50 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~   50 (148)
                      |..+.+..++  +.++|+|||+|.+.++|+.|+..+++..+.|+++.++
T Consensus        26 v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362       26 IESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             EEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            5677888776  7899999999999999999999999999999988763

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

Probab=98.72  E-value=1.6e-08  Score=60.65  Aligned_cols=55  Identities=29%  Similarity=0.538  Sum_probs=50.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .|+.|.+-.|+-||=.+|||+|+|.+.+.|+.|+..+|+..+.++++.|.|+-..
T Consensus        98 eiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~  152 (170)
T KOG0130|consen   98 EIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVK  152 (170)
T ss_pred             cccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEec
Confidence            3678888899999999999999999999999999999999999999999987543

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.70  E-value=5.4e-08  Score=72.45  Aligned_cols=80  Identities=28%  Similarity=0.536  Sum_probs=70.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCC---CCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGES---GRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ..+.+|++||++.++++.|...|..||++.++.+++.+..   ...+.++||-|-+..+|++|+..|+|..+.+..+++-
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~g  252 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLG  252 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeec
Confidence            3467999999999999999999999999999999876422   3456789999999999999999999999999999998


Q ss_pred             ecc
Q 032044          142 LAQ  144 (148)
Q Consensus       142 ~~~  144 (148)
                      |.+
T Consensus       253 Wgk  255 (877)
T KOG0151|consen  253 WGK  255 (877)
T ss_pred             ccc
Confidence            874

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.69  E-value=1.7e-08  Score=76.69  Aligned_cols=131  Identities=17%  Similarity=0.265  Sum_probs=106.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHH
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTE   81 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~   81 (148)
                      |++|.|-+-+ -++...|||+.|.+.+++-.|...+.+..|....+.+.+...       .......+++++|+.++...
T Consensus       399 ve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~-------kst~ttr~~sgglg~w~p~~  470 (975)
T KOG0112|consen  399 VEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQP-------KSTPTTRLQSGGLGPWSPVS  470 (975)
T ss_pred             ccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccccccccc-------ccccceeeccCCCCCCChHH
Confidence            5566665553 456778999999999999999999999888777766666543       22355679999999999999


Q ss_pred             HHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEeccCC
Q 032044           82 SLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG--RAMRVSLAQGR  146 (148)
Q Consensus        82 ~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g--~~l~v~~~~~~  146 (148)
                      .+...|..||.|..|.+-..      ..|+|+.|++...|+.|+..+-|..++|  +.++|.++.+.
T Consensus       471 ~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~  531 (975)
T KOG0112|consen  471 RLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPP  531 (975)
T ss_pred             HHHHHhhccCcceeeecccC------CcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCC
Confidence            99999999999988766433      3489999999999999999999999986  67888887653

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.66  E-value=6.4e-08  Score=56.85  Aligned_cols=70  Identities=21%  Similarity=0.388  Sum_probs=44.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCC-----ceeCCeEEEEE
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNG-----VELEGRAMRVS  141 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~-----~~i~g~~l~v~  141 (148)
                      +.|++.+++..++.++|++.|++||.|.+|.+..+      ...|||.|.+++.|+.|+..+..     ..+.+..+.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            46889999999999999999999999999887654      22699999999999999987643     45666666555


Q ss_pred             e
Q 032044          142 L  142 (148)
Q Consensus       142 ~  142 (148)
                      .
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            4

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

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

Probab=98.64  E-value=1.3e-08  Score=65.86  Aligned_cols=79  Identities=24%  Similarity=0.336  Sum_probs=70.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      +....+|+|.|+...++++-|.++|-+-|+|.++.|..+.+ +.++ +|||.|.++...+-|++.+||..+.|..+.+.+
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhccc
Confidence            34567999999999999999999999999999999988755 4445 999999999999999999999999998888876


Q ss_pred             c
Q 032044          143 A  143 (148)
Q Consensus       143 ~  143 (148)
                      -
T Consensus        84 r   84 (267)
T KOG4454|consen   84 R   84 (267)
T ss_pred             c
Confidence            4

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.63  E-value=3.6e-07  Score=50.51  Aligned_cols=69  Identities=22%  Similarity=0.335  Sum_probs=46.5

Q ss_pred             eEEEcCCCCCCCHHHHH----HHHhhcCC-eeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           68 KLFVGNLSWSVTTESLT----QAFQEYGN-VVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        68 ~l~i~nlp~~~~~~~l~----~~f~~~g~-v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      .|+|.|||.+.+...|+    .++..+|. |..+  .        .+.|+|.|.+.+.|.+|.+.|+|-.+-|++|.|++
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~--------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S--------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e--------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            68999999998887655    55557764 4443  1        24699999999999999999999999999999999


Q ss_pred             ccCC
Q 032044          143 AQGR  146 (148)
Q Consensus       143 ~~~~  146 (148)
                      ....
T Consensus        74 ~~~~   77 (90)
T PF11608_consen   74 SPKN   77 (90)
T ss_dssp             S--S
T ss_pred             cCCc
Confidence            7433

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

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.59  E-value=3.5e-07  Score=60.55  Aligned_cols=52  Identities=10%  Similarity=0.140  Sum_probs=45.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      +|++|+|+++.   +.+++|||+|.++++|+.|+. |+|..|.+++|.|.......
T Consensus        31 ~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~y~   82 (243)
T PLN03121         31 AIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQYE   82 (243)
T ss_pred             CeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcccc
Confidence            58899999984   455899999999999999996 99999999999999876543

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.59  E-value=1.7e-07  Score=69.87  Aligned_cols=140  Identities=13%  Similarity=0.053  Sum_probs=104.1

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC------------------------
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP------------------------   57 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~------------------------   57 (148)
                      |.+..|..+...+-..|-++|.|....++++|+. .+.+.+-++.+.+.......-                        
T Consensus       337 ~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~-rn~~~~~~R~~q~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~  415 (944)
T KOG4307|consen  337 AQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFT-RNPSDDVNRPFQTGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIA  415 (944)
T ss_pred             ccccchhhhhcCCCcCCceEEEecCcchHHHHHh-cCchhhhhcceeecCCCccccccCccccccCCCCcccccCCCCCC
Confidence            3445556665555558999999999999999997 566677777777764322100                        


Q ss_pred             ----------CCCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEEEEcCCCCCceeEEEEEecCHHHHHHHHH
Q 032044           58 ----------KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVG-ARVLYDGESGRSRGYGFVCYSTKAEMETALE  126 (148)
Q Consensus        58 ----------~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~-~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~  126 (148)
                                ..+.+.....+|||..||..+++.++.++|.....|+. |.+.+. .+++.++.|||.|..++.+..|..
T Consensus       416 ~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~  494 (944)
T KOG4307|consen  416 PPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASS  494 (944)
T ss_pred             CcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccC-Ccccccchhhheeccccccchhhh
Confidence                      00112234568999999999999999999998777766 555444 557778899999999999999998


Q ss_pred             HhCCceeCCeEEEEEec
Q 032044          127 SLNGVELEGRAMRVSLA  143 (148)
Q Consensus       127 ~l~~~~i~g~~l~v~~~  143 (148)
                      .-+.+.++.+.|+|+..
T Consensus       495 ~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  495 VKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             cccccccCceEEEeech
Confidence            77777788889998764

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.59  E-value=2.9e-07  Score=68.66  Aligned_cols=75  Identities=21%  Similarity=0.391  Sum_probs=66.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCee-EEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVV-GARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~-~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      +.|-+.|+|++++.+||.++|..|-.+- +|.+-++ +.|.+.|.|-|-|++.+.|..|...|++..|.++.|.+.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            4789999999999999999999996543 4444444 7799999999999999999999999999999999998875

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=98.59  E-value=4.1e-07  Score=49.30  Aligned_cols=49  Identities=41%  Similarity=0.763  Sum_probs=42.9

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEee
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF   51 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~   51 (148)
                      |..+.+..++.+ .++|+|||+|.+.++|..|+..+++..+.|+.+.+.+
T Consensus        26 i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590          26 VESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             EEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            567788887644 7899999999999999999999999999999998764

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).

>PLN03120 nucleic acid binding protein; Provisional

Probab=98.58  E-value=3.6e-07  Score=61.37  Aligned_cols=51  Identities=12%  Similarity=0.231  Sum_probs=45.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      +|++|.|++++.   ++|||||+|.++++|..|+. |++..+.|+.|.|.++...
T Consensus        30 ~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120         30 DIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCC
Confidence            588999998863   56999999999999999996 9999999999999987643

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

Probab=98.58  E-value=1.5e-07  Score=56.03  Aligned_cols=52  Identities=19%  Similarity=0.413  Sum_probs=46.9

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      |..|-+-.|+.+...-|||||+|.+.++|..|+..+++..+..++|.+.|.-
T Consensus        63 irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   63 IRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            5566667788899999999999999999999999999999999999998753

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

Probab=98.56  E-value=1.1e-07  Score=65.75  Aligned_cols=53  Identities=28%  Similarity=0.456  Sum_probs=50.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      +|.+|.+++|..||.+.-||||+|.+.+++++|.-+|++..|.++.|+|.++.
T Consensus       265 ~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  265 KIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             cceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            58899999999999999999999999999999999999999999999999864

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

Probab=98.53  E-value=2e-07  Score=58.46  Aligned_cols=40  Identities=33%  Similarity=0.590  Sum_probs=36.8

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044           16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus        16 ~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      ..|||||||.+..||+.|+..|+|..|.|..+.|+.+...
T Consensus        46 PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~   85 (195)
T KOG0107|consen   46 PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGR   85 (195)
T ss_pred             CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCC
Confidence            4589999999999999999999999999999999987644

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

Probab=98.40  E-value=3.8e-07  Score=63.04  Aligned_cols=82  Identities=26%  Similarity=0.387  Sum_probs=73.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCee--------EEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCe
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVV--------GARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR  136 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~--------~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~  136 (148)
                      ...+|++.++|..+++++|.++|.++|.|.        .+.+.++..++.+++-|.|.|++...|+.|+.-+++..+.|.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            456899999999999999999999998653        356777888999999999999999999999999999999999


Q ss_pred             EEEEEeccCC
Q 032044          137 AMRVSLAQGR  146 (148)
Q Consensus       137 ~l~v~~~~~~  146 (148)
                      .|+|.++..+
T Consensus       145 ~ikvs~a~~r  154 (351)
T KOG1995|consen  145 TIKVSLAERR  154 (351)
T ss_pred             Cchhhhhhhc
Confidence            9999888655

>PLN03213 repressor of silencing 3; Provisional

Probab=98.38  E-value=8.7e-07  Score=63.98  Aligned_cols=50  Identities=18%  Similarity=0.399  Sum_probs=43.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCH--HHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTV--EDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~--~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      .|.++.|++.  +|  +|||||+|.+.  .++.+|+..|+|..+.|+.|+|..+.+
T Consensus        36 sVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213         36 TVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             CeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            4788999944  66  99999999987  679999999999999999999987654

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

Probab=98.32  E-value=3.2e-07  Score=60.74  Aligned_cols=49  Identities=24%  Similarity=0.508  Sum_probs=45.0

Q ss_pred             eEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            5 LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         5 i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      -++++|+-||+++||+||.|.+..++..|++.++|..++.++|..+.+.
T Consensus       220 akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  220 AKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSE  268 (290)
T ss_pred             ccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhh
Confidence            4789999999999999999999999999999999999999998887543

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

Probab=98.31  E-value=1.8e-07  Score=60.66  Aligned_cols=110  Identities=25%  Similarity=0.414  Sum_probs=87.3

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcC----CCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGN----LSWS   77 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~n----lp~~   77 (148)
                      |.++.|..++ .+..+ ||||.|.++-.+..|+..+||..+.+.++.+.+-                  .++    |...
T Consensus        36 V~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r------------------~G~shapld~r   95 (267)
T KOG4454|consen   36 VYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR------------------CGNSHAPLDER   95 (267)
T ss_pred             eEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc------------------cCCCcchhhhh
Confidence            3455555564 55555 9999999999999999999999999999888743                  233    5556


Q ss_pred             CCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCce
Q 032044           78 VTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVE  132 (148)
Q Consensus        78 ~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~  132 (148)
                      .+++.+...+..-|++..+++..+.+ +.++.++|+++........++....+..
T Consensus        96 ~~~ei~~~v~s~a~p~~~~R~~~~~d-~rnrn~~~~~~qr~~~~P~~~~~y~~l~  149 (267)
T KOG4454|consen   96 VTEEILYEVFSQAGPIEGVRIPTDND-GRNRNFGFVTYQRLCAVPFALDLYQGLE  149 (267)
T ss_pred             cchhhheeeecccCCCCCcccccccc-CCccCccchhhhhhhcCcHHhhhhcccC
Confidence            78888889999999999999988755 7788889999988888888887666644

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.23  E-value=5.5e-06  Score=57.25  Aligned_cols=79  Identities=20%  Similarity=0.341  Sum_probs=61.2

Q ss_pred             cceEEEcCCCCCCCHHH------HHHHHhhcCCeeEEEEEEcCCC-CCcee--EEEEEecCHHHHHHHHHHhCCceeCCe
Q 032044           66 DFKLFVGNLSWSVTTES------LTQAFQEYGNVVGARVLYDGES-GRSRG--YGFVCYSTKAEMETALESLNGVELEGR  136 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~------l~~~f~~~g~v~~~~~~~~~~~-~~~~~--~~fv~f~~~~~a~~a~~~l~~~~i~g~  136 (148)
                      ..-+||-++|+.+..++      -.++|.+||.|..+.+-+.-.+ +...+  -.||+|.+.++|.+|++..+|..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            34589999999887776      3489999999998877543211 11112  249999999999999999999999999


Q ss_pred             EEEEEecc
Q 032044          137 AMRVSLAQ  144 (148)
Q Consensus       137 ~l~v~~~~  144 (148)
                      .|+..|-.
T Consensus       194 ~lkatYGT  201 (480)
T COG5175         194 VLKATYGT  201 (480)
T ss_pred             eEeeecCc
Confidence            99988743

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.16  E-value=5.1e-08  Score=73.78  Aligned_cols=132  Identities=16%  Similarity=0.169  Sum_probs=97.0

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCC-----CCcceEEEcCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYA-----ETDFKLFVGNLSW   76 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~-----~~~~~l~i~nlp~   76 (148)
                      |++|++......-....++++++....+++.|.. ..+..+.++...+..+.+.........     ....+++++||++
T Consensus       599 vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~  677 (881)
T KOG0128|consen  599 VEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAVGLADAEEKEENFKVSPNEIRDLIKIFVSNLSP  677 (881)
T ss_pred             cccccCccccccccccchhhhhhccccchhhccc-ccccccCCccccCCCCCchhhhhccCcCchHHHHHHHHHHhhcch
Confidence            4555555422222333378899999999998886 567777888888777655543222111     2346899999999


Q ss_pred             CCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC
Q 032044           77 SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELE  134 (148)
Q Consensus        77 ~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~  134 (148)
                      .+.+.+|...|.++|.+..+.+.-..+.+..+|+||++|..++++.+|+....++.++
T Consensus       678 ~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  678 KMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             hhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            9999999999999998877766545566788999999999999999999866655544

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=98.12  E-value=1.8e-06  Score=57.32  Aligned_cols=73  Identities=19%  Similarity=0.298  Sum_probs=61.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCC--------CCc----eeEEEEEecCHHHHHHHHHHhCCce
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGES--------GRS----RGYGFVCYSTKAEMETALESLNGVE  132 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~--------~~~----~~~~fv~f~~~~~a~~a~~~l~~~~  132 (148)
                      ....||++++|+..+...|+++|..||.|-.+.+.....+        +.+    -.-|.|+|.+-..|......||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4568999999999999999999999999999888665443        222    2346799999999999999999999


Q ss_pred             eCCeE
Q 032044          133 LEGRA  137 (148)
Q Consensus       133 i~g~~  137 (148)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99864

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=98.11  E-value=1.3e-05  Score=41.07  Aligned_cols=52  Identities=21%  Similarity=0.366  Sum_probs=41.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHH
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL  125 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~  125 (148)
                      +.|-|.|.|++.. +.+..+|..||.|..+.+..      .....+|.|.++.+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            4688899998765 56666889999999887751      2347899999999999985

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=98.07  E-value=1.9e-05  Score=52.58  Aligned_cols=103  Identities=28%  Similarity=0.369  Sum_probs=83.9

Q ss_pred             HHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCc
Q 032044           28 EDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRS  107 (148)
Q Consensus        28 ~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~  107 (148)
                      .-|..|-..|++....++.+.+.|+..            ..|+|.||+..++.+.+.+.|+.||++....+..+ +.+.+
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~------------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~   71 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH------------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKP   71 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc------------ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccc
Confidence            346677778899999999999999864            26999999999999999999999999988777766 55778


Q ss_pred             eeEEEEEecCHHHHHHHHHHhCC----ceeCCeEEEEEec
Q 032044          108 RGYGFVCYSTKAEMETALESLNG----VELEGRAMRVSLA  143 (148)
Q Consensus       108 ~~~~fv~f~~~~~a~~a~~~l~~----~~i~g~~l~v~~~  143 (148)
                      .+-++|.|.....|.+|+..++.    ....+...-|.+.
T Consensus        72 t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   72 TREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             cccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            88899999999999999987743    3344555555443

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=98.04  E-value=6.1e-05  Score=43.73  Aligned_cols=77  Identities=17%  Similarity=0.244  Sum_probs=51.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEE-EEEcC------CCCCceeEEEEEecCHHHHHHHHHHhCCceeCCe-E
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGAR-VLYDG------ESGRSRGYGFVCYSTKAEMETALESLNGVELEGR-A  137 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~-~~~~~------~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~-~  137 (148)
                      ..-|.|-|.|+. ....+.+.|++||.|.... ..++.      ........-.|+|.++.+|++||+ -||..++|. .
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            345888899988 5678999999999987664 00000      001123467899999999999999 999999885 5


Q ss_pred             EEEEecc
Q 032044          138 MRVSLAQ  144 (148)
Q Consensus       138 l~v~~~~  144 (148)
                      +-|.+++
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            5577763

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=98.03  E-value=3.3e-05  Score=52.51  Aligned_cols=65  Identities=17%  Similarity=0.213  Sum_probs=53.3

Q ss_pred             HHHHHHHHhhcCCeeEEEEEEcCCCCCce-eEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           80 TESLTQAFQEYGNVVGARVLYDGESGRSR-GYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        80 ~~~l~~~f~~~g~v~~~~~~~~~~~~~~~-~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ++++.+.|++||.|..+.|...+...... .--||+|...+.|.+|+-.|||..++|+.+...+.+
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            35788899999999999887665443322 236999999999999999999999999999987754

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.99  E-value=2.2e-07  Score=65.69  Aligned_cols=117  Identities=27%  Similarity=0.392  Sum_probs=95.2

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCC-eecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCee
Q 032044           16 SRGFAFVTMSTVEDCNAVIENLDGR-EYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVV   94 (148)
Q Consensus        16 ~~g~afv~f~~~~~a~~a~~~l~~~-~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~   94 (148)
                      -.|||||...+..-|.+|++.+++. .+.|+.+.+..+.+++.       .++.+-|+|+|+...++-+..++..||.+.
T Consensus        36 k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkq-------rsrk~Qirnippql~wevld~Ll~qyg~ve  108 (584)
T KOG2193|consen   36 KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQ-------RSRKIQIRNIPPQLQWEVLDSLLAQYGTVE  108 (584)
T ss_pred             ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHH-------HhhhhhHhcCCHHHHHHHHHHHHhccCCHh
Confidence            3589999999999999999999886 68899999988765543       334688999999999999999999999988


Q ss_pred             EEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           95 GARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        95 ~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      .+..... ++.  ....=++|...+.++.|+..++|..+.+..+.+.|
T Consensus       109 ~~eqvnt-~~e--tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Y  153 (584)
T KOG2193|consen  109 NCEQVNT-DSE--TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGY  153 (584)
T ss_pred             Hhhhhcc-chH--HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhccc
Confidence            8765322 211  11233788899999999999999999988888776

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

Probab=97.98  E-value=4.3e-05  Score=56.21  Aligned_cols=77  Identities=29%  Similarity=0.405  Sum_probs=60.8

Q ss_pred             CCcceEEEcCCCCCCCH------HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCe-
Q 032044           64 ETDFKLFVGNLSWSVTT------ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR-  136 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~------~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~-  136 (148)
                      .-...|.|.|+|.--..      .-|..+|+++|.+....++.+.. |..+|+.|++|.+..+|+.|++.|||+.++-+ 
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            34567899999874332      34668899999999888887755 44899999999999999999999999998754 


Q ss_pred             EEEEE
Q 032044          137 AMRVS  141 (148)
Q Consensus       137 ~l~v~  141 (148)
                      ...|.
T Consensus       135 tf~v~  139 (698)
T KOG2314|consen  135 TFFVR  139 (698)
T ss_pred             eEEee
Confidence            44443

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

Probab=97.97  E-value=3.1e-05  Score=44.68  Aligned_cols=51  Identities=22%  Similarity=0.348  Sum_probs=43.7

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      |..|+|-..+   ..+|.|||.|++..+|.+|+..|+|..+.++.+.|.+..+.
T Consensus        45 IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   45 IRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             eEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHH
Confidence            5566666655   46799999999999999999999999999999999988654

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

Probab=97.95  E-value=4.8e-06  Score=55.34  Aligned_cols=62  Identities=24%  Similarity=0.383  Sum_probs=49.5

Q ss_pred             HHHHHHHh-hcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           81 ESLTQAFQ-EYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        81 ~~l~~~f~-~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      +++...++ +||.|..+.+..+.. .-..|-+||.|...++|++|++.||+.+++|++|...++
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~-~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLG-DHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccc-hhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            34455555 899998887765522 224678999999999999999999999999999998875

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

Probab=97.82  E-value=0.00016  Score=44.57  Aligned_cols=56  Identities=30%  Similarity=0.535  Sum_probs=44.1

Q ss_pred             HHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           82 SLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        82 ~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      +|.+.|..||.+.-+++.-+        .-+|+|.+.+.|.+|+. ++|.+++|+.|.|++..+.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            67778889998877776532        36899999999999999 9999999999999987653

; PDB: 1UFW_A 2DNR_A.

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.81  E-value=0.00018  Score=52.44  Aligned_cols=66  Identities=21%  Similarity=0.504  Sum_probs=49.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEE--cC-CCCCcee---EEEEEecCHHHHHHHHHHhC
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLY--DG-ESGRSRG---YGFVCYSTKAEMETALESLN  129 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~--~~-~~~~~~~---~~fv~f~~~~~a~~a~~~l~  129 (148)
                      ...+++|++++||++++|+.|...|..||.+ .+.+..  +. ..-.++|   |+|+.|+++...+.-+..+.
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            4467899999999999999999999999974 344441  11 1123456   99999999998887776554

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

Probab=97.77  E-value=5.7e-05  Score=50.54  Aligned_cols=52  Identities=31%  Similarity=0.530  Sum_probs=46.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      |..+.+..++.+|.++|||||+|.+.+.+..|+. |++..+.+..+.+.+..-
T Consensus       128 i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r~  179 (231)
T KOG4209|consen  128 INRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKRT  179 (231)
T ss_pred             ccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeeee
Confidence            4567899999999999999999999999999999 999999999999986543

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.63  E-value=0.00085  Score=35.31  Aligned_cols=55  Identities=16%  Similarity=0.209  Sum_probs=43.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhc---CCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHh
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEY---GNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL  128 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~---g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l  128 (148)
                      +..|+|+|+.. ++.++|..+|..|   .....+.++-+.       .|=|.|.+.+.|.+|+..|
T Consensus         5 peavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            45799999855 7889999999998   134677777553       3779999999999999754

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=97.60  E-value=0.00031  Score=51.81  Aligned_cols=72  Identities=8%  Similarity=0.254  Sum_probs=57.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhh--cCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCC--ceeCCeEEE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQE--YGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNG--VELEGRAMR  139 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~--~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~--~~i~g~~l~  139 (148)
                      ...|.+.|+-+|.+...++++.+|+.  +..+.++.+..+..       =||+|++..||+.|.+.|..  .+|.|+.|.
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-------WyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-------WYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-------eEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            35667888999999999999999985  55677777765522       58999999999999998865  567888777


Q ss_pred             EEe
Q 032044          140 VSL  142 (148)
Q Consensus       140 v~~  142 (148)
                      .++
T Consensus       246 ARI  248 (684)
T KOG2591|consen  246 ARI  248 (684)
T ss_pred             hhh
Confidence            665

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.58  E-value=0.00053  Score=38.10  Aligned_cols=55  Identities=15%  Similarity=0.303  Sum_probs=39.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNG  130 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~  130 (148)
                      ...++. .|..+-..||.++|++||.|. +.++-+       ..|||...+.+.|..++..+.-
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhcc
Confidence            345555 999999999999999999874 344422       2599999999999999987753

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.56  E-value=0.00023  Score=39.55  Aligned_cols=43  Identities=23%  Similarity=0.379  Sum_probs=30.3

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044           16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus        16 ~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      +.+.|+|.|.+.+.|.+|...++|..+.|..|.+.+.......
T Consensus        38 ~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~r~~   80 (90)
T PF11608_consen   38 SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKNREF   80 (90)
T ss_dssp             -TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S---
T ss_pred             eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCcccc
Confidence            3478999999999999999999999999999999998655443

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

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.51  E-value=0.00015  Score=53.76  Aligned_cols=78  Identities=21%  Similarity=0.240  Sum_probs=61.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhc-CCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee---CCeE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEY-GNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL---EGRA  137 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~-g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i---~g~~  137 (148)
                      ....++.|||.||-..+|.-+|+.++..- |.|....|-+      -+..|||.|.+.+.|......|||...   +++.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDk------IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDK------IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHH------hhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            45567899999999999999999999954 4455552211      244699999999999999999999765   5688


Q ss_pred             EEEEeccC
Q 032044          138 MRVSLAQG  145 (148)
Q Consensus       138 l~v~~~~~  145 (148)
                      |.+.|...
T Consensus       514 L~adf~~~  521 (718)
T KOG2416|consen  514 LIADFVRA  521 (718)
T ss_pred             eEeeecch
Confidence            88888653

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.48  E-value=0.0008  Score=48.22  Aligned_cols=67  Identities=22%  Similarity=0.268  Sum_probs=56.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEc---CCCCC----------ceeEEEEEecCHHHHHHHHHHhCC
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYD---GESGR----------SRGYGFVCYSTKAEMETALESLNG  130 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~---~~~~~----------~~~~~fv~f~~~~~a~~a~~~l~~  130 (148)
                      -++++|.+.|||.+-..+.|.++|..+|.|..|+|...   +.+..          .+-.|+|+|...+.|.+|...++.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            36789999999999999999999999999999999866   22211          134689999999999999997754

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

Probab=97.47  E-value=0.00066  Score=39.20  Aligned_cols=49  Identities=12%  Similarity=0.369  Sum_probs=39.5

Q ss_pred             eEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeec----CcEEEEeecC
Q 032044            5 LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL----GRILRVNFSD   53 (148)
Q Consensus         5 i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~----~~~i~v~~~~   53 (148)
                      +.+..|-.++.+.|||||-|.++++|......++|..+.    .+...+.|+.
T Consensus        33 ~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAr   85 (97)
T PF04059_consen   33 FYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYAR   85 (97)
T ss_pred             EEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhH
Confidence            456778888999999999999999999999999998774    3444555543

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

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.45  E-value=0.00023  Score=49.72  Aligned_cols=78  Identities=24%  Similarity=0.480  Sum_probs=65.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYG--NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ...++||+||-|++|++||.+.+..-|  .+..+.+..++-+|-++|||+|-..+....++.+..|-.++|.|..-.|-.
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeec
Confidence            345799999999999999999998776  366677777778888999999999999999999998888999886555543

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=97.39  E-value=0.0067  Score=35.95  Aligned_cols=68  Identities=12%  Similarity=0.176  Sum_probs=49.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYG-NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG  135 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g  135 (148)
                      ...+.+...|+..+.++|..+...+- .|..+++.++.  ..++-.+++.|.+.++|+.....+||+.++.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            34455555666666677776666654 36777887763  2356678999999999999999999988764

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.38  E-value=0.00053  Score=48.58  Aligned_cols=77  Identities=18%  Similarity=0.166  Sum_probs=60.0

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCC---CceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESG---RSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~---~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ...|.|.||.+.++.++++.+|...|.|..+.++.+....   ...-.|||.|.+...+..|.- |.+..+=|+.|.|.+
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEe
Confidence            3479999999999999999999999999998887543321   234589999999998887755 777766666666654


Q ss_pred             c
Q 032044          143 A  143 (148)
Q Consensus       143 ~  143 (148)
                      .
T Consensus        86 ~   86 (479)
T KOG4676|consen   86 Y   86 (479)
T ss_pred             c
Confidence            3

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=97.35  E-value=0.00031  Score=45.19  Aligned_cols=79  Identities=10%  Similarity=0.110  Sum_probs=49.0

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhh-cCCe---eEEEEEEc--CCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC---
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQE-YGNV---VGARVLYD--GESGRSRGYGFVCYSTKAEMETALESLNGVELEG---  135 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~-~g~v---~~~~~~~~--~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g---  135 (148)
                      ...+|.|++||++++++++.+.+.+ ++.-   .++.-...  ........-|||.|.+.++.......++|+.+-+   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4458999999999999999997776 5543   22221111  1112224568999999999999999999977632   


Q ss_pred             --eEEEEEec
Q 032044          136 --RAMRVSLA  143 (148)
Q Consensus       136 --~~l~v~~~  143 (148)
                        .+..|++|
T Consensus        86 ~~~~~~VE~A   95 (176)
T PF03467_consen   86 NEYPAVVEFA   95 (176)
T ss_dssp             -EEEEEEEE-
T ss_pred             CCcceeEEEc
Confidence              34555554

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

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

Probab=97.23  E-value=0.00076  Score=51.66  Aligned_cols=73  Identities=21%  Similarity=0.345  Sum_probs=51.8

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHh
Q 032044           16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQ   88 (148)
Q Consensus        16 ~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~   88 (148)
                      ++|+|||.+...++|.+|+.+|.+..+.++.|++.|+...-...+....-...+=|.-+|+.--..+++.+++
T Consensus       456 ~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~kse~k~~wD~~lGVt~IP~~kLt~dl~~~~e  528 (894)
T KOG0132|consen  456 PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKSEYKDYWDVELGVTYIPWEKLTDDLEAWCE  528 (894)
T ss_pred             CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcchhhhhhhhcccCeeEeehHhcCHHHHHhhh
Confidence            4589999999999999999999999999999999998765544421111111122333576655556676665

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.10  E-value=0.0001  Score=52.03  Aligned_cols=128  Identities=16%  Similarity=0.140  Sum_probs=89.5

Q ss_pred             CcceeEeeecCCC---CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC-CCC-----------------
Q 032044            1 MLSKLTVLYDRET---GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK-PKL-----------------   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~---~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~-~~~-----------------   59 (148)
                      +|.+++++-+..+   ......|||-|.+.+.+..|.. |.++.+-++-+.|.++.... +..                 
T Consensus        33 kI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~~~~~~p~r~af~~l~~~navprll~  111 (479)
T KOG4676|consen   33 KIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPYGDEVIPDRFAFVELADQNAVPRLLP  111 (479)
T ss_pred             ccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEecCCCCCccHHHHHhcCcccccccccC
Confidence            4566666653221   2455689999999999999987 77888777777776543211 000                 


Q ss_pred             ---------CC----------------C--------CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCC
Q 032044           60 ---------PL----------------Y--------AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGR  106 (148)
Q Consensus        60 ---------~~----------------~--------~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~  106 (148)
                               +.                +        ..-..++++.+|+..+...++.+.|..+|.+.+..+...    .
T Consensus       112 pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask----~  187 (479)
T KOG4676|consen  112 PDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILPESGESFERKGEVSYAHTASK----S  187 (479)
T ss_pred             CCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhcc----C
Confidence                     00                0        001357999999999999999999999999887766533    2


Q ss_pred             ceeEEEEEecCHHHHHHHHHHhCCceeC
Q 032044          107 SRGYGFVCYSTKAEMETALESLNGVELE  134 (148)
Q Consensus       107 ~~~~~fv~f~~~~~a~~a~~~l~~~~i~  134 (148)
                      ...+|-++|........|+. .+|..+.
T Consensus       188 ~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  188 RSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             CCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            34467899999888888888 6776554

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.96  E-value=0.0011  Score=47.51  Aligned_cols=73  Identities=32%  Similarity=0.461  Sum_probs=57.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCe-eEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCc-eeCCeEEEEEecc
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNV-VGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV-ELEGRAMRVSLAQ  144 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v-~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~-~i~g~~l~v~~~~  144 (148)
                      ..+|++||.+..+..++..+|...-.. ..-.++       ..||+|+...+...|.+|++.++|. ++.|+++.+..+-
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            368999999999999999999865211 111122       2569999999999999999999985 7889999888765


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      ++
T Consensus        75 ~k   76 (584)
T KOG2193|consen   75 PK   76 (584)
T ss_pred             hH
Confidence            44

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.94  E-value=0.00031  Score=48.74  Aligned_cols=81  Identities=20%  Similarity=0.357  Sum_probs=60.3

Q ss_pred             CcceEEEcCCCCCCCHHHHH---HHHhhcCCeeEEEEEEcCC--C-CCceeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 032044           65 TDFKLFVGNLSWSVTTESLT---QAFQEYGNVVGARVLYDGE--S-GRSRGYGFVCYSTKAEMETALESLNGVELEGRAM  138 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~---~~f~~~g~v~~~~~~~~~~--~-~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l  138 (148)
                      ...-+|+-+|+.....+.+.   +.|.+||.|..+.+..++.  . ......++|+|...++|..|+...+|...+|+.+
T Consensus        76 qknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   76 QKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            33457888888777665554   5778889998887776542  1 1123347999999999999999999999999887


Q ss_pred             EEEeccC
Q 032044          139 RVSLAQG  145 (148)
Q Consensus       139 ~v~~~~~  145 (148)
                      ++.+...
T Consensus       156 ka~~gtt  162 (327)
T KOG2068|consen  156 KASLGTT  162 (327)
T ss_pred             HHhhCCC
Confidence            7766543

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

Probab=96.86  E-value=0.0029  Score=47.22  Aligned_cols=54  Identities=28%  Similarity=0.424  Sum_probs=47.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      ||.-.+++.+.-+-..+-|+||.+.+.++|.++|..|+.+.++|+.|.|+.+..
T Consensus       431 KVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  431 KVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            456678888877766777999999999999999999999999999999987654

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=96.84  E-value=0.013  Score=42.52  Aligned_cols=68  Identities=18%  Similarity=0.265  Sum_probs=58.2

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYG-NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG  135 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g  135 (148)
                      +..|.|-.+|...+-.||..|+..+- .|..+++++++  -.++-..+|.|.+..+|......+||..++.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~--~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG--MPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC--CCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            77899999999999999999999765 48889998853  2345568999999999999999999988763

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

Probab=96.82  E-value=0.0031  Score=44.11  Aligned_cols=47  Identities=23%  Similarity=0.387  Sum_probs=37.2

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHH-hCCCeecCcEEEEeecCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIEN-LDGREYLGRILRVNFSDK   54 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-l~~~~~~~~~i~v~~~~~   54 (148)
                      |++|.++..      +++|||+|.+..+|+.|.+. ++...|.|+.|.|.|...
T Consensus       255 irsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  255 IRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             eeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            445555544      36999999999999998875 455678999999999877

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

Probab=96.70  E-value=0.0028  Score=47.10  Aligned_cols=48  Identities=21%  Similarity=0.479  Sum_probs=37.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeec-CcEEEEe
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL-GRILRVN   50 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~-~~~i~v~   50 (148)
                      |..+.+..+.. |..+||.|++|.+..+|+.|+..|+|..+. +.+..+.
T Consensus        91 ~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~  139 (698)
T KOG2314|consen   91 IVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVR  139 (698)
T ss_pred             ccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccceEEee
Confidence            44555666754 459999999999999999999999999885 4555553

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=96.52  E-value=0.0045  Score=35.03  Aligned_cols=68  Identities=12%  Similarity=0.147  Sum_probs=46.7

Q ss_pred             EEEEeCCHHHHHHHHHHhCCC--eecCcEEEEeecCC--CCCC--CCCCCCCcceEEEcCCCCCCCHHHHHHHHh
Q 032044           20 AFVTMSTVEDCNAVIENLDGR--EYLGRILRVNFSDK--PKPK--LPLYAETDFKLFVGNLSWSVTTESLTQAFQ   88 (148)
Q Consensus        20 afv~f~~~~~a~~a~~~l~~~--~~~~~~i~v~~~~~--~~~~--~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~   88 (148)
                      |.|.|.++.-|+..+.. ...  .+.++.+.+....-  ....  .-.....+++|.+.|+|...++++|++.++
T Consensus         1 AlITF~e~~VA~~i~~~-~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKK-KKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             CEEEeCcHHHHHHHHhC-CEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeEE
Confidence            68999999999998873 333  45666665653322  1111  112344677999999999999999988765

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

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

Probab=96.52  E-value=0.011  Score=39.88  Aligned_cols=55  Identities=29%  Similarity=0.540  Sum_probs=46.6

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      ++.+-+-+++ .|++.|.|=|.|...++|..|++.+++..+.|.++.+.....+..
T Consensus       110 ~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~~~  164 (243)
T KOG0533|consen  110 LKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSPSQ  164 (243)
T ss_pred             ceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCccc
Confidence            3455667775 899999999999999999999999999999999999987655443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.31  E-value=0.026  Score=34.79  Aligned_cols=71  Identities=13%  Similarity=0.172  Sum_probs=50.3

Q ss_pred             CcceEEEcC----CCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           65 TDFKLFVGN----LSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        65 ~~~~l~i~n----lp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      +-.+|.++=    +.+.-+...+...++.||+|.++...       .+..|.|.|.+..+|-.|+..++. ...|..+.-
T Consensus        85 PMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-------GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qC  156 (166)
T PF15023_consen   85 PMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-------GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQC  156 (166)
T ss_pred             CceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-------CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEe
Confidence            445677754    44444445566777899999988664       244699999999999999998877 445555555


Q ss_pred             Eec
Q 032044          141 SLA  143 (148)
Q Consensus       141 ~~~  143 (148)
                      .|-
T Consensus       157 sWq  159 (166)
T PF15023_consen  157 SWQ  159 (166)
T ss_pred             ecc
Confidence            553

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

Probab=96.22  E-value=0.0024  Score=42.82  Aligned_cols=40  Identities=30%  Similarity=0.478  Sum_probs=36.4

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044           15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus        15 ~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      .-.|=+||.|..+++|+.|+..||+..+.|++|+.+++..
T Consensus       108 hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen  108 HLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             hhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            5667799999999999999999999999999999998754

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

Probab=96.20  E-value=0.0034  Score=44.06  Aligned_cols=53  Identities=26%  Similarity=0.529  Sum_probs=47.5

Q ss_pred             eeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         4 ~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.+-+++.|++.+|-|.|.|.+...|+.|+.-+++..+.+.+|.|..+....
T Consensus       103 ki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  103 KIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERRT  155 (351)
T ss_pred             chhccccccccCcCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhcc
Confidence            46778899999999999999999999999999999999999999998776543

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=95.91  E-value=0.079  Score=36.76  Aligned_cols=69  Identities=19%  Similarity=0.255  Sum_probs=51.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCe-EEEEEeccC
Q 032044           69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR-AMRVSLAQG  145 (148)
Q Consensus        69 l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~-~l~v~~~~~  145 (148)
                      |.|-+.|+.- ..-|...|.+||.|.+....      .+-.+-+|.|.+.-+|++|+. -+|..|+|. .|-|+.|..
T Consensus       200 VTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  200 VTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             EEEeccCccc-hhHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCC
Confidence            5566777763 45778899999998776443      123377899999999999999 899999875 456666543

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=95.88  E-value=0.015  Score=44.59  Aligned_cols=52  Identities=17%  Similarity=0.417  Sum_probs=43.8

Q ss_pred             cceeEeeecCCC---CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            2 LSKLTVLYDRET---GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         2 i~~i~~~~~~~~---~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      |.+++|+.-+..   .+.+.+|||.|-+..+|++|+..|+|..+.+..+++.|..
T Consensus       201 lasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gWgk  255 (877)
T KOG0151|consen  201 LASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGWGK  255 (877)
T ss_pred             ccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeecccc
Confidence            456777765432   3667799999999999999999999999999999999984

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.82  E-value=0.0062  Score=44.39  Aligned_cols=73  Identities=21%  Similarity=0.319  Sum_probs=58.4

Q ss_pred             cceEEEcCCCCCC-CHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           66 DFKLFVGNLSWSV-TTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        66 ~~~l~i~nlp~~~-~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      .+.+-+.-.|... +..+|..+|.+||.|..|.+-...      -.|.|+|.+.-+|-+|.. .++..|+|+.|+|.|-+
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whn  444 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHN  444 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCch------hhheeeeeccccccchhc-cccceecCceeEEEEec
Confidence            3455566666664 447899999999999988775442      258999999999988888 89999999999999976


Q ss_pred             C
Q 032044          145 G  145 (148)
Q Consensus       145 ~  145 (148)
                      +
T Consensus       445 p  445 (526)
T KOG2135|consen  445 P  445 (526)
T ss_pred             C
Confidence            5

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.81  E-value=0.046  Score=35.53  Aligned_cols=60  Identities=22%  Similarity=0.285  Sum_probs=43.3

Q ss_pred             CHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhC--CceeCCeEEEEEecc
Q 032044           79 TTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN--GVELEGRAMRVSLAQ  144 (148)
Q Consensus        79 ~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~--~~~i~g~~l~v~~~~  144 (148)
                      ..+.|+++|..++.+....+.+.      -+-..|.|.+.+.|..|...|+  +..+.|..+++-++.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~   69 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQ   69 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE---
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcc
Confidence            45789999999998766655533      2237899999999999999999  999999999998874

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=95.58  E-value=0.0027  Score=49.52  Aligned_cols=78  Identities=23%  Similarity=0.292  Sum_probs=63.0

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...+|+++||+..+++.+|+..|..+|.+..+.|-.... +.-..++||.|.+...+..|...+.+..|....+++.+.
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            357899999999999999999999999999998865422 222347999999999999999999988776555555443

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=95.55  E-value=0.014  Score=41.15  Aligned_cols=51  Identities=18%  Similarity=0.339  Sum_probs=44.1

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      +.++++.-++.+|+++|||++...+..++.+.++-|....++|+.-.|..+
T Consensus       109 ~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen  109 FADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             HhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            346788888889999999999999999999999999999999887666543

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

Probab=95.52  E-value=0.015  Score=43.22  Aligned_cols=125  Identities=18%  Similarity=0.169  Sum_probs=74.7

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC-----------------CCCCCCCCcceEEEcCCC
Q 032044           13 TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP-----------------KLPLYAETDFKLFVGNLS   75 (148)
Q Consensus        13 ~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~-----------------~~~~~~~~~~~l~i~nlp   75 (148)
                      |-...|..||+|.+..+|+.|+..|++..|.|+.+..........                 ......+....++.- |+
T Consensus       108 t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~  186 (549)
T KOG4660|consen  108 TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LS  186 (549)
T ss_pred             ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCcccccchhcccchhhhhccchhhcCCCCCCcCCcceee-ec
Confidence            445678999999999999999999999999999888322211110                 011111122233333 88


Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           76 WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        76 ~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      +..+..-++..+.-+|.+.. +.     ++.-...-+++|.+..++..+.... |..+.|......++.+
T Consensus       187 P~~s~~~~~~~~~~~~~~~~-~~-----~~~~~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  187 PTRSSILLEHISSVDGSSPG-RE-----TPLLNHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             cchhhhhhhcchhccCcccc-cc-----ccchhhhhhhhhccccchhhcccCC-ceecCCCCceEEecCC
Confidence            88777556666666665543 21     1211224567777777774444422 6666666666555543

>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=94.96  E-value=0.23  Score=27.14  Aligned_cols=59  Identities=24%  Similarity=0.357  Sum_probs=33.3

Q ss_pred             CCCCHHHHHHHHhhcCCe-----eEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           76 WSVTTESLTQAFQEYGNV-----VGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        76 ~~~~~~~l~~~f~~~g~v-----~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ..++..+|..++...+.+     -.+.+..        .++||+.... .|+.++..|++..+.|++++|+.+
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            346677888888766543     3444532        2688887654 788999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

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

Probab=94.79  E-value=0.14  Score=27.35  Aligned_cols=30  Identities=7%  Similarity=0.295  Sum_probs=27.0

Q ss_pred             EEEEeCCHHHHHHHHHHhCCCeecCcEEEE
Q 032044           20 AFVTMSTVEDCNAVIENLDGREYLGRILRV   49 (148)
Q Consensus        20 afv~f~~~~~a~~a~~~l~~~~~~~~~i~v   49 (148)
                      -||.|++..+|+++....++..+.+..+.+
T Consensus        36 fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   36 FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            699999999999999999999988877765

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

>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=94.69  E-value=0.32  Score=26.01  Aligned_cols=55  Identities=18%  Similarity=0.312  Sum_probs=41.9

Q ss_pred             CCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           77 SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        77 ~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      .++-++++..+..|+- ..  +..+ .    .| =||.|.+.++|++|....+|..+.+..+.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~--I~~d-~----tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DR--IRDD-R----TG-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ce--EEec-C----CE-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            3567899999999963 23  3333 2    12 489999999999999999999988877654

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

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=94.67  E-value=0.033  Score=42.36  Aligned_cols=73  Identities=18%  Similarity=0.214  Sum_probs=61.0

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      .+..+..+++++|+.+.+..+-++.++..+|.|.+....         .|||..|........|+..++...++|..+.+
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~---------~fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~  105 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD---------KFGFCEFLKHIGDLRASRLLTELNIDDQKLIE  105 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhh---------hhcccchhhHHHHHHHHHHhcccCCCcchhhc
Confidence            344566799999999999999999999999987654332         17999999999999999999999999887766


Q ss_pred             Ee
Q 032044          141 SL  142 (148)
Q Consensus       141 ~~  142 (148)
                      ..
T Consensus       106 ~~  107 (668)
T KOG2253|consen  106 NV  107 (668)
T ss_pred             cc
Confidence            54

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

Probab=94.47  E-value=0.1  Score=32.43  Aligned_cols=34  Identities=26%  Similarity=0.426  Sum_probs=30.0

Q ss_pred             EEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044           19 FAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus        19 ~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .-+|.|.+.++|.+|+. ++|..+.|+.+.|..-.
T Consensus        72 ~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKt  105 (146)
T PF08952_consen   72 TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKT  105 (146)
T ss_dssp             CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE--
T ss_pred             eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCC
Confidence            47999999999999998 89999999999998654

; PDB: 1UFW_A 2DNR_A.

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

Probab=94.40  E-value=0.079  Score=38.80  Aligned_cols=50  Identities=22%  Similarity=0.270  Sum_probs=38.4

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      |+...|......++...||||+|.+.++++.|+. .+...++++++.|+--
T Consensus       315 Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~-Asp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  315 IKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIE-ASPLEIGGRKLNVEEK  364 (419)
T ss_pred             ccccceEEeccCCCcCceEEEEEeecchhhhhhh-cCccccCCeeEEEEec
Confidence            4455555543344555999999999999999998 4688899999999843

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=94.30  E-value=0.039  Score=43.29  Aligned_cols=71  Identities=31%  Similarity=0.412  Sum_probs=56.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee--CCeEEEEEeccC
Q 032044           69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL--EGRAMRVSLAQG  145 (148)
Q Consensus        69 l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i--~g~~l~v~~~~~  145 (148)
                      ..+.|.+-..+-.-|..+|.+||.+.+.+..++-.      .|.|+|.+.+.|..|+..++|.++  .|.+.+|.+++.
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            44445555666677889999999999988776632      689999999999999999999875  577888888753

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=94.14  E-value=0.21  Score=29.67  Aligned_cols=40  Identities=13%  Similarity=0.395  Sum_probs=33.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeec
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL   43 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~   43 (148)
                      |+.++|+++..  .++-.+.+.|.+.++|+.....+||..+.
T Consensus        41 i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   41 IEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             EEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            56788888743  36777899999999999999999998874

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=93.99  E-value=0.17  Score=35.75  Aligned_cols=33  Identities=33%  Similarity=0.603  Sum_probs=31.1

Q ss_pred             EEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044           21 FVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus        21 fv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      ||.|.+.++|.+|+...+|..++|+-|+..|..
T Consensus       169 YITy~~kedAarcIa~vDgs~~DGr~lkatYGT  201 (480)
T COG5175         169 YITYSTKEDAARCIAEVDGSLLDGRVLKATYGT  201 (480)
T ss_pred             EEEecchHHHHHHHHHhccccccCceEeeecCc
Confidence            999999999999999999999999999998754

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=93.41  E-value=0.13  Score=35.67  Aligned_cols=51  Identities=20%  Similarity=0.353  Sum_probs=37.8

Q ss_pred             ceeEeeecCCCCCccc-EEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            3 SKLTVLYDRETGRSRG-FAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         3 ~~i~~~~~~~~~~~~g-~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      ..|-|.-.+..-.... --||+|...++|.+|+-.|||..|+|+.+...|..
T Consensus       314 ~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  314 GNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             eeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            3344444433222222 46999999999999999999999999999887764

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=93.26  E-value=0.035  Score=34.69  Aligned_cols=83  Identities=12%  Similarity=0.083  Sum_probs=59.5

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC-CCCCCCCCCcceEEEcCCCCC-CCHHHHHHHHhhcCCe
Q 032044           16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK-PKLPLYAETDFKLFVGNLSWS-VTTESLTQAFQEYGNV   93 (148)
Q Consensus        16 ~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~-~~~~~~~~~~~~l~i~nlp~~-~~~~~l~~~f~~~g~v   93 (148)
                      ..++..++|.+.+++..++. .....+.+..+.+....+.. .........+.=|.|.|||.. .+++-+..+.+.+|.+
T Consensus        54 ~~~~fl~~F~~~~d~~~vl~-~~p~~~~~~~~~l~~W~~~~~~~~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~  132 (153)
T PF14111_consen   54 GDNLFLFQFESEEDRQRVLK-GGPWNFNGHFLILQRWSPDFNPSEVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEP  132 (153)
T ss_pred             CCCeEEEEEEeccceeEEEe-cccccccccchhhhhhcccccccccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCe
Confidence            45789999999999999997 45566777777776554322 222222223445888999998 7778899999999998


Q ss_pred             eEEEEE
Q 032044           94 VGARVL   99 (148)
Q Consensus        94 ~~~~~~   99 (148)
                      ..+...
T Consensus       133 i~vD~~  138 (153)
T PF14111_consen  133 IEVDEN  138 (153)
T ss_pred             EEEEcC
Confidence            877543

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=91.04  E-value=1.5  Score=32.45  Aligned_cols=41  Identities=15%  Similarity=0.408  Sum_probs=34.7

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG   44 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~   44 (148)
                      |.+|+++||..  -++-...|.|.+..+|...-..+||..|..
T Consensus       102 I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen  102 ISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             hheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            78899999643  356678999999999999999999998753

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=90.89  E-value=0.17  Score=35.25  Aligned_cols=77  Identities=26%  Similarity=0.206  Sum_probs=59.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ...+.+++++...+.+.+...++..+|......+.........++++++.|...+.+..|+.....+...++.+...
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~d  163 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKD  163 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCc
Confidence            46789999999999999899999999977666666555667788999999999999999998443345555444433

>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=89.45  E-value=0.63  Score=25.36  Aligned_cols=34  Identities=29%  Similarity=0.552  Sum_probs=19.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044           18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus        18 g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      .|+||+-... .|..++..+++..+.|+++.++.+
T Consensus        41 ~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   41 NFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             S-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             eEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3688887655 788899999999999999998753

; PDB: 2G0C_A 3MOJ_B.

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=88.54  E-value=2.1  Score=29.87  Aligned_cols=46  Identities=13%  Similarity=0.218  Sum_probs=35.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCe-eEEEEEEcCCCCCceeEEEEEecCH
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNV-VGARVLYDGESGRSRGYGFVCYSTK  118 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v-~~~~~~~~~~~~~~~~~~fv~f~~~  118 (148)
                      .-|++.|||.++.-.||+..+.+.+.+ .++.+  .    .+.+-||+.|.+.
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~~~pm~isw--k----g~~~k~flh~~~~  377 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRECTPMSISW--K----GHFGKCFLHFGNR  377 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcCCCceeEee--e----cCCcceeEecCCc
Confidence            459999999999999999999987642 33333  2    2466799999664

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=87.36  E-value=0.9  Score=26.48  Aligned_cols=37  Identities=11%  Similarity=0.246  Sum_probs=29.1

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCCeecCcE-EEEeec
Q 032044           15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRI-LRVNFS   52 (148)
Q Consensus        15 ~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~-i~v~~~   52 (148)
                      .....--|.|.++.+|++||. .||..+.|.- +-|.+.
T Consensus        52 ~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mvGV~~~   89 (100)
T PF05172_consen   52 SGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLMVGVKPC   89 (100)
T ss_dssp             CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEEEEEEE-
T ss_pred             CCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEEEEEEEc
Confidence            345678999999999999998 7999998754 446655

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth

Probab=85.47  E-value=3.2  Score=22.30  Aligned_cols=64  Identities=17%  Similarity=0.243  Sum_probs=44.1

Q ss_pred             HHHHHHHhhcCC-eeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           81 ESLTQAFQEYGN-VVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        81 ~~l~~~f~~~g~-v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      ++|.+-|...|- +..+.-+..+.+..+...-||++....+..++   ++=..+++..|.|+..+.++
T Consensus         2 ~~I~~~L~~~G~~v~~i~~~~~~~~k~pl~mf~veL~p~~~~k~i---~~Ik~l~~~~V~vE~~~k~~   66 (68)
T PF07530_consen    2 EEIKEELKDQGHPVRNIHNMHSRNTKKPLNMFFVELEPKPNNKEI---YKIKTLCGQRVKVERPRKRR   66 (68)
T ss_pred             HHHHHHHHHcCCceEEEEccccCCCCCCceEEEEeeccCccccce---eehHhhCCeEEEEecCCCCC
Confidence            578888888774 66666666665666777788888766553332   44456788889988876654

These proteins are possibly involved in RNA binding or single strand DNA binding.

>smart00596 PRE_C2HC PRE_C2HC domain

Probab=85.04  E-value=2.7  Score=22.65  Aligned_cols=64  Identities=17%  Similarity=0.185  Sum_probs=43.1

Q ss_pred             HHHHHHHhhcCC-eeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           81 ESLTQAFQEYGN-VVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        81 ~~l~~~f~~~g~-v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      .+|.+.|...|- +..+.-+..++++.|...-+|+.....+-..   .++=..++|.++.|+....++
T Consensus         2 ~~I~~~L~~~G~~v~~i~~m~~~~~r~P~nmf~vel~~~~~~~~---Il~ik~Lg~~~V~VEr~~k~~   66 (69)
T smart00596        2 SQIEEALKDIGFPVLFIHNMLNRDTKNPQNMFEVELVPAANGKE---ILNIKTLGGQRVTVERPHKRK   66 (69)
T ss_pred             HHHHHHHHHcCCceeEEEcccccCCCCcceeEEEEeeecCCCcc---eEeehhhCCeeEEEecCcccC
Confidence            478888998884 6677767776766666677787765432222   344456788888888766554

>PF03468 XS: XS domain; InterPro: IPR005380 The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X Q9SBW2 from SWISSPROT and SGS3 Q9LDX1 from SWISSPROT

Probab=82.37  E-value=8.4  Score=23.11  Aligned_cols=56  Identities=16%  Similarity=0.343  Sum_probs=31.3

Q ss_pred             eEEEcCCCCC---------CCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEec-CHHHHHHHHH
Q 032044           68 KLFVGNLSWS---------VTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYS-TKAEMETALE  126 (148)
Q Consensus        68 ~l~i~nlp~~---------~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~-~~~~a~~a~~  126 (148)
                      ++.|.|+|..         .+.+.|.+.|..|.++ .+....++.  .+.|++.|+|. +-.--..|+.
T Consensus        10 mgIi~N~~~~~~~~g~~~g~~~~~l~~~l~~f~p~-kv~~l~~~~--gh~g~aiv~F~~~w~Gf~~A~~   75 (116)
T PF03468_consen   10 MGIIVNIPTEKDDDGRWVGMSNEELLDKLAEFNPL-KVKPLYGKQ--GHTGFAIVEFNKDWSGFKNAMR   75 (116)
T ss_dssp             EEEEE----EE-TTS-EE---SHHHHHHHHH---S-EEEEEEETT--EEEEEEEEE--SSHHHHHHHHH
T ss_pred             EEEEEcCccccCCCCceeccCHHHHHHHHHhcCCc-eeEECcCCC--CCcEEEEEEECCChHHHHHHHH
Confidence            5666677543         3557899999999775 455555543  57899999997 5555555655

SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain containing proteins contain coiled-coils, which suggests that they will oligomerise. Most coiled-coil proteins form either a dimeric or a trimeric structure. It is possible that different members of the XS domain family could oligomerise via their coiled-coils forming a variety of complexes [].; PDB: 4E8U_C.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=81.25  E-value=3.8  Score=26.74  Aligned_cols=37  Identities=24%  Similarity=0.304  Sum_probs=29.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhC--CCeecCcEEEEeecC
Q 032044           17 RGFAFVTMSTVEDCNAVIENLD--GREYLGRILRVNFSD   53 (148)
Q Consensus        17 ~g~afv~f~~~~~a~~a~~~l~--~~~~~~~~i~v~~~~   53 (148)
                      -+-..|.|.+.++|..|...++  +..+.|..+.+.++.
T Consensus        31 FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~   69 (184)
T PF04847_consen   31 FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQ   69 (184)
T ss_dssp             TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE---
T ss_pred             CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcc
Confidence            3568999999999999999999  899999999998774

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.12  E-value=14  Score=28.61  Aligned_cols=80  Identities=20%  Similarity=0.406  Sum_probs=57.8

Q ss_pred             CCCcceEEEcCCCCC-CCHHHHHHHHhhc----CCeeEEEEEEcC----------CCCC---------------------
Q 032044           63 AETDFKLFVGNLSWS-VTTESLTQAFQEY----GNVVGARVLYDG----------ESGR---------------------  106 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~-~~~~~l~~~f~~~----g~v~~~~~~~~~----------~~~~---------------------  106 (148)
                      ....++|-|-|+.|+ +...+|.-+|..|    |.|.+|.|....          -+|+                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            456778999999997 6778888888755    467777764321          0111                     


Q ss_pred             ----------------ceeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEe
Q 032044          107 ----------------SRGYGFVCYSTKAEMETALESLNGVELEG--RAMRVSL  142 (148)
Q Consensus       107 ----------------~~~~~fv~f~~~~~a~~a~~~l~~~~i~g--~~l~v~~  142 (148)
                                      ..=||.|+|.+...|......++|.++..  ..+-++|
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                            11278899999999999999999998864  4555554

>PF02714 DUF221: Domain of unknown function DUF221; InterPro: IPR003864 This domain is found in a family of hypothetical transmembrane proteins none of which have any known function, the aligned region is at 538 residues at maximum length

Probab=80.63  E-value=6  Score=28.03  Aligned_cols=57  Identities=23%  Similarity=0.288  Sum_probs=37.3

Q ss_pred             EEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhh
Q 032044           20 AFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQE   89 (148)
Q Consensus        20 afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~   89 (148)
                      |||.|++..+|+.|.+.+....  ...+.++.+.++.           -|.=.||..+..+..++..+..
T Consensus         1 aFVtF~~~~~a~~~~q~~~~~~--~~~~~v~~APeP~-----------DI~W~NL~~~~~~r~~R~~~~~   57 (325)
T PF02714_consen    1 AFVTFNSQKSAQIALQLLLSKR--PNSWRVSPAPEPD-----------DIIWENLSISSKQRFLRRIIVN   57 (325)
T ss_pred             CEEEECCHHHHHHHHHHHhcCC--CCCceEeeCCCcc-----------cccccccCCChHHHHHHHHHHH
Confidence            7999999999999998443332  2334555544332           3556778777777666655543

; GO: 0016020 membrane

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	148
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		2e-19
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		4e-07
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		6e-14
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-07
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		6e-14
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-13
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		8e-07
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		4e-13
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		8e-06
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		6e-13
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		7e-13
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		9e-13
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-12
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-12
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		5e-12
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		9e-09
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		5e-12
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		8e-09
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-11
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-11
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		3e-11
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		5e-11
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		6e-11
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		6e-11
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		5e-09
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		6e-11
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		3e-09
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		6e-11
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-09
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		6e-11
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-09
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		6e-11
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		3e-09
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		7e-11
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-09
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		5e-10
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-09
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		1e-09
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		3e-09
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		5e-09
1sxl_A	97	Resonance Assignments And Solution Structure Of The		5e-09
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		7e-09
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		8e-09
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		8e-06
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		8e-09
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		9e-09
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		1e-08
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-08
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		1e-08
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		1e-08
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		1e-08
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		2e-08
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		2e-08
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		2e-08
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-08
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		2e-08
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		2e-08
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		3e-08
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		5e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		3e-08
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		3e-08
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		3e-08
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		4e-08
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		4e-08
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		4e-08
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		4e-08
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		6e-08
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		7e-08
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		7e-08
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		7e-08
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		7e-08
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		8e-08
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		9e-08
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		1e-07
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		1e-07
2yka_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		1e-07
2kt5_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		1e-07
3ulh_A	107	Crystal Structure Of A Rna Binding Domain Of Tho Co		2e-07
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		2e-07
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		2e-07
2khc_A	118	Bruno Rrm3+ Length = 118		2e-07
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		2e-07
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		2e-07
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		3e-07
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		3e-07
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		3e-07
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		4e-07
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		4e-07
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		5e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		6e-07
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		2e-06
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		2e-06
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		2e-06
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		3e-06
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		3e-06
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		4e-06
2dnp_A	90	Solution Structure Of Rna Binding Domain 2 In Rna-B		4e-06
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		5e-06
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		6e-06
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		6e-06
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		6e-06
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		6e-06
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		6e-06
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		7e-06
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		8e-06
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		9e-06
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-05
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		1e-05
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		1e-05
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		1e-05
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		1e-05
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-05
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		2e-05
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		2e-05
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		2e-05
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		3e-05
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		3e-05
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		3e-05
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		3e-05
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		3e-05
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		3e-05
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		4e-05
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		5e-05
2dnh_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		6e-05
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		6e-05
2cqh_A	93	Solution Structure Of The Rna Binding Domain Of Igf		7e-05
3lqv_A	115	Branch Recognition By Sf3b14 Length = 115		8e-05
2cpx_A	115	Solution Structure Of Rna Binding Domain In Hypothe		8e-05
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		9e-05
1x4h_A	111	Solution Structure Of Rrm Domain In Rna-Binding Pro		1e-04
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		1e-04
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		1e-04
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		2e-04
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		2e-04
1wf1_A	110	Solution Structure Of Rrm Domain In Rna-Binding Pro		3e-04
2lxi_A	91	Nmr Structure Of The N-Terminal Rna Binding Domain		3e-04
2f9d_A	125	2.5 Angstrom Resolution Structure Of The Spliceosom		4e-04
3p5t_L	90	Cfim25-Cfim68 Complex Length = 90		4e-04
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		4e-04
2cpe_A	113	Solution Structure Of The Rna Recognition Motif Of		5e-04
1fjc_A	96	Solution Structure Of Nucleolin Rbd2 Length = 96		5e-04
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		5e-04
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		5e-04
2fho_B	87	Nmr Solution Structure Of The Human Spliceosomal Pr		6e-04
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		6e-04
3n9u_C	156	Crystal Structure Of The Complex Between The 25 Kda		7e-04
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		7e-04
3q2s_C	229	Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX Lengt		8e-04

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 91.3 bits (225), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/142 (27%), Positives = 88/142 (61%), Gaps = 4/142 (2%)
Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPL 61
           ++ + ++ D+   ++  +AFV      D N  ++ L+G++    I+++N++ + +     
Sbjct: 27  IANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQS--- 82
Query: 62  YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEM 121
            ++  F LFVG+L+ +V  E+L  AF+++ + +   V++D ++G SRGYGFV ++++ + 
Sbjct: 83  SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 142
Query: 122 ETALESLNGVELEGRAMRVSLA 143
           + A++S+ G +L GR +R++ A
Sbjct: 143 QNAMDSMQGQDLNGRPLRINWA 164

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VGNL  ++T + L Q FQ  G +   +++ D ++ ++  Y FV Y    +   AL++L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 129 NGVELEGRAMRVSLA 143
           NG ++E   ++++ A
Sbjct: 62  NGKQIENNIVKINWA 76

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 73.2 bits (178), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 38/133 (28%), Positives = 72/133 (54%), Gaps = 5/133 (3%)
Query: 10  DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKL 69
           D+ TG+S G+ FV  S   D +  I  L+G +   + ++V+++      +      D  L
Sbjct: 39  DKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSASI-----RDANL 93
Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           +V  L  +++ + + Q F +YG ++ +R+L D  +G SRG GF+ +  + E E A++ LN
Sbjct: 94  YVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153
Query: 130 GVELEGRAMRVSL 142
           G +  G A  +++
Sbjct: 154 GQKPLGAAEPITV 166

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 45/76 (59%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L  ++T +     F   G++   +++ D  +G+S GYGFV YS   + + A+ +L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 129 NGVELEGRAMRVSLAQ 144
           NG++L+ + ++VS A+
Sbjct: 67  NGLKLQTKTIKVSYAR 82

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 72.8 bits (177), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 55/77 (71%)
Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           F LFVG+L+ +V  E+L  AF+++ + +   V++D ++G SRGYGFV ++++ + + A++
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 127 SLNGVELEGRAMRVSLA 143
           S+ G +L GR +R++ A
Sbjct: 62  SMQGQDLNGRPLRINWA 78

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 38/126 (30%), Positives = 66/126 (52%), Gaps = 5/126 (3%)
Query: 10  DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKL 69
           D+ TG+S G+ FV     +D    I  L+G     + ++V+++      +      D  L
Sbjct: 37  DKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASI-----RDANL 91
Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           +V  L  ++T + L Q F +YG ++ +R+L D  +G SRG GF+ +  + E E A++ LN
Sbjct: 92  YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 151
Query: 130 GVELEG 135
           G +  G
Sbjct: 152 GQKPSG 157

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 49.3 bits (116), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 42/76 (55%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L  ++T E     F   G +   +++ D  +G+S GYGFV Y    + E A+ +L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 129 NGVELEGRAMRVSLAQ 144
           NG+ L+ + ++VS A+
Sbjct: 65  NGLRLQTKTIKVSYAR 80

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 43/136 (31%), Positives = 76/136 (55%), Gaps = 5/136 (3%)
Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           ++ D +TG S G+AFV  ++  D    I+ L+G     + L+V+++ +P  +    +  D
Sbjct: 35  IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA-RPGGE----SIKD 89
Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             L+V NL  ++T + L   F +YG++V   +L D  +GR RG  FV Y+ + E + A+ 
Sbjct: 90  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 127 SLNGVELEGRAMRVSL 142
           +LN V  EG +  +S+
Sbjct: 150 ALNNVIPEGGSQPLSV 165

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 45/80 (56%)
Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           ++  L V  L   +T   L   F+  G +   R++ D ++G S GY FV ++++ + + A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 125 LESLNGVELEGRAMRVSLAQ 144
           ++ LNG+ +  + ++VS A+
Sbjct: 62  IKVLNGITVRNKRLKVSYAR 81

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 69.7 bits (169), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 32/77 (41%), Positives = 49/77 (63%)
Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           F +FVG+LS  +TTE +  AF  +G +  ARV+ D  +G+S+GYGFV +  K + E A++
Sbjct: 16  FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
Query: 127 SLNGVELEGRAMRVSLA 143
            + G  L GR +R + A
Sbjct: 76  QMGGQWLGGRQIRTNWA 92

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 69.3 bits (168), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 33/80 (41%), Positives = 48/80 (60%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FVGN+ +  T E L   F E G VV  R++YD E+G+ +GYGF  Y  +    +A+ +L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 129 NGVELEGRAMRVSLAQGRRS 148
           NG E  GRA+RV  A   ++
Sbjct: 71  NGREFSGRALRVDNAASEKN 90

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 68.9 bits (167), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 45/137 (32%), Positives = 76/137 (55%), Gaps = 7/137 (5%)
Query: 10  DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKL 69
           D +TG S G+AFV  ++  D    I+ L+G     + L+V+++ +P  +    +  D  L
Sbjct: 49  DYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYA-RPGGE----SIKDTNL 103
Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           +V NL  ++T + L   F +YG++V   +L D  +GR RG  FV Y+ + E + A+ +LN
Sbjct: 104 YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Query: 130 GVELEG--RAMRVSLAQ 144
            V  EG  + + V LA+
Sbjct: 164 NVIPEGGSQPLSVRLAE 180

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 68.6 bits (166), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 32/77 (41%), Positives = 48/77 (62%)
Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           F +FVG+LS  +TTE +  AF  +G +  ARV+ D  +G+S+GYGFV +  K + E A+ 
Sbjct: 16  FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 75
Query: 127 SLNGVELEGRAMRVSLA 143
            + G  L GR +R + A
Sbjct: 76  HMGGQWLGGRQIRTNWA 92

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 49/73 (67%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +L+VG+L +++T + L   F+ +G +   +++ D E+GRS+GYGF+ +S     + ALE 
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 128 LNGVELEGRAMRV 140
           LNG EL GR M+V
Sbjct: 88  LNGFELAGRPMKV 100

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 66.6 bits (161), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 35/136 (25%), Positives = 71/136 (52%), Gaps = 5/136 (3%)
Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           ++ D+  G S G+ FV   T +D    I  L+G     + ++V+++ +P  ++      D
Sbjct: 34  LIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA-RPSSEVI----KD 88
Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             L++  L  ++T + +   F  +G ++ +RVL D  +G SRG  F+ +  ++E E A+ 
Sbjct: 89  ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 127 SLNGVELEGRAMRVSL 142
           S NG +  G +  +++
Sbjct: 149 SFNGHKPPGSSEPITV 164

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 55.8 bits (133), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L  ++T + L   F   G V  A+++ D  +G S GYGFV Y T  + E A+ +L
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 129 NGVELEGRAMRVSLAQ 144
           NG+ L+ + ++VS A+
Sbjct: 65  NGLRLQSKTIKVSYAR 80

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 66.6 bits (161), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 35/136 (25%), Positives = 71/136 (52%), Gaps = 5/136 (3%)
Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           ++ D+  G S G+ FV   T +D    I  L+G     + ++V+++ +P  ++      D
Sbjct: 34  LIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA-RPSSEVI----KD 88
Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             L++  L  ++T + +   F  +G ++ +RVL D  +G SRG  F+ +  ++E E A+ 
Sbjct: 89  ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 127 SLNGVELEGRAMRVSL 142
           S NG +  G +  +++
Sbjct: 149 SFNGHKPPGSSEPITV 164

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 55.8 bits (133), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L  ++T + L   F   G V  A+++ D  +G S GYGFV Y T  + E A+ +L
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 129 NGVELEGRAMRVSLAQ 144
           NG+ L+ + ++VS A+
Sbjct: 65  NGLRLQSKTIKVSYAR 80

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 65.5 bits (158), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/81 (39%), Positives = 49/81 (60%)
Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A  + KLFVG LS+    +SL Q F +YG +    V+ D E+ RSRG+GFV +    + +
Sbjct: 9   ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 123 TALESLNGVELEGRAMRVSLA 143
            A+ ++NG  ++GR +RV  A
Sbjct: 69  DAMMAMNGKSVDGRQIRVDQA 89

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/150 (24%), Positives = 75/150 (50%), Gaps = 16/150 (10%)
Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIEN---LDGREYLGRILRVNFSDKPKPK 58
           ++ L ++ D  TGRSRGF F++       + V++    LDG+              PK  
Sbjct: 30  VTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVI-----------DPKRA 78
Query: 59  LPLYAETDF-KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
           +P   +    K+FVG +   V  +   + F ++G ++ A+++ D ++G+SRG+GFV Y +
Sbjct: 79  IPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS 138
Query: 118 KAEMETALESLNGVELEGRAMRVSLAQGRR 147
              ++   ++   ++ + R + +  A+ R 
Sbjct: 139 ADAVDRVCQN-KFIDFKDRKIEIKRAEPRH 167

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 63.9 bits (154), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 30/72 (41%), Positives = 46/72 (63%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VG+L +++T + L   F+ +G +    ++ D ++GRS+GYGF+ +S       ALE L
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 129 NGVELEGRAMRV 140
           NG EL GR MRV
Sbjct: 68  NGFELAGRPMRV 79

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 63.2 bits (152), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 75/143 (52%), Gaps = 5/143 (3%)
Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAE 64
           + V  D  T RS G+A+V      D    ++ ++     G+ +R+ +S +  P L     
Sbjct: 40  IRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR-DPSLRKSGV 98
Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
            +  +F+ NL  S+  ++L   F  +GN++  +V+ D E+G S+GYGFV + T+   E A
Sbjct: 99  GN--IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERA 154
Query: 125 LESLNGVELEGRAMRVSLAQGRR 147
           +E +NG+ L  R + V   + R+
Sbjct: 155 IEKMNGMLLNDRKVFVGRFKSRK 177

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 63.2 bits (152), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 75/143 (52%), Gaps = 5/143 (3%)
Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAE 64
           + V  D  T RS G+A+V      D    ++ ++     G+ +R+ +S +  P L     
Sbjct: 45  IRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR-DPSLRKSGV 103
Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
            +  +F+ NL  S+  ++L   F  +GN++  +V+ D E+G S+GYGFV + T+   E A
Sbjct: 104 GN--IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERA 159
Query: 125 LESLNGVELEGRAMRVSLAQGRR 147
           +E +NG+ L  R + V   + R+
Sbjct: 160 IEKMNGMLLNDRKVFVGRFKSRK 182

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 63.2 bits (152), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR----VNFSDKPKP 57
           L+   V+ D  T RSRGF FVT +TVE+ +A + N    +  GR++     V+  D  +P
Sbjct: 33  LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRP 91
Query: 58  KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
              L  +   K+FVG +        L   F++YG +    ++ D  SG+ RG+ FV +  
Sbjct: 92  GAHLTVK---KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 148
Query: 118 KAEMETAL----ESLNGVELEGR 136
              ++  +     ++NG   E R
Sbjct: 149 HDSVDKIVIQKYHTVNGHNCEVR 171

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 56.6 bits (135), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 47/79 (59%), Gaps = 1/79 (1%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLF+G LS+  T ESL   F+++G +    V+ D  + RSRG+GFV Y+T  E++ A+ +
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 128 LNGVELEGRAMRVSLAQGR 146
               +++GR +    A  R
Sbjct: 68  RPH-KVDGRVVEPKRAVSR 85

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 62.8 bits (151), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR----VNFSDKPKP 57
           L+   V+ D  T RSRGF FVT +TVE+ +A + N    +  GR++     V+  D  +P
Sbjct: 39  LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRP 97
Query: 58  KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
              L  +   K+FVG +        L   F++YG +    ++ D  SG+ RG+ FV +  
Sbjct: 98  GAHLTVK---KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 154
Query: 118 KAEMETAL----ESLNGVELEGR 136
              ++  +     ++NG   E R
Sbjct: 155 HDSVDKIVIQKYHTVNGHNCEVR 177

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 57.4 bits (137), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 1/91 (1%)
Query: 56  KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           K + P   E   KLF+G LS+  T ESL   F+++G +    V+ D  + RSRG+GFV Y
Sbjct: 2   KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 61
Query: 116 STKAEMETALESLNGVELEGRAMRVSLAQGR 146
           +T  E++ A+ +    +++GR +    A  R
Sbjct: 62  ATVEEVDAAMNARPH-KVDGRVVEPKRAVSR 91

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 62.8 bits (151), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR----VNFSDKPKP 57
           L+   V+ D  T RSRGF FVT +TVE+ +A + N    +  GR++     V+  D  +P
Sbjct: 40  LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRP 98
Query: 58  KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
              L  +   K+FVG +        L   F++YG +    ++ D  SG+ RG+ FV +  
Sbjct: 99  GAHLTVK---KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
Query: 118 KAEMETAL----ESLNGVELEGR 136
              ++  +     ++NG   E R
Sbjct: 156 HDSVDKIVIQKYHTVNGHNCEVR 178

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 57.4 bits (137), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 1/91 (1%)
Query: 56  KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           K + P   E   KLF+G LS+  T ESL   F+++G +    V+ D  + RSRG+GFV Y
Sbjct: 3   KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
Query: 116 STKAEMETALESLNGVELEGRAMRVSLAQGR 146
           +T  E++ A+ +    +++GR +    A  R
Sbjct: 63  ATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR 92

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 62.8 bits (151), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR----VNFSDKPKP 57
           L+   V+ D  T RSRGF FVT +TVE+ +A + N    +  GR++     V+  D  +P
Sbjct: 38  LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRP 96
Query: 58  KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
              L  +   K+FVG +        L   F++YG +    ++ D  SG+ RG+ FV +  
Sbjct: 97  GAHLTVK---KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 153
Query: 118 KAEMETAL----ESLNGVELEGR 136
              ++  +     ++NG   E R
Sbjct: 154 HDSVDKIVIQKYHTVNGHNCEVR 176

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 1/91 (1%)
Query: 56  KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           K + P   E   KLF+G LS+  T ESL   F+++G +    V+ D  + RSRG+GFV Y
Sbjct: 1   KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 60
Query: 116 STKAEMETALESLNGVELEGRAMRVSLAQGR 146
           +T  E++ A+ +    +++GR +    A  R
Sbjct: 61  ATVEEVDAAMNARPH-KVDGRVVEPKRAVSR 90

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 62.8 bits (151), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR----VNFSDKPKP 57
           L+   V+ D  T RSRGF FVT +TVE+ +A + N    +  GR++     V+  D  +P
Sbjct: 41  LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRP 99
Query: 58  KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
              L  +   K+FVG +        L   F++YG +    ++ D  SG+ RG+ FV +  
Sbjct: 100 GAHLTVK---KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 156
Query: 118 KAEMETAL----ESLNGVELEGR 136
              ++  +     ++NG   E R
Sbjct: 157 HDSVDKIVIQKYHTVNGHNCEVR 179

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 57.4 bits (137), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 1/91 (1%)
Query: 56  KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           K + P   E   KLF+G LS+  T ESL   F+++G +    V+ D  + RSRG+GFV Y
Sbjct: 4   KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 63
Query: 116 STKAEMETALESLNGVELEGRAMRVSLAQGR 146
           +T  E++ A+ +    +++GR +    A  R
Sbjct: 64  ATVEEVDAAMNARPH-KVDGRVVEPKRAVSR 93

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 62.8 bits (151), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 12/143 (8%)
Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR----VNFSDKPKP 57
           L+   V+ D  T RSRGF FVT +TVE+ +A + N    +  GR++     V+  D  +P
Sbjct: 40  LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRP 98
Query: 58  KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
              L  +   K+FVG +        L   F++YG +    ++ D  SG+ RG+ FV +  
Sbjct: 99  GAHLTVK---KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
Query: 118 KAEMETAL----ESLNGVELEGR 136
              ++  +     ++NG   E R
Sbjct: 156 HDSVDKIVIQKYHTVNGHNCEVR 178

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 1/91 (1%)
Query: 56  KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           K + P   E   KLF+G LS+  T ESL   F+++G +    V+ D  + RSRG+GFV Y
Sbjct: 3   KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
Query: 116 STKAEMETALESLNGVELEGRAMRVSLAQGR 146
           +T  E++ A+ +    +++GR +    A  R
Sbjct: 63  ATVEEVDAAMNARPH-KVDGRVVEPKRAVSR 92

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 60.1 bits (144), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 47/76 (61%), Gaps = 2/76 (2%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V NL   +  E L +AF  +G +  A+V+ +G  GRS+G+GFVC+S+  E   A+  +
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 129 NGVELEGRAMRVSLAQ 144
           NG  +  + + V+LAQ
Sbjct: 76  NGRIVATKPLYVALAQ 91

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 48/76 (63%), Gaps = 1/76 (1%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG L +  T  SL + F+ +G++  A V+ D ++G+SRGYGFV  + +A  E A + 
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 128 LNGVELEGRAMRVSLA 143
            N + ++GR   V+LA
Sbjct: 79  PNPI-IDGRKANVNLA 93

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++VGNL +S T+E + + F ++G V   +++YD E+ + +G+GFV    ++  E A+  L
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKL 62
Query: 129 NGVELEGRAMRVSLAQGRRS 148
           +  +  GR +RV+ A  ++S
Sbjct: 63  DNTDFMGRTIRVTEANPKKS 82

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 57.4 bits (137), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 45/78 (57%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV  +++  T   L + F+ YG +    ++Y   SG+ RGY F+ Y  + +M +A +  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 129 NGVELEGRAMRVSLAQGR 146
           +G +++GR + V + +GR
Sbjct: 165 DGKKIDGRRVLVDVERGR 182

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 56.6 bits (135), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 44/79 (55%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  LS   T   L + F +YG +    ++YD +S RSRG+ FV +    + + A E  
Sbjct: 15  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 129 NGVELEGRAMRVSLAQGRR 147
           NG+EL+GR +RV  +  +R
Sbjct: 75  NGMELDGRRIRVDFSITKR 93

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 56.6 bits (135), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/81 (37%), Positives = 47/81 (58%), Gaps = 2/81 (2%)
Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D  L+V NL  ++T + L   F +YG++V   +L D  +GR RG  FV Y+ + E + A+
Sbjct: 13  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 126 ESLNGVELEG--RAMRVSLAQ 144
            +LN V  EG  + + V LA+
Sbjct: 73  SALNNVIPEGGSQPLSVRLAE 93

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 56.2 bits (134), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 44/79 (55%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  LS   T   L + F +YG +    ++YD +S RSRG+ FV +    + + A E  
Sbjct: 18  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 129 NGVELEGRAMRVSLAQGRR 147
           NG+EL+GR +RV  +  +R
Sbjct: 78  NGMELDGRRIRVDFSITKR 96

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 55.8 bits (133), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 34/148 (22%), Positives = 71/148 (47%), Gaps = 6/148 (4%)
Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD---KPKPK 58
           +  + + +D  T + +GFAFV     E     +E ++     GR ++V       + +P 
Sbjct: 55  IKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPI 114
Query: 59  LPLYAETD---FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           +   AE      +++V ++   ++ + +   F+ +G +  A +  D  +G+ +GYGF+ Y
Sbjct: 115 IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEY 174
Query: 116 STKAEMETALESLNGVELEGRAMRVSLA 143
                 + A+ S+N  +L G+ +RV  A
Sbjct: 175 EKAQSSQDAVSSMNLFDLGGQYLRVGKA 202

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 42/73 (57%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +++VG++ + +  +++ QAF  +G +    + +D  + + +G+ FV Y      + ALE 
Sbjct: 30  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 128 LNGVELEGRAMRV 140
           +N V L GR ++V
Sbjct: 90  MNSVMLGGRNIKV 102

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score = 55.8 bits (133), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KL V NL + V+   + + F E+G +  A V YD  SGRS G   V +  KA+   A++ 
Sbjct: 30  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 88
Query: 128 LNGVELEGRAMRVSL 142
            NGV L+GR M + L
Sbjct: 89  YNGVPLDGRPMNIQL 103

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 55.8 bits (133), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 46/77 (59%)
Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D  L+V  L  +++ + + Q F +YG ++ +R+L D  +G SRG GF+ +  + E E A+
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 126 ESLNGVELEGRAMRVSL 142
           + LNG +  G A  +++
Sbjct: 61  KGLNGQKPLGAAEPITV 77

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 55.5 bits (132), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 31/79 (39%), Positives = 50/79 (63%)
Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           + F +FVG+LS  +TT ++  AF  +G +  ARV+ D  +G+S+GYGFV +  K + E A
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 125 LESLNGVELEGRAMRVSLA 143
           ++ + G  L GR +R + A
Sbjct: 65  IQQMGGQWLGGRQIRTNWA 83

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 55.5 bits (132), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L  ++T + L   F   G V  A+++ D  +G S GYGFV Y T  + E A+ +L
Sbjct: 7   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 129 NGVELEGRAMRVSLAQ 144
           NG+ L+ + ++VS A+
Sbjct: 67  NGLRLQSKTIKVSYAR 82

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/87 (31%), Positives = 50/87 (57%)
Query: 58  KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
           + P   E    L V NL++  + ++L + F++YG V    +  D  +  SRG+ FV +  
Sbjct: 39  RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 98
Query: 118 KAEMETALESLNGVELEGRAMRVSLAQ 144
           K + E A+++++G  L+GR +RV +A+
Sbjct: 99  KRDAEDAMDAMDGAVLDGRELRVQMAR 125

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 44/79 (55%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  LS   T   L + F +YG +    ++YD +S RSRG+ FV +    + + A E  
Sbjct: 49  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 129 NGVELEGRAMRVSLAQGRR 147
           NG+EL+GR +RV  +  +R
Sbjct: 109 NGMELDGRRIRVDFSITKR 127

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 45/78 (57%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV  +++  T   L + F+ YG +    ++Y   SG+ RGY F+ Y  + +M +A +  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 129 NGVELEGRAMRVSLAQGR 146
           +G +++GR + V + +GR
Sbjct: 165 DGKKIDGRRVLVDVERGR 182

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 39/58 (67%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           KLF+G LS+  T ESL   ++++G +    V+ D  S RSRG+GFV +S+ AE++ A+
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 47/76 (61%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V NL++  + ++L + F++YG V    +  D  +  SRG+ FV +  K + E A++++
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 129 NGVELEGRAMRVSLAQ 144
           +G  L+GR +RV +A+
Sbjct: 133 DGAVLDGRELRVQMAR 148

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K FVG LSW  + + L   F ++G VV   +  D  +GRSRG+GF+ +   A +E  L+ 
Sbjct: 13  KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 128 LNGVELEGRAM 138
                L+GR +
Sbjct: 73  KEH-RLDGRVI 82

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 42/73 (57%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  LS   T   L + F +YG +    ++YD +S RSRG+ FV +    + + A E  
Sbjct: 18  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 129 NGVELEGRAMRVS 141
           NG+EL+GR +RVS
Sbjct: 78  NGMELDGRRIRVS 90

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 48/79 (60%), Gaps = 2/79 (2%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +F+ NL  S+  ++L   F  +GN++  +V+ D E+G S+GYGFV + T+   E A+E +
Sbjct: 14  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 129 NGVELEGRAMRVSLAQGRR 147
           NG+ L  R + V   + R+
Sbjct: 72  NGMLLNDRKVFVGRFKSRK 90

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 43/76 (56%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L  + T + L   F   G V  A+++ D  +G S GYGFV Y T  + E A+ +L
Sbjct: 22  LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 129 NGVELEGRAMRVSLAQ 144
           NG+ L+ + ++VS A+
Sbjct: 82  NGLRLQSKTIKVSYAR 97

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/148 (22%), Positives = 70/148 (47%), Gaps = 6/148 (4%)
Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD---KPKPK 58
           +  + + +D  T + +GFAFV     E     +E ++     GR ++V       + +P 
Sbjct: 40  IKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPI 99
Query: 59  LPLYAETD---FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
           +   AE      +++V ++   ++ + +   F+ +G +    +  D  +G+ +GYGF+ Y
Sbjct: 100 IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEY 159
Query: 116 STKAEMETALESLNGVELEGRAMRVSLA 143
                 + A+ S+N  +L G+ +RV  A
Sbjct: 160 EKAQSSQDAVSSMNLFDLGGQYLRVGKA 187

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 42/73 (57%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +++VG++ + +  +++ QAF  +G +    + +D  + + +G+ FV Y      + ALE 
Sbjct: 15  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 128 LNGVELEGRAMRV 140
           +N V L GR ++V
Sbjct: 75  MNSVMLGGRNIKV 87

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 42/74 (56%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LF+ +L      + L Q F  +GNVV A+V  D ++  S+ +GFV Y      + A++S+
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 129 NGVELEGRAMRVSL 142
           NG ++  + ++V L
Sbjct: 88  NGFQIGMKRLKVQL 101

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 43/75 (57%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++V NL +S+T   L + F +YG VV   ++ D ++ +S+G  F+ +  K   +    ++
Sbjct: 19  VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 129 NGVELEGRAMRVSLA 143
           N  +L GR ++ S+A
Sbjct: 79  NNKQLFGRVIKASIA 93

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 48/79 (60%), Gaps = 2/79 (2%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +F+ NL  S+  ++L   F  +GN++  +V+ D E+G S+GYGFV + T+   E A+E +
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 129 NGVELEGRAMRVSLAQGRR 147
           NG+ L  R + V   + R+
Sbjct: 66  NGMLLNDRKVFVGRFKSRK 84

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFVG L WS T E+L   F +YG VV   ++ D  + +SRG+GFV +     + T L S
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 128 LNGVELEGRAM 138
                L+GR +
Sbjct: 78  RPHT-LDGRNI 87

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 34/132 (25%), Positives = 68/132 (51%), Gaps = 9/132 (6%)
Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
            + D  TG +R F +V   + ED    +E L G +  G  +++   +KPK +        
Sbjct: 44  AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL---EKPKGRDSKKVRAA 99
Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             L   NLS+++T + L + F+   + +  R++   + G+S+G  ++ + ++A+ E  LE
Sbjct: 100 RTLLAKNLSFNITEDELKEVFE---DALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLE 154
Query: 127 SLNGVELEGRAM 138
              G E++GR++
Sbjct: 155 EKQGAEIDGRSV 166

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 1/83 (1%)
Query: 59  LPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTK 118
            P   E D  +FVGNL   V  E L + F + G +    +  D E G+ + +GFVC+   
Sbjct: 9   FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHP 67
Query: 119 AEMETALESLNGVELEGRAMRVS 141
             +  A+  LNG+ L GR + VS
Sbjct: 68  ESVSYAIALLNGIRLYGRPINVS 90

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           ET  KL V NL + V+   + + F E+G +  A V YD  SGRS G   V +  +A+   
Sbjct: 86  ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALK 144
Query: 124 ALESLNGVELEGRAMRVSL 142
           A++   GV L+GR M + L
Sbjct: 145 AMKQYKGVPLDGRPMDIQL 163

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 52.8 bits (125), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 46/79 (58%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VG L+  V  + L  AF  +G++   ++  D E+ + RG+ FV +    +   A++++
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 129 NGVELEGRAMRVSLAQGRR 147
           N  EL GR +RV+LA+  R
Sbjct: 75  NESELFGRTIRVNLAKPMR 93

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 39/112 (34%), Positives = 51/112 (45%), Gaps = 12/112 (10%)
Query: 15  RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNL 74
           R RGF F+ + +          LDG     R LR+ F           A     L V NL
Sbjct: 56  RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF-----------ATHGAALTVKNL 104
Query: 75  SWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           S  V+ E L QAF ++G V  A V+ D + GR+ G GFV ++ K     ALE
Sbjct: 105 SPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALE 155

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFVGNL   +T E   + F+ YG      +       R RG+GF+   ++   E A   
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 128 LNGVELEGRAMRVSLA 143
           L+G  L+ R +R+  A
Sbjct: 78  LDGTILKSRPLRIRFA 93

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 45/76 (59%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VG L+  V  + L  AF  +G++   ++  D E+ + RG+ FV +    +   A++++
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 129 NGVELEGRAMRVSLAQ 144
           N  EL GR +RV+LA+
Sbjct: 68  NESELFGRTIRVNLAK 83

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 34/132 (25%), Positives = 62/132 (46%), Gaps = 9/132 (6%)
Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
            + D   G +R F +V   + ED    +E L G +  G  +++   +KPK K        
Sbjct: 38  AVVDVRIGMTRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL---EKPKGKDSKKERDA 93
Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             L   NL + VT + L + F++      A +    + G+S+G  ++ + T+A+ E   E
Sbjct: 94  RTLLAKNLPYKVTQDELKEVFED-----AAEIRLVSKDGKSKGIAYIEFKTEADAEKTFE 148
Query: 127 SLNGVELEGRAM 138
              G E++GR++
Sbjct: 149 EKQGTEIDGRSI 160

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 45/76 (59%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VG L+  V  + L  AF  +G++   ++  D E+ + RG+ FV +    +   A++++
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 129 NGVELEGRAMRVSLAQ 144
           N  EL GR +RV+LA+
Sbjct: 70  NESELFGRTIRVNLAK 85

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 52.4 bits (124), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 44/75 (58%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VG L+  V  + L  AF  +G++   ++  D E+ + RG+ FV +    +   A++++
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 129 NGVELEGRAMRVSLA 143
           N  EL GR +RV+LA
Sbjct: 65  NESELFGRTIRVNLA 79

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 52.4 bits (124), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V NL++  + +SL + F++YG V    +  +  +   RG+ FV +  + + + A  ++
Sbjct: 16  LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 129 NGVELEGRAMRVSLAQ-GRR 147
           +G EL+GR +RV +A+ GRR
Sbjct: 76  DGAELDGRELRVQVARYGRR 95

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/141 (23%), Positives = 65/141 (46%), Gaps = 6/141 (4%)
Query: 9   YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD---KPKPKLPLYAET 65
           +D  T + +GFAFV     E     +E  +     GR ++V       + +P +   AE 
Sbjct: 46  WDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEE 105
Query: 66  D---FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
                +++V ++   ++ + +   F+ +G +    +  D  +G+ +GYGF+ Y      +
Sbjct: 106 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQ 165
Query: 123 TALESLNGVELEGRAMRVSLA 143
            A+ S N  +L G+ +RV  A
Sbjct: 166 DAVSSXNLFDLGGQYLRVGKA 186

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 45/76 (59%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L  ++T +     F   G++   +++ D  +G+S GYGFV YS   + + A+ +L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 129 NGVELEGRAMRVSLAQ 144
           NG++L+ + ++VS A+
Sbjct: 67  NGLKLQTKTIKVSYAR 82

>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs Orf57 Peptide Length = 124

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           ET  KL V NL + V+   + + F E+G +  A V YD  SGRS G   V +  +A+   
Sbjct: 33  ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALK 91
Query: 124 ALESLNGVELEGRAMRVSL 142
           A++   GV L+GR M + L
Sbjct: 92  AMKQYKGVPLDGRPMDIQL 110

>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1 Icp27 Peptide Length = 124

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           ET  KL V NL + V+   + + F E+G +  A V YD  SGRS G   V +  +A+   
Sbjct: 33  ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALK 91
Query: 124 ALESLNGVELEGRAMRVSL 142
           A++   GV L+GR M + L
Sbjct: 92  AMKQYKGVPLDGRPMDIQL 110

>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A Resolution Length = 107

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KL V NL + V+   + + F E+G +  A V YD  SGRS G   V +  KA+   A + 
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAXKQ 89
Query: 128 LNGVELEGRAMRVSL 142
            NGV L+GR   + L
Sbjct: 90  YNGVPLDGRPXNIQL 104

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/81 (34%), Positives = 47/81 (58%), Gaps = 1/81 (1%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+F+G LSW  T E L + F ++G V    V+ D  + RSRG+GFV +  +A ++  L +
Sbjct: 27  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 85
Query: 128 LNGVELEGRAMRVSLAQGRRS 148
            +  EL+ + +   +A  RR+
Sbjct: 86  QSRHELDSKTIDPKVAFPRRA 106

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 44/75 (58%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VG L+  V  + L  AF  +G++   ++  D E+ + RG+ FV +    +   A++++
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 129 NGVELEGRAMRVSLA 143
           N  EL GR +RV+LA
Sbjct: 126 NESELFGRTIRVNLA 140

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 41/74 (55%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LF+ +L    T   L   F  +GNV+ A+V  D ++  S+ +GFV +      + A++++
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 129 NGVELEGRAMRVSL 142
           NG ++  + ++V L
Sbjct: 103 NGFQVGTKRLKVQL 116

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 57  PKLPLYAETDF--KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVC 114
           P   +  E D    L V  +  +V    L Q F+ YG +   +++ D E+ +SRGYGFV 
Sbjct: 31  PPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVK 90
Query: 115 YSTKAEMETALESLNGVELEGRAMRVSLA 143
           + + +  + A+  LNG  +  + ++V+LA
Sbjct: 91  FQSGSSAQQAIAGLNGFNILNKRLKVALA 119

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/99 (29%), Positives = 52/99 (52%), Gaps = 11/99 (11%)
Query: 48  RVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRS 107
            +N  +K +PK         +L V N+ +      L Q F ++G ++   ++++ E G S
Sbjct: 20  HMNTENKSQPK---------RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG-S 68
Query: 108 RGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
           +G+GFV +   A+ + A E L+G  +EGR + V+ A  R
Sbjct: 69  KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY----STKAEMETA 124
           +F+G LSW  T + L   F ++G VV   +  D  +GRSRG+GFV +    S    M+  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 125 LESLNG 130
              LNG
Sbjct: 62  EHKLNG 67

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 41/139 (29%), Positives = 70/139 (50%), Gaps = 13/139 (9%)
Query: 4   KLTVLYDRETG--RSRGFAFVTMST----VEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
           ++ VL DR     +S+G  FVT  T    +E  NA + N+     +   +++  +D  K 
Sbjct: 44  EINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA-LHNMKVLPGMHHPIQMKPADSEKN 102
Query: 58  KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
                A  D KLF+G +S   T   +   F  +G +   R+L  G  G SRG  FV ++T
Sbjct: 103 N----AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILR-GPDGLSRGCAFVTFTT 157
Query: 118 KAEMETALESLNGVE-LEG 135
           +A  +TA+++++  + +EG
Sbjct: 158 RAMAQTAIKAMHQAQTMEG 176

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 41/139 (29%), Positives = 70/139 (50%), Gaps = 13/139 (9%)
Query: 4   KLTVLYDRETG--RSRGFAFVTMST----VEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
           ++ VL DR     +S+G  FVT  T    +E  NA + N+     +   +++  +D  K 
Sbjct: 32  EINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA-LHNMKVLPGMHHPIQMKPADSEKN 90
Query: 58  KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
                A  D KLF+G +S   T   +   F  +G +   R+L  G  G SRG  FV ++T
Sbjct: 91  N----AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILR-GPDGLSRGCAFVTFTT 145
Query: 118 KAEMETALESLNGVE-LEG 135
           +A  +TA+++++  + +EG
Sbjct: 146 RAMAQTAIKAMHQAQTMEG 164

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           T  +L V N+ +      L Q F ++G ++   ++++ E G S+G+GFV +   A+ + A
Sbjct: 14  TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG-SKGFGFVTFENSADADRA 71
Query: 125 LESLNGVELEGRAMRVSLAQGR 146
            E L+G  +EGR + V+ A  R
Sbjct: 72  REKLHGTVVEGRKIEVNNATAR 93

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           K+F+G LSW  T E L + F ++G V    V+ D  + RSRG+GFV +  +A ++  L
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 49/79 (62%), Gaps = 5/79 (6%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L + NLS+S T E+L + F++   +     +   ++G+S+GY F+ +++  + + AL S 
Sbjct: 18  LVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 129 NGVELEGRAMRVSLAQGRR 147
           N  E+EGRA+R+ L QG R
Sbjct: 74  NKREIEGRAIRLEL-QGPR 91

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A+   KLF+G L+     + L   F ++G +    ++ D  + +SRG+ F+ +   A+ +
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAK 62
Query: 123 TALESLNGVELEGRAMRVSLAQ 144
            A + +NG  L G+A++V  A+
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAK 84

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 53  DKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGF 112
           D+P P+  +     + LFV  +    T E +   F EYG +    +  D  +G  +GY  
Sbjct: 12  DEPGPQRSVEG---WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 68
Query: 113 VCYSTKAEMETALESLNGVELEGRAMRVS 141
           V Y T  E + A+E LNG +L G+ + V 
Sbjct: 69  VEYETYKEAQAAMEGLNGQDLMGQPISVD 97

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 53  DKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGF 112
           D+P P+  +     + LFV  +    T E +   F EYG +    +  D  +G  +GY  
Sbjct: 13  DEPGPQRSVEG---WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 69
Query: 113 VCYSTKAEMETALESLNGVELEGRAMRVS 141
           V Y T  E + A+E LNG +L G+ + V 
Sbjct: 70  VEYETYKEAQAAMEGLNGQDLMGQPISVD 98

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 47/78 (60%), Gaps = 3/78 (3%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV  LS   T E+L ++F      V AR++ D E+G S+G+GFV ++++ + + A E++
Sbjct: 18  LFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 129 NGVELEGRAMRVSLAQGR 146
              E++G  + +  A+ +
Sbjct: 75  EDGEIDGNKVTLDWAKPK 92

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 35/58 (60%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           +FVG LS + T E +   F+++G V  A +++D  + R RG+GFV + ++  +E   E
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVV-GARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +F+GNL   +  + L   F  +G ++   +++ D ++G S+GY F+ +++    + A+E+
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 128 LNGVELEGRAMRVSLA 143
           +NG  L  R + VS A
Sbjct: 68  MNGQYLCNRPITVSYA 83

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 40/137 (29%), Positives = 62/137 (45%), Gaps = 16/137 (11%)
Query: 4   KLTVLYDRETG--RSRGFAFVTMST----VEDCNAVIEN--LDGREYLGRILRVNFSDKP 55
           ++ VL DR     +S+G  FVT  T    +E  NA+     L G  +           KP
Sbjct: 32  EINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNXKVLPGXHH-------PIQXKP 84
Query: 56  KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
                  A  D KLF+G +S   T   +   F  +G +   R+L  G  G SRG  FV +
Sbjct: 85  ADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILR-GPDGLSRGCAFVTF 143
Query: 116 STKAEMETALESLNGVE 132
           +T+A  +TA+++ +  +
Sbjct: 144 TTRAXAQTAIKAXHQAQ 160

>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding Protein 14 Length = 90

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 8/77 (10%)
Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           +K+FVGN+S + T++ L   F+  G V+   V+ D        Y FV    +A+ + A+ 
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIA 61
Query: 127 SLNGVELEGRAMRVSLA 143
            LNG E++G+ + V L+
Sbjct: 62  QLNGKEVKGKRINVELS 78

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 31/132 (23%), Positives = 61/132 (46%), Gaps = 6/132 (4%)
Query: 12  ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFV 71
           +  + + FAF+   +V++    +   DG  + G+ L++    +P    PL      KLF+
Sbjct: 46  QINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR---RPHDYQPLPGAH--KLFI 99
Query: 72  GNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV 131
           G L   +  + + +    +G +    ++ D  +G S+GY F  Y      + A+  LNG+
Sbjct: 100 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 159
Query: 132 ELEGRAMRVSLA 143
           +L  + + V  A
Sbjct: 160 QLGDKKLLVQRA 171

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 36/73 (49%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV  +    T E +   F EYG +    +  D  +G  +GY  V Y T  E + A+E L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 129 NGVELEGRAMRVS 141
           NG +L G+ + V 
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 31/132 (23%), Positives = 61/132 (46%), Gaps = 6/132 (4%)
Query: 12  ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFV 71
           +  + + FAF+   +V++    +   DG  + G+ L++    +P    PL      KLF+
Sbjct: 48  QINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR---RPHDYQPLPGAH--KLFI 101
Query: 72  GNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV 131
           G L   +  + + +    +G +    ++ D  +G S+GY F  Y      + A+  LNG+
Sbjct: 102 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 161
Query: 132 ELEGRAMRVSLA 143
           +L  + + V  A
Sbjct: 162 QLGDKKLLVQRA 173

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 22/81 (27%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG +  +     L + F+++G V    ++YD E  R RG+GF+ +  +  ++ A+ +
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-N 70
Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           ++  ++ G+ + V  A+ R S
Sbjct: 71  MHFHDIMGKKVEVKRAEPRDS 91

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 36/73 (49%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV  +    T E +   F EYG +    +  D  +G  +GY  V Y T  E + A+E L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 129 NGVELEGRAMRVS 141
           NG +L G+ + V 
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 36/73 (49%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV  +    T E +   F EYG +    +  D  +G  +GY  V Y T  E + A+E L
Sbjct: 12  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 129 NGVELEGRAMRVS 141
           NG +L G+ + V 
Sbjct: 72  NGQDLMGQPISVD 84

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 36/73 (49%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV  +    T E +   F EYG +    +  D  +G  +GY  V Y T  E + A+E L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 129 NGVELEGRAMRVS 141
           NG +L G+ + V 
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 43/76 (56%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L   +T   L   F+  G +   R++ D ++G S GY FV ++++ + + A++ L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 129 NGVELEGRAMRVSLAQ 144
           NG+ +  + ++VS A+
Sbjct: 66  NGITVRNKRLKVSYAR 81

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 45.8 bits (107), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 8/79 (10%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KL VGN+S + T + L   F+EYG V+   ++ D        Y FV      +   A+  
Sbjct: 12  KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRG 63
Query: 128 LNGVELEGRAMRVSLAQGR 146
           L+  E +G+ M V L+  R
Sbjct: 64  LDNTEFQGKRMHVQLSTSR 82

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFVGNL   +T E + + F++YG   G   ++     + +G+GF+   T+   E A   
Sbjct: 24  RLFVGNLPPDITEEEMRKLFEKYGK-AGEVFIH-----KDKGFGFIRLETRTLAEIAKVE 77
Query: 128 LNGVELEGRAMRVSLA 143
           L+ + L G+ +RV  A
Sbjct: 78  LDNMPLRGKQLRVRFA 93

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 46/81 (56%)
Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D  ++VG L   V+   L + F + G VV   +  D  +G+ +GYGFV + ++ + + A+
Sbjct: 15  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 126 ESLNGVELEGRAMRVSLAQGR 146
           + ++ ++L G+ +RV+ A   
Sbjct: 75  KIMDMIKLYGKPIRVNKASAH 95

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV ++      + + + F +YG +    +  D  +G S+GY  V Y T  +   A E+L
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 129 NGVELEGRAMRVS 141
           NG E+ G+ ++V 
Sbjct: 135 NGAEIMGQTIQVD 147

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 41/72 (56%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +++G++ +  T E +       G V+  ++++D ++GRS+GY F+ +       +A+ +L
Sbjct: 7   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 129 NGVELEGRAMRV 140
           NG +L  R ++ 
Sbjct: 67  NGYQLGSRFLKC 78

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV ++      + + + F +YG +    +  D  +G S+GY  V Y T  +   A E+L
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 129 NGVELEGRAMRVS 141
           NG E+ G+ ++V 
Sbjct: 89  NGAEIMGQTIQVD 101

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFVG L+   + + + + F+ +GN+    +L  G  G S+G  FV YS+ AE + A+ +
Sbjct: 17  KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILR-GPDGNSKGCAFVKYSSHAEAQAAINA 75
Query: 128 LNGVE 132
           L+G +
Sbjct: 76  LHGSQ 80

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFVGNL   +T E + + F++YG      +  D      +G+GF+   T+   E A   
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 128 LNGVELEGRAMRVSLA 143
           L+ + L G+ +RV  A
Sbjct: 71  LDNMPLRGKQLRVRFA 86

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 18/71 (25%), Positives = 41/71 (57%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +++G++ +  T E +       G V+  ++++D ++GRS+GY F+ +       +A+ +L
Sbjct: 5   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 129 NGVELEGRAMR 139
           NG +L  R ++
Sbjct: 65  NGYQLGSRFLK 75

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 41/72 (56%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +++G++ +  T E +       G V+  ++++D ++GRS+GY F+ +       +A+ +L
Sbjct: 6   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 129 NGVELEGRAMRV 140
           NG +L  R ++ 
Sbjct: 66  NGYQLGSRFLKC 77

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 31/147 (21%), Positives = 65/147 (44%), Gaps = 16/147 (10%)
Query: 12  ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV----------NFSDKPKPKLP- 60
           +  + + FAF+   +V++    +   DG  + G+ L++            S+ P   +P 
Sbjct: 46  QINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPG 104
Query: 61  ----LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYS 116
               +  ++  KLF+G L   +  + + +    +G +    ++ D  +G S+GY F  Y 
Sbjct: 105 VVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 164
Query: 117 TKAEMETALESLNGVELEGRAMRVSLA 143
                + A+  LNG++L  + + V  A
Sbjct: 165 DINVTDQAIAGLNGMQLGDKKLLVQRA 191

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 35/124 (28%), Positives = 50/124 (40%), Gaps = 11/124 (8%)
Query: 17  RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSW 76
           +G AFVT+   E   A I          R L V               TD  L V NL  
Sbjct: 57  KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ-----------PTDALLCVANLPP 105
Query: 77  SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR 136
           S+T +   +  + +G++    ++Y   +G+S+GYGF  Y  K     A   L G  L  R
Sbjct: 106 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 165
Query: 137 AMRV 140
            + V
Sbjct: 166 TLYV 169

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV NL+ +VT E L +AF ++G +   + L D        Y F+ +  +     A+E +
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 129 NGVELEGRAMRVSLAQ 144
           NG +LEG  + +  A+
Sbjct: 66  NGKDLEGENIEIVFAK 81

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 35/124 (28%), Positives = 50/124 (40%), Gaps = 11/124 (8%)
Query: 17  RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSW 76
           +G AFVT+   E   A I          R L V               TD  L V NL  
Sbjct: 57  KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ-----------PTDALLCVANLPP 105
Query: 77  SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR 136
           S+T +   +  + +G++    ++Y   +G+S+GYGF  Y  K     A   L G  L  R
Sbjct: 106 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 165
Query: 137 AMRV 140
            + V
Sbjct: 166 TLYV 169

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 41/77 (53%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VGNLS+  T E + + F + G++    +  D     + G+ FV Y ++A+ E A+  +
Sbjct: 42  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 129 NGVELEGRAMRVSLAQG 145
           NG  L+ R +R     G
Sbjct: 102 NGTRLDDRIIRTDWDAG 118

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 35/124 (28%), Positives = 50/124 (40%), Gaps = 11/124 (8%)
Query: 17  RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSW 76
           +G AFVT+   E   A I          R L V               TD  L V NL  
Sbjct: 55  KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ-----------PTDALLCVANLPP 103
Query: 77  SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR 136
           S+T +   +  + +G++    ++Y   +G+S+GYGF  Y  K     A   L G  L  R
Sbjct: 104 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 163
Query: 137 AMRV 140
            + V
Sbjct: 164 TLYV 167

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FV NL + V  + L + F   G VV A +L D + G+SRG G V +    E   A+   
Sbjct: 18  VFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 129 NGVELEGRAMRVSL 142
           NG  L  R M V +
Sbjct: 77  NGQLLFDRPMHVKM 90

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++FV NL +  T + L   F E G+V+ A +    E+G+S+G G V + +    E A   
Sbjct: 10  QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACRM 67
Query: 128 LNGVELEGRAMRVSL 142
           +NG++L GR + V +
Sbjct: 68  MNGMKLSGREIDVRI 82

>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5 Rna Binding Protein Length = 105

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D KLFVG L+   + E + + FQ +G +    VL  G  G S+G  FV +S+  E + A+
Sbjct: 15  DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLR-GPDGSSKGCAFVKFSSHTEAQAAI 73
Query: 126 ESLNGVE 132
            +L+G +
Sbjct: 74  HALHGSQ 80

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FV NL +  T + L   F E G+V+ A +    E+G+S+G G V + +    E A   +
Sbjct: 8   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACRMM 65
Query: 129 NGVELEGRAMRVSL 142
           NG++L GR + V +
Sbjct: 66  NGMKLSGREIDVRI 79

>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii Mrna- Binding Protein 2 Length = 93

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 7/81 (8%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KL++GNLS +VT + L Q F +    +  +VL         GY FV Y  +     A+E+
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIET 63
Query: 128 LNG-VELEGRAMRVSLAQGRR 147
           L+G VEL G+ M V  +  ++
Sbjct: 64  LSGKVELHGKIMEVDYSVSKK 84

>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14 Length = 115

Iteration: 1
 Score = 42.7 bits (99), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 3/88 (3%)
Query: 61  LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAE 120
           L  E +  L++ NL + +T E +   F +YG +   RV   G +  +RG  +V Y    +
Sbjct: 3   LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFD 59
Query: 121 METALESLNGVELEGRAMRVSLAQGRRS 148
            + A++ L+G  +  R + V      R+
Sbjct: 60  AKNAVDHLSGFNVSNRYLVVLYYNANRA 87

>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical Protein Flj11016 Length = 115

Iteration: 1
 Score = 42.7 bits (99), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 5/95 (5%)
Query: 58  KLPLYA-----ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGF 112
           K+P+++     E +  L++ NLS  VT   L   F  +    G  + +   +GR RG  F
Sbjct: 12  KIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAF 71
Query: 113 VCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
           + +  K     AL  +NG +L G+ + +   + ++
Sbjct: 72  ITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK 106

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 42.4 bits (98), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VGNLS+  T E + + F + G++    +  D +   + G+ FV Y ++A+ E A+  +
Sbjct: 21  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD-KMKTACGFCFVEYYSRADAENAMRYI 79
Query: 129 NGVELEGRAMRVSLAQG 145
           NG  L+ R +R     G
Sbjct: 80  NGTRLDDRIIRTDWDAG 96

>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28 Length = 111

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/84 (27%), Positives = 46/84 (54%), Gaps = 6/84 (7%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +F+ NLS+    E+L +  Q++G++   RV+   ++  S+G  F  + T+   +  L + 
Sbjct: 18  VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 129 N------GVELEGRAMRVSLAQGR 146
           +      G++L+GR ++V LA  R
Sbjct: 78  SLEAEGGGLKLDGRQLKVDLAVTR 101

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 50/85 (58%), Gaps = 3/85 (3%)
Query: 66  DFKLFVGNLSWSVTTESLTQAF-QEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           ++ LFVG+L+  V    L + F + Y +  G +V+ D ++G S+GYGFV ++ + E + A
Sbjct: 9   EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRA 67
Query: 125 LESLNG-VELEGRAMRVSLAQGRRS 148
           L    G V L  + +R+S+A  + S
Sbjct: 68  LTECQGAVGLGSKPVRLSVAIPKAS 92

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++VGN+ +  T E L   F   G+V    +L D  SG  +G+ ++ +S K  + T+L +L
Sbjct: 8   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 66
Query: 129 NGVELEGRAMRV 140
           +     GR ++V
Sbjct: 67  DESLFRGRQIKV 78

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLF+GNL    T + +   F++YG V+   ++        + YGFV    K   E A+ +
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
Query: 128 LNGVELEGRAMRVSLAQGR 146
           L+  +L G  + V  ++ +
Sbjct: 62  LHHYKLHGVNINVEASKNK 80

>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens At 1.95 A Resolution Length = 89

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++VGN+ +  T E L   F   G+V    +L D  SG  +G+ ++ +S K  + T+L +L
Sbjct: 9   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 67
Query: 129 NGVELEGRAMRV 140
           +     GR ++V
Sbjct: 68  DESLFRGRQIKV 79

>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein Np_057951 Length = 110

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/95 (28%), Positives = 47/95 (49%), Gaps = 14/95 (14%)
Query: 50  NFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQA-FQEYGNVVGARVLYDGESGRSR 108
           N ++K  PK       + ++F+GNL+ ++  +S  +  F +YG V G  V         +
Sbjct: 16  NVTNKNDPK-----SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HK 62
Query: 109 GYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
           GY FV YS +     A+   NG  L G+ + +++A
Sbjct: 63  GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA 97

>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1 (Rrm1) Of The Protein Rbm10 From Homo Sapiens Length = 91

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 37/57 (64%), Gaps = 2/57 (3%)
Query: 4  KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIE-NLDGREYLGRILRVNFSDKPKPKL 59
          ++ ++ ++ +G+SRGFAFV  S ++D    +E N      LG+ + +++SD PKPK+
Sbjct: 31 EVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD-PKPKI 86

>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal Protein P14 Bound To Region Of Sf3b155 Length = 125

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 3/88 (3%)
Query: 61  LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAE 120
           L  E +  L++ NL + +T E +   F +YG +   RV   G +  +RG  +V Y    +
Sbjct: 13  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFD 69
Query: 121 METALESLNGVELEGRAMRVSLAQGRRS 148
            + A + L+G  +  R + V      R+
Sbjct: 70  AKNACDHLSGFNVCNRYLVVLYYNANRA 97

>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex Length = 90

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYG--NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           L++GNL+W  T E LT+A    G  +++  +   +  +G+S+G+  V   ++A  +  ++
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 127 SLNGVELEGR 136
            L   EL G+
Sbjct: 64  LLPKRELHGQ 73

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 35/73 (47%)
Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFV NLS++ + E L + F  YG +       D  + + +G+ FV +        A   
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 128 LNGVELEGRAMRV 140
           ++G   +GR + V
Sbjct: 70  VDGQVFQGRMLHV 82

>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing Sarcoma(Ews) Protein Length = 113

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 8/86 (9%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNV-----VGARVLY---DGESGRSRGYGFVCYSTKAE 120
           ++V  L+ SVT + L   F++ G V      G  +++   D E+G+ +G   V Y     
Sbjct: 18  IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 121 METALESLNGVELEGRAMRVSLAQGR 146
            + A+E  +G + +G  ++VSLA+ +
Sbjct: 78  AKAAVEWFDGKDFQGSKLKVSLARKK 103

>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2 Length = 96

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 19/70 (27%), Positives = 42/70 (60%), Gaps = 5/70 (7%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L   NLS+++T + L + F+   + +  R++   + G+S+G  ++ + ++A+ E  LE  
Sbjct: 19  LLAKNLSFNITEDELKEVFE---DALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 129 NGVELEGRAM 138
            G E++GR++
Sbjct: 74  QGAEIDGRSV 83

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/89 (24%), Positives = 45/89 (50%), Gaps = 6/89 (6%)
Query: 57  PKLPLYAETDFKL-----FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
           P  PL AE   ++     +VGN+ +  T + L   F   G++    +L D  SG  +GY 
Sbjct: 22  PPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYA 81
Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRV 140
           ++ ++ +  ++ A+ +++     GR ++V
Sbjct: 82  YIEFAERNSVDAAV-AMDETVFRGRTIKV 109

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/73 (23%), Positives = 37/73 (50%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++  L    T + L +  Q YG +V  + + D  + + +GYGFV + + +  + A+ +L
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 129 NGVELEGRAMRVS 141
               ++ +  + S
Sbjct: 68  KASGVQAQMAKQS 80

>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein Complex P14-Sf3b155 Length = 87

Iteration: 1
 Score = 39.7 bits (91), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 58  KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
           +LP   E +  L++ NL + +T E +   F +YG +   RV   G +  +RG  +V Y  
Sbjct: 6   RLP--PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYED 60
Query: 118 KAEMETALESLNGVELEGRAMRV 140
             + + A + L+G  +  R + V
Sbjct: 61  IFDAKNACDHLSGFNVCNRYLVV 83

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 39.7 bits (91), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L V  L W  T + L + F  +G V+  +V  D ++G S+G+GFV ++   E ET ++ +
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT---EYETQVKVM 74
Query: 129 NGVEL-EGRAMRVSLAQGRRS 148
           +   + +GR     L   ++S
Sbjct: 75  SQRHMIDGRWCDCKLPNSKQS 95

>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda Subunit And The 59 Kda Subunit (Rrm Domain) Of Human Cleavage Factor Im Length = 156

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 31/106 (29%), Positives = 50/106 (47%), Gaps = 9/106 (8%)
Query: 47  LRVNFSDKPKPKLP--LYAETDFK-----LFVGNLSWSVTTESLTQAFQEYG--NVVGAR 97
           +R   S KP  K P  LY  +  +     ++VG+ SW  T + L Q  +  G  +VV  +
Sbjct: 29  VRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELK 88
Query: 98  VLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
              +  +G+S+GY  V  +++  +   LE L G  L G  + V  A
Sbjct: 89  FAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA 134

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score = 39.3 bits (90), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++ NL  S+  + L    + +G V+  R+L D  SG SRG GF    +  + E  +   
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 129 NG 130
           NG
Sbjct: 87  NG 88

>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX Length = 229

Iteration: 1
 Score = 39.3 bits (90), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 69  LFVGNLSWSVTTESLTQAFQEYG--NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           L++GNL+W  T E LT+A    G  +++  +   +  +G+S+G+  V   ++A  +  ++
Sbjct: 71  LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 127 SLNGVELEGRAMRVS 141
            L   EL G+   V+
Sbjct: 131 LLPKRELHGQNPVVT 145

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	148
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-59
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	9e-30
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-58
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-26
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-57
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-28
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-54
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-27
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-53
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-53
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-22
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	8e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-51
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-27
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-47
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-46
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-11
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-45
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-26
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-08
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	8e-43
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-25
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-42
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-22
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-42
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-25
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-42
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-35
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-17
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-39
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-16
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-39
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-15
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-38
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-19
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-37
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-15
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-36
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-14
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-36
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-17
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-35
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-18
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-35
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-17
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-35
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-19
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	6e-35
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-18
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-34
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-17
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-34
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-19
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-34
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	6e-19
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-34
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-18
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-34
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-34
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-18
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-34
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-18
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-33
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	7e-14
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-33
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-17
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	8e-33
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-17
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-32
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-13
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-32
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-14
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-32
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-32
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-14
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-32
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-18
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-32
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-18
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	6e-32
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-16
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	6e-32
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-14
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-32
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-18
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-32
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-19
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	8e-32
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-13
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	9e-32
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-13
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-31
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-17
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-31
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-18
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-31
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	9e-19
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-31
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	7e-17
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-31
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-17
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-31
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-16
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-31
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	8e-13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	6e-31
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-12
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-31
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-18
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-30
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	4e-14
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-30
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-15
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-30
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-15
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-30
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-13
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-30
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-13
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-30
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-13
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	5e-30
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-30
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-30
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-17
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	8e-30
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	5e-16
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-29
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-19
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-29
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-17
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-29
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-29
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-14
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-28
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-15
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-28
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-15
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	4e-28
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-06
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-28
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	8e-15
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-27
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-19
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-06
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-27
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-13
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-27
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	7e-13
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-27
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-14
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-27
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-14
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	6e-27
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-26
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	5e-17
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-26
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-26
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	9e-16
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-26
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-25
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-17
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-06
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-25
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	6e-16
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-25
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-25
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-14
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-25
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-12
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-25
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-12
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-25
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	8e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	4e-25
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-09
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-25
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	7e-25
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	6e-11
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	4e-24
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-10
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	5e-24
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-24
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	7e-05
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	6e-24
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-11
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	9e-24
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-10
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	9e-24
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-23
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-10
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-23
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-08
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-23
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-10
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-23
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-10
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-23
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-11
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-23
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	8e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-23
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-10
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-22
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-07
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-22
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-10
2div_A	99	TRNA selenocysteine associated protein; structural	2e-22
2div_A	99	TRNA selenocysteine associated protein; structural	9e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-22
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-08
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-22
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-10
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-21
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-07
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-21
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-11
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-21
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-08
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	4e-21
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	5e-21
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	5e-11
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	7e-21
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	9e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-20
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-20
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-20
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-08
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-20
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-09
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-20
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	5e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-20
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	8e-20
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-14
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	9e-20
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-06
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-19
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	6e-19
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-08
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-18
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-04
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-18
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	6e-11
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-18
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-18
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	9e-18
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-11
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-17
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	8e-17
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-17
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	9e-17
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-06
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-16
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-16
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-16
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-16
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-04
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-16
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	7e-16
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-15
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-09
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-15
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	8e-04
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	6e-15
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-14
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-14
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-14
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	6e-14
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-13
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	7e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-13
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-13
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-12
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-12
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-12
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-12
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-04
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-12
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-12
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-05
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-11
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-11
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-11
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	6e-11
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-10
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-09
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	4e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-07
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-07
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	2e-07
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	2e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	3e-04
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-06
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-05
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	3e-04
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	8e-04

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  182 bits (465), Expect = 1e-59
 Identities = 32/148 (21%), Positives = 66/148 (44%), Gaps = 6/148 (4%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           + +D  T + +GFAFV     E     +E ++     GR ++V          P+  +  
Sbjct: 60  MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLA 119

Query: 67  ------FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAE 120
                  +++V ++   ++ + +   F+ +G +  A +  D  +G+ +GYGF+ Y     
Sbjct: 120 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQS 179

Query: 121 METALESLNGVELEGRAMRVSLAQGRRS 148
            + A+ S+N  +L G+ +RV  A     
Sbjct: 180 SQDAVSSMNLFDLGGQYLRVGKAVTPPM 207

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  106 bits (267), Expect = 9e-30
 Identities = 22/104 (21%), Positives = 51/104 (49%), Gaps = 4/104 (3%)

Query: 44  GRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGE 103
           G+ +    + + +  L + +    +++VG++ + +  +++ QAF  +G +    + +D  
Sbjct: 10  GQQMGRGSAAQRQGALAIMS----RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSV 65

Query: 104 SGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
           + + +G+ FV Y      + ALE +N V L GR ++V       
Sbjct: 66  TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIG 109

>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 =  178 bits (454), Expect = 1e-58
 Identities = 39/138 (28%), Positives = 85/138 (61%), Gaps = 4/138 (2%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           ++ D+   ++  +AFV      D N  ++ L+G++    I+++N++ + +      ++  
Sbjct: 32  IMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQS---SSDDT 87

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           F LFVG+L+ +V  E+L  AF+++ + +   V++D ++G SRGYGFV ++++ + + A++
Sbjct: 88  FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 147

Query: 127 SLNGVELEGRAMRVSLAQ 144
           S+ G +L GR +R++ A 
Sbjct: 148 SMQGQDLNGRPLRINWAA 165

>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 = 95.3 bits (238), Expect = 6e-26
 Identities = 23/80 (28%), Positives = 45/80 (56%), Gaps = 1/80 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+VGNL  ++T + L Q FQ  G +   +++ D ++ ++  Y FV Y    +   AL++L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 129 NGVELEGRAMRVSLAQGRRS 148
           NG ++E   ++++ A   + 
Sbjct: 62  NGKQIENNIVKINWAFQSQQ 81

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 61.8 bits (151), Expect = 5e-13
 Identities = 17/48 (35%), Positives = 34/48 (70%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
           V++D +TG SRG+ FV+ ++ +D    ++++ G++  GR LR+N++ K
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>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 =  174 bits (443), Expect = 7e-57
 Identities = 44/139 (31%), Positives = 74/139 (53%), Gaps = 7/139 (5%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           ++ D +TG S G+AFV  ++  D    I+ L+G     + L+V+++      +      D
Sbjct: 35  IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIK-----D 89

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             L+V NL  ++T + L   F +YG++V   +L D  +GR RG  FV Y+ + E + A+ 
Sbjct: 90  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149

Query: 127 SLNGVELEG--RAMRVSLA 143
           +LN V  EG  + + V LA
Sbjct: 150 ALNNVIPEGGSQPLSVRLA 168

>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 =  101 bits (255), Expect = 2e-28
 Identities = 22/83 (26%), Positives = 44/83 (53%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           +  L V  L   +T   L   F+  G +   R++ D ++G S GY FV ++++ + + A+
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 126 ESLNGVELEGRAMRVSLAQGRRS 148
           + LNG+ +  + ++VS A+    
Sbjct: 63  KVLNGITVRNKRLKVSYARPGGE 85

>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 =  168 bits (428), Expect = 1e-54
 Identities = 40/139 (28%), Positives = 70/139 (50%), Gaps = 7/139 (5%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           ++ D+ TG+S G+ FV     +D    I  L+G     + ++V+++             D
Sbjct: 34  LVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSAS-----IRD 88

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             L+V  L  ++T + L Q F +YG ++ +R+L D  +G SRG GF+ +  + E E A++
Sbjct: 89  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148

Query: 127 SLNGVELEG--RAMRVSLA 143
            LNG +  G    + V  A
Sbjct: 149 GLNGQKPSGATEPITVKFA 167

>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 = 98.8 bits (247), Expect = 2e-27
 Identities = 25/81 (30%), Positives = 43/81 (53%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L V  L  ++T E     F   G +   +++ D  +G+S GYGFV Y    + E A+ +
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           LNG+ L+ + ++VS A+   +
Sbjct: 64  LNGLRLQTKTIKVSYARPSSA 84

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 60.7 bits (148), Expect = 1e-12
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 2/48 (4%)

Query: 6   TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG--RILRVNF 51
            +L D+ TG SRG  F+      +    I+ L+G++  G    + V F
Sbjct: 119 RILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF 166

>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 =  164 bits (418), Expect = 3e-53
 Identities = 29/137 (21%), Positives = 60/137 (43%), Gaps = 6/137 (4%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
            +   +  + + FAF+   +V++    +   DG  + G+ L++      +P         
Sbjct: 41  PVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPHDYQPL-----PGA 94

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
            KLF+G L   +  + + +    +G +    ++ D  +G S+GY F  Y      + A+ 
Sbjct: 95  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154

Query: 127 SLNGVELEGRAMRVSLA 143
            LNG++L  + + V  A
Sbjct: 155 GLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 82.7 bits (205), Expect = 6e-21
 Identities = 13/86 (15%), Positives = 39/86 (45%), Gaps = 6/86 (6%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVG-----ARVLYDGESGRSRGYGFVCYSTKAEME 122
           +L+VGN+ + +T E++   F     + G        +   +  + + + F+ + +  E  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 123 TALESLNGVELEGRAMRVSLAQGRRS 148
            A+   +G+  +G+++++      + 
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQP 90

>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 =  165 bits (420), Expect = 4e-53
 Identities = 29/153 (18%), Positives = 63/153 (41%), Gaps = 16/153 (10%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP--------- 57
            +   +  + + FAF+   +V++    +   DG  + G+ L++      +P         
Sbjct: 41  PVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPS 99

Query: 58  ------KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
                    +  ++  KLF+G L   +  + + +    +G +    ++ D  +G S+GY 
Sbjct: 100 VYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 159

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLAQ 144
           F  Y      + A+  LNG++L  + + V  A 
Sbjct: 160 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 192

>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 = 85.9 bits (213), Expect = 6e-22
 Identities = 13/85 (15%), Positives = 39/85 (45%), Gaps = 6/85 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVG-----ARVLYDGESGRSRGYGFVCYSTKAEME 122
           +L+VGN+ + +T E++   F     + G        +   +  + + + F+ + +  E  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 123 TALESLNGVELEGRAMRVSLAQGRR 147
            A+   +G+  +G+++++      +
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQ 89

>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 = 64.7 bits (158), Expect = 8e-14
 Identities = 12/48 (25%), Positives = 22/48 (45%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
           ++ D  TG S+G+AF     +   +  I  L+G +   + L V  +  
Sbjct: 146 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASV 193

>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 =  159 bits (405), Expect = 4e-51
 Identities = 33/137 (24%), Positives = 65/137 (47%), Gaps = 9/137 (6%)

Query: 10  DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKL 69
           D  TG +R F +V   + ED    +E L G +  G  +++    KPK +          L
Sbjct: 47  DVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE---KPKGRDSKKVRAARTL 102

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
              NLS+++T + L + F++   +         + G+S+G  ++ + ++A+ E  LE   
Sbjct: 103 LAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQ 157

Query: 130 GVELEGRAMRVSLAQGR 146
           G E++GR++ +     +
Sbjct: 158 GAEIDGRSVSLYYTGEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 99.6 bits (249), Expect = 1e-27
 Identities = 25/86 (29%), Positives = 46/86 (53%), Gaps = 2/86 (2%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           + T F LF+GNL+ + +   L  A  E        V+    +G +R +G+V + +  ++E
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLE 68

Query: 123 TALESLNGVELEGRAMRVSLAQGRRS 148
            ALE L G+++ G  +++   +GR S
Sbjct: 69  KALE-LTGLKVFGNEIKLEKPKGRDS 93

>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 = 63.8 bits (156), Expect = 1e-13
 Identities = 10/49 (20%), Positives = 23/49 (46%)

Query: 6   TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
            +    + G+S+G A++   +  D    +E   G E  GR + + ++ +
Sbjct: 125 EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173

>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 =  152 bits (387), Expect = 5e-47
 Identities = 30/139 (21%), Positives = 57/139 (41%), Gaps = 4/139 (2%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           ++Y   TG+S+G+ F      +       +L G+    R L V+++D  +    L     
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR- 185

Query: 67  FKLFVGNLSWSVT-TESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
             L V  L       ++L +A     +    ++    + G+ +G+  + Y T    E A 
Sbjct: 186 -CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEYETAEMAEEAQ 243

Query: 126 ESLNGVELEGRAMRVSLAQ 144
           +  +G+ L G  +RVS   
Sbjct: 244 QQADGLSLGGSHLRVSFCA 262

>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 =  151 bits (383), Expect = 2e-46
 Identities = 35/138 (25%), Positives = 52/138 (37%), Gaps = 11/138 (7%)

Query: 10  DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKL 69
                + +G AFVT+   E   A I          R L V               TD  L
Sbjct: 50  YCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL-----------QPTDALL 98

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
            V NL  S+T +   +  + +G++    ++Y   +G+S+GYGF  Y  K     A   L 
Sbjct: 99  CVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL 158

Query: 130 GVELEGRAMRVSLAQGRR 147
           G  L  R + V      +
Sbjct: 159 GKPLGPRTLYVHWTDAGQ 176

>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 = 78.5 bits (194), Expect = 1e-18
 Identities = 18/95 (18%), Positives = 33/95 (34%), Gaps = 11/95 (11%)

Query: 54  KPKPKLPLYAETDF----KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRG 109
           +   K   + E  F    K+ +  L   VT + +     +Y  +    V       + +G
Sbjct: 6   EEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKG 58

Query: 110 YGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ 144
             FV      + E A+ + +   L  R + V L  
Sbjct: 59  TAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP 93

>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 = 58.1 bits (141), Expect = 4e-11
 Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 1/52 (1%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           +    + G+ +GFA +   T E      +  DG    G  LRV+F     P 
Sbjct: 217 LACG-QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG 267

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score =  145 bits (369), Expect = 4e-45
 Identities = 38/140 (27%), Positives = 67/140 (47%), Gaps = 5/140 (3%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
           V  D  T RS G+A+V      D    ++ ++     G+ +R+ +S +            
Sbjct: 47  VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLR---KSGV 103

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             +F+ NL  S+  ++L   F  +GN++  +V+ D     S+GYGFV + T+   E A+E
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIE 161

Query: 127 SLNGVELEGRAMRVSLAQGR 146
            +NG+ L  R + V   + R
Sbjct: 162 KMNGMLLNDRKVFVGRFKSR 181

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 96.2 bits (240), Expect = 8e-26
 Identities = 26/85 (30%), Positives = 44/85 (51%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
                L+VG+L   VT   L + F   G ++  RV  D  + RS GY +V +   A+ E 
Sbjct: 13  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72

Query: 124 ALESLNGVELEGRAMRVSLAQGRRS 148
           AL+++N   ++G+ +R+  +Q   S
Sbjct: 73  ALDTMNFDVIKGKPVRIMWSQRDPS 97

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 48.4 bits (116), Expect = 8e-08
 Identities = 12/48 (25%), Positives = 19/48 (39%)

Query: 11  RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
            +   S+G+ FV   T E     IE ++G     R + V      K +
Sbjct: 137 CDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKER 184

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  138 bits (350), Expect = 8e-43
 Identities = 34/144 (23%), Positives = 73/144 (50%), Gaps = 14/144 (9%)

Query: 6   TVLYDRETGRSRGFAFVTMSTVEDCNAVIEN---LDGREYLGRILRVNFSDKPKPKLPLY 62
            ++ D  TGRSRGF F++       + V++    LDG+     ++    +  P+ +    
Sbjct: 34  KIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGK-----VIDPKRA-IPRDE---- 83

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
            +   K+FVG +   V  +   + F ++G ++ A+++ D ++G+SRG+GFV Y +   ++
Sbjct: 84  QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVD 143

Query: 123 TALESLNGVELEGRAMRVSLAQGR 146
              +    ++ + R + +  A+ R
Sbjct: 144 RVCQ-NKFIDFKDRKIEIKRAEPR 166

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 93.4 bits (233), Expect = 3e-25
 Identities = 23/85 (27%), Positives = 48/85 (56%), Gaps = 2/85 (2%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           +   K+F+G L+W  T ++L + F +YG V   +++ D  +GRSRG+GF+ +   + ++ 
Sbjct: 1   KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60

Query: 124 ALESLNGVELEGRAMRVSLAQGRRS 148
            +++ +   L+G+ +    A  R  
Sbjct: 61  VVKTQH--ILDGKVIDPKRAIPRDE 83

>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 =  140 bits (355), Expect = 2e-42
 Identities = 41/131 (31%), Positives = 56/131 (42%), Gaps = 13/131 (9%)

Query: 15  RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNL 74
           R RGF F+ + +          LDG     R LR+ F+                L V NL
Sbjct: 56  RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH-----------GAALTVKNL 104

Query: 75  SWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN-GVEL 133
           S  V+ E L QAF ++G V  A V+ D + GR+ G GFV ++ K     ALE    G  L
Sbjct: 105 SPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFL 163

Query: 134 EGRAMRVSLAQ 144
                R  + +
Sbjct: 164 LTTTPRPVIVE 174

>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 = 89.4 bits (222), Expect = 1e-22
 Identities = 28/102 (27%), Positives = 44/102 (43%), Gaps = 9/102 (8%)

Query: 43  LGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDG 102
           +G  + +    KP  K         +LFVGNL   +T E   + F+ YG      +    
Sbjct: 2   MGFTIDIKSFLKPGEKTY---TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN--- 55

Query: 103 ESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ 144
              R RG+GF+   ++   E A   L+G  L+ R +R+  A 
Sbjct: 56  ---RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT 94

>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 = 49.3 bits (118), Expect = 5e-08
 Identities = 10/54 (18%), Positives = 18/54 (33%), Gaps = 2/54 (3%)

Query: 6   TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL-GRILRVNFSDKPKPK 58
            V+ D + GR+ G  FV  +        +E      +L     R    +  +  
Sbjct: 127 VVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF 179

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score =  138 bits (349), Expect = 2e-42
 Identities = 37/142 (26%), Positives = 63/142 (44%), Gaps = 3/142 (2%)

Query: 6   TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD-KPKPKLPLYAE 64
            V+ D  T RSRGF FVT +TVE+ +A +      +  GR++    +  +   + P    
Sbjct: 44  VVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHL 102

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           T  K+FVG +        L   F++YG +    ++ D  SG+ RG+ FV +     ++  
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 162

Query: 125 LESLNGVELEGRAMRVSLAQGR 146
           +       + G    V  A  +
Sbjct: 163 VIQ-KYHTVNGHNCEVRKALSK 183

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 95.4 bits (238), Expect = 1e-25
 Identities = 34/97 (35%), Positives = 52/97 (53%), Gaps = 4/97 (4%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
           S    PK P   E   KLF+G LS+  T ESL   F+++G +    V+ D  + RSRG+G
Sbjct: 2   SKSESPKEP---EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 58

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRRS 148
           FV Y+T  E++ A+ +    +++GR +    A  R  
Sbjct: 59  FVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSRED 94

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  140 bits (356), Expect = 3e-42
 Identities = 34/144 (23%), Positives = 63/144 (43%), Gaps = 5/144 (3%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETD 66
            L       SR FA++ +++ ED    +E L+G +  G  L    S+  +      + T 
Sbjct: 149 RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATL 208

Query: 67  --FKLFVGNLSWSVTTE-SLTQAFQEYGNVVGARVLYDG-ESGRSRGYGFVCYSTKAEME 122
              ++ + NLS  +  E  L ++F+ +G++    +     E   +    F+ +  K   E
Sbjct: 209 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 268

Query: 123 TALESLNGVELEGRAMRVSLAQGR 146
            AL+ +N   L  R + VSLA  +
Sbjct: 269 RALQ-MNRSLLGNREISVSLADKK 291

>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 =  122 bits (307), Expect = 6e-35
 Identities = 22/134 (16%), Positives = 49/134 (36%), Gaps = 13/134 (9%)

Query: 11  RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLF 70
               ++  FA +  +  +   A I            + V+              T+  L+
Sbjct: 75  DSLKKNFRFARIEFARYDGALAAITKTHKVVG-QNEIIVS------------HLTECTLW 121

Query: 71  VGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNG 130
           + N   S T  ++    Q+   V  +  L       SR + ++  ++K +    +E LNG
Sbjct: 122 MTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNG 181

Query: 131 VELEGRAMRVSLAQ 144
           +++EG  +   ++ 
Sbjct: 182 LKIEGYTLVTKVSN 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 = 76.2 bits (188), Expect = 1e-17
 Identities = 13/104 (12%), Positives = 31/104 (29%), Gaps = 3/104 (2%)

Query: 44  GRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGE 103
           G       + K   +          + V NL  S     + + F+  G ++   V     
Sbjct: 19  GSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS-- 76

Query: 104 SGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
             ++  +  + ++       A+   + V +    + VS      
Sbjct: 77  LKKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSHLTECT 119

>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 =  126 bits (320), Expect = 2e-39
 Identities = 29/80 (36%), Positives = 55/80 (68%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           F LFVG+L+ +V  E+L  AF+++ + +   V++D ++G SRGYGFV ++++ + + A++
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 127 SLNGVELEGRAMRVSLAQGR 146
           S+ G +L GR +R++ A   
Sbjct: 62  SMQGQDLNGRPLRINWAAKL 81

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 67.9 bits (167), Expect = 3e-16
 Identities = 16/51 (31%), Positives = 33/51 (64%), Gaps = 1/51 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
          V++D +TG SRG+ FV+ ++ +D    ++++ G++  GR LR+N++     
Sbjct: 33 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA-AKLE 82

>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 =  126 bits (318), Expect = 6e-39
 Identities = 31/82 (37%), Positives = 51/82 (62%)

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           + F +FVG+LS  +TT ++  AF  +G +  ARV+ D  +G+S+GYGFV +  K + E A
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64

Query: 125 LESLNGVELEGRAMRVSLAQGR 146
           ++ + G  L GR +R + A  +
Sbjct: 65  IQQMGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 65.7 bits (161), Expect = 3e-15
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
          V+ D  TG+S+G+ FV+     D    I+ + G+   GR +R N++   KP
Sbjct: 38 VVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA-TRKP 87

>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 =  126 bits (320), Expect = 3e-38
 Identities = 40/144 (27%), Positives = 62/144 (43%), Gaps = 7/144 (4%)

Query: 5   LTVLYDRETG--RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLY 62
           + VL DR     +S+G  FVT  T +        L   + L  +       KP       
Sbjct: 33  INVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ-MKPADSEKNN 91

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A  D KLF+G +S   T   +   F  +G +   R+L     G SRG  FV ++T+A  +
Sbjct: 92  AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQ 150

Query: 123 TALESLNG---VELEGRAMRVSLA 143
           TA+++++    +E     M V  A
Sbjct: 151 TAIKAMHQAQTMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 79.2 bits (196), Expect = 1e-19
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESG--RSRGYGFVCYSTKAEMETAL 125
           K+FVG +  + + + L + F++YG V    VL D      +S+G  FV + T+     A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 126 ESLNGVELEGRAMRVSLAQ 144
            +L+ +++          +
Sbjct: 65  NALHNMKVLPGMHHPIQMK 83

>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 =  122 bits (307), Expect = 4e-37
 Identities = 32/86 (37%), Positives = 50/86 (58%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
               F +FVG+LS  +TTE +  AF  +G +  ARV+ D  +G+S+GYGFV +  K + E
Sbjct: 12  TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 71

Query: 123 TALESLNGVELEGRAMRVSLAQGRRS 148
            A++ + G  L GR +R + A  +  
Sbjct: 72  NAIQQMGGQWLGGRQIRTNWATRKPP 97

>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 = 66.2 bits (162), Expect = 3e-15
 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
          V+ D  TG+S+G+ FV+     D    I+ + G+   GR +R N++   KP  P
Sbjct: 47 VVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA-TRKPPAP 99

>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 =  121 bits (305), Expect = 1e-36
 Identities = 34/116 (29%), Positives = 53/116 (45%), Gaps = 3/116 (2%)

Query: 34  IENLDGREYLGRILRVNFSDKP--KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYG 91
           + ++ G + +GR       D            ET  KL V NL + V+   + + F E+G
Sbjct: 1   MASMTGGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG 60

Query: 92  NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
            +  A V YD  SGRS G   V +  +A+   A++   GV L+GR M + L   + 
Sbjct: 61  TLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 115

>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 = 64.3 bits (157), Expect = 2e-14
 Identities = 16/56 (28%), Positives = 21/56 (37%), Gaps = 1/56 (1%)

Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
           L K  V YDR +GRS G A V      D    ++   G    GR + +        
Sbjct: 62  LKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 116

>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 =  119 bits (300), Expect = 4e-36
 Identities = 32/97 (32%), Positives = 54/97 (55%)

Query: 50  NFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRG 109
           + +      L   +    +L+VG+L +++T + L   F+ +G +   +++ D E+GRS+G
Sbjct: 10  HMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKG 69

Query: 110 YGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
           YGF+ +S     + ALE LNG EL GR M+V     R
Sbjct: 70  YGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER 106

>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 = 72.3 bits (178), Expect = 1e-17
 Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
           ++ D ETGRS+G+ F+T S  E     +E L+G E  GR ++V      + 
Sbjct: 58  LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV-TERT 107

>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 =  117 bits (295), Expect = 2e-35
 Identities = 32/86 (37%), Positives = 49/86 (56%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A  + KLFVG LS+    +SL Q F +YG +    V+ D E+ RSRG+GFV +    + +
Sbjct: 9   ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68

Query: 123 TALESLNGVELEGRAMRVSLAQGRRS 148
            A+ ++NG  ++GR +RV  A     
Sbjct: 69  DAMMAMNGKSVDGRQIRVDQAGKSSD 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 = 74.2 bits (183), Expect = 2e-18
 Identities = 20/52 (38%), Positives = 30/52 (57%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          V+ DRET RSRGF FVT   ++D    +  ++G+   GR +RV+ + K    
Sbjct: 44 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 95

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score =  117 bits (296), Expect = 4e-35
 Identities = 28/96 (29%), Positives = 48/96 (50%)

Query: 48  RVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRS 107
            V+            A T   L+VG L+  V  + L  AF  +G++   ++  D E+ + 
Sbjct: 45  HVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKH 104

Query: 108 RGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
           RG+ FV +    +   A++++N  EL GR +RV+LA
Sbjct: 105 RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 72.1 bits (177), Expect = 3e-17
 Identities = 20/46 (43%), Positives = 27/46 (58%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
           +  D ET + RGFAFV     ED  A I+N++  E  GR +RVN +
Sbjct: 95  IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>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 =  117 bits (295), Expect = 4e-35
 Identities = 29/96 (30%), Positives = 46/96 (47%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
                       + +  L V  LS   T   L + F +YG +    ++YD +S RSRG+ 
Sbjct: 32  RGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 91

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
           FV +    + + A E  NG+EL+GR +RV  +  +R
Sbjct: 92  FVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 127

>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 = 77.1 bits (190), Expect = 3e-19
 Identities = 22/51 (43%), Positives = 32/51 (62%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
           ++YD+++ RSRGFAFV    V+D     E  +G E  GR +RV+FS   +P
Sbjct: 78  IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128

>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 =  116 bits (292), Expect = 6e-35
 Identities = 31/79 (39%), Positives = 47/79 (59%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L+VG+L +++T + L   F+ +G +    ++ D ++GRS+GYGF+ +S       ALE 
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 128 LNGVELEGRAMRVSLAQGR 146
           LNG EL GR MRV     R
Sbjct: 67  LNGFELAGRPMRVGHVTER 85

>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 = 74.5 bits (184), Expect = 1e-18
 Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
          ++ D +TGRS+G+ F+T S  E     +E L+G E  GR +RV      + 
Sbjct: 37 LMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV-TERL 86

>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 =  114 bits (289), Expect = 1e-34
 Identities = 27/82 (32%), Positives = 47/82 (57%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A T   L+VG L+  V  + L  AF  +G++   ++  D E+ + RG+ FV +    +  
Sbjct: 4   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

Query: 123 TALESLNGVELEGRAMRVSLAQ 144
            A++++N  EL GR +RV+LA+
Sbjct: 64  AAIDNMNESELFGRTIRVNLAK 85

>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 = 71.0 bits (175), Expect = 2e-17
 Identities = 20/44 (45%), Positives = 26/44 (59%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
          +  D ET + RGFAFV     ED  A I+N++  E  GR +RVN
Sbjct: 39 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 82

>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 =  115 bits (290), Expect = 1e-34
 Identities = 34/88 (38%), Positives = 49/88 (55%)

Query: 60  PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKA 119
           P    +   +FVGN+ +  T E L   F E G VV  R++YD E+G+ +GYGF  Y  + 
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 120 EMETALESLNGVELEGRAMRVSLAQGRR 147
              +A+ +LNG E  GRA+RV  A   +
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEK 89

>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 = 76.1 bits (188), Expect = 3e-19
 Identities = 21/52 (40%), Positives = 32/52 (61%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          ++YDRETG+ +G+ F      E   + + NL+GRE+ GR LRV+ +   K K
Sbjct: 40 LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNK 91

>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 =  114 bits (288), Expect = 2e-34
 Identities = 23/81 (28%), Positives = 45/81 (55%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A +   ++V NL +S+T   L + F +YG VV   ++ D ++ +S+G  F+ +  K   +
Sbjct: 13  APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72

Query: 123 TALESLNGVELEGRAMRVSLA 143
               ++N  +L GR ++ S+A
Sbjct: 73  NCTRAINNKQLFGRVIKASIA 93

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 75.3 bits (186), Expect = 6e-19
 Identities = 9/47 (19%), Positives = 26/47 (55%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          T++ D++T +S+G AF+     +        ++ ++  GR+++ + +
Sbjct: 47 TIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>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 =  114 bits (288), Expect = 2e-34
 Identities = 29/82 (35%), Positives = 44/82 (53%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
            + +  L V  LS   T   L + F +YG +    ++YD +S RSRG+ FV +    + +
Sbjct: 12  PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAK 71

Query: 123 TALESLNGVELEGRAMRVSLAQ 144
            A E  NG+EL+GR +RVS   
Sbjct: 72  EAKERANGMELDGRRIRVSGPS 93

>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 = 73.4 bits (181), Expect = 3e-18
 Identities = 19/46 (41%), Positives = 28/46 (60%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          ++YD+++ RSRGFAFV    V+D     E  +G E  GR +RV+  
Sbjct: 47 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP 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 =  114 bits (287), Expect = 3e-34
 Identities = 26/92 (28%), Positives = 47/92 (51%), Gaps = 2/92 (2%)

Query: 57  PKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYS 116
           P     + T F LF+GNL+ + +   L  A  E        V+ D  +G +R +G+V + 
Sbjct: 8   PVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFE 66

Query: 117 TKAEMETALESLNGVELEGRAMRVSLAQGRRS 148
           +  ++E ALE L G+++ G  +++   +GR  
Sbjct: 67  SAEDLEKALE-LTGLKVFGNEIKLEKPKGRDG 97

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 60.0 bits (146), Expect = 5e-13
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 2/52 (3%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           + D  TG +R F +V   + ED    +E L G +  G  +++    K +  
Sbjct: 48 AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP-KGRDG 97

>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 =  114 bits (287), Expect = 4e-34
 Identities = 28/86 (32%), Positives = 48/86 (55%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A T   L+VG L+  V  + L  AF  +G++   ++  D E+ + RG+ FV +    +  
Sbjct: 9   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68

Query: 123 TALESLNGVELEGRAMRVSLAQGRRS 148
            A++++N  EL GR +RV+LA+  R 
Sbjct: 69  AAIDNMNESELFGRTIRVNLAKPMRI 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 = 74.2 bits (183), Expect = 2e-18
 Identities = 21/52 (40%), Positives = 29/52 (55%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          +  D ET + RGFAFV     ED  A I+N++  E  GR +RVN +   + K
Sbjct: 44 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK 95

>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 =  115 bits (290), Expect = 5e-34
 Identities = 32/144 (22%), Positives = 60/144 (41%), Gaps = 13/144 (9%)

Query: 17  RGFAFVTMSTVE-----DCNAVIENLDGREYLGRILRVNFSDKPKPKL--------PLYA 63
            G      +T E         V +       +      + + K              +  
Sbjct: 8   NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           E    L V NL++  + ++L + F++YG V    +  D  +  SRG+ FV +  K + E 
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127

Query: 124 ALESLNGVELEGRAMRVSLAQGRR 147
           A+++++G  L+GR +RV +A+  R
Sbjct: 128 AMDAMDGAVLDGRELRVQMARYGR 151

>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 = 74.9 bits (184), Expect = 4e-18
 Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
           +  DR T  SRGFAFV      D    ++ +DG    GR LRV  + +      
Sbjct: 102 IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA-RYGRPPD 154

>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 =  112 bits (283), Expect = 2e-33
 Identities = 32/82 (39%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
            ET  KL V NL + V+   + + F E+G +  A V YD  SGRS G   V +  KA+  
Sbjct: 26  VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADAL 84

Query: 123 TALESLNGVELEGRAMRVSLAQ 144
            A++  NGV L+GR M + L  
Sbjct: 85  KAMKQYNGVPLDGRPMNIQLVT 106

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 62.7 bits (153), Expect = 7e-14
 Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
           L K  V YDR +GRS G A V      D    ++  +G    GR + +  
Sbjct: 56  LKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 104

>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 =  113 bits (284), Expect = 3e-33
 Identities = 25/94 (26%), Positives = 47/94 (50%)

Query: 55  PKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVC 114
           P  ++    +    L V  +  +V    L Q F+ YG +   +++ D E+ +SRGYGFV 
Sbjct: 31  PPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVK 90

Query: 115 YSTKAEMETALESLNGVELEGRAMRVSLAQGRRS 148
           + + +  + A+  LNG  +  + ++V+LA     
Sbjct: 91  FQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ 124

>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 = 72.1 bits (177), Expect = 3e-17
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAET- 65
           ++ DRET +SRG+ FV   +       I  L+G   L + L+V  +     + P  A   
Sbjct: 74  IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA-ASGHQRPGIAGAV 132

Query: 66  -DFKLFV 71
            D   ++
Sbjct: 133 GDGNGYL 139

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score =  112 bits (282), Expect = 8e-33
 Identities = 30/109 (27%), Positives = 48/109 (44%), Gaps = 9/109 (8%)

Query: 47  LRVNFSDKPKPKLPLYAETD-------FKLFVGNLSWSVTTESLTQAFQEYG--NVVGAR 97
           +R   S KP  K P    T          ++VG+ SW  T + L Q  +  G  +VV  +
Sbjct: 29  VRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELK 88

Query: 98  VLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
              +  +G+S+GY  V  +++  +   LE L G  L G  + V  A  +
Sbjct: 89  FAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ 137

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 71.9 bits (176), Expect = 5e-17
 Identities = 11/49 (22%), Positives = 25/49 (51%)

Query: 6   TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
               +R  G+S+G+A V +++    + ++E L G+   G  + V  + +
Sbjct: 88  KFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATR 136

>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 =  110 bits (278), Expect = 1e-32
 Identities = 27/84 (32%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
                 +FV NL + V  + L + F   G VV A +L D + G+SRG G V +    E  
Sbjct: 12  GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAV 70

Query: 123 TALESLNGVELEGRAMRVSLAQGR 146
            A+   NG  L  R M V + +  
Sbjct: 71  QAISMFNGQLLFDRPMHVKMDERA 94

>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 = 60.8 bits (148), Expect = 4e-13
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          +L D++ G+SRG   VT     +    I   +G+    R + V   ++  PK
Sbjct: 47 ILEDKD-GKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPK 97

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score =  109 bits (276), Expect = 2e-32
 Identities = 23/84 (27%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVV-GARVLYDGESGRSRGYGFVCYSTKAEMETA 124
              +F+GNL   +  + L   F  +G ++   +++ D ++G S+GY F+ +++    + A
Sbjct: 5   SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64

Query: 125 LESLNGVELEGRAMRVSLAQGRRS 148
           +E++NG  L  R + VS A  + S
Sbjct: 65  IEAMNGQYLCNRPITVSYAFKKDS 88

>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 = 63.0 bits (154), Expect = 4e-14
 Identities = 16/58 (27%), Positives = 34/58 (58%)

Query: 1  MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          +L    ++ D +TG S+G+AF+  ++ +  +A IE ++G+    R + V+++ K   K
Sbjct: 32 ILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK 89

>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 =  109 bits (276), Expect = 2e-32
 Identities = 28/80 (35%), Positives = 47/80 (58%), Gaps = 2/80 (2%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             L+V NL   +  E L +AF  +G +  A+V+ +   GRS+G+GFVC+S+  E   A+ 
Sbjct: 16  VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVT 73

Query: 127 SLNGVELEGRAMRVSLAQGR 146
            +NG  +  + + V+LAQ +
Sbjct: 74  EMNGRIVATKPLYVALAQRK 93

>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 = 58.8 bits (143), Expect = 2e-12
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 11 RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
           E GRS+GF FV  S+ E+    +  ++GR    + L V  + + K 
Sbjct: 49 MEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA-QRKE 94

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  110 bits (277), Expect = 2e-32
 Identities = 22/101 (21%), Positives = 46/101 (45%), Gaps = 2/101 (1%)

Query: 44  GRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGE 103
              L    +     ++         LF+ +L    T   L   F  +GNV+ A+V  D +
Sbjct: 20  SVALSAAAAAAAGKQIEGPEGC--NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQ 77

Query: 104 SGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ 144
           +  S+ +GFV +      + A++++NG ++  + ++V L +
Sbjct: 78  TSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 63.9 bits (156), Expect = 3e-14
 Identities = 11/45 (24%), Positives = 22/45 (48%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
           V  D++T  S+ F FV+    +     I+ ++G +   + L+V  
Sbjct: 72  VFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL 116

>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 =  109 bits (275), Expect = 2e-32
 Identities = 18/81 (22%), Positives = 42/81 (51%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            +++G++ +  T E +       G V+  ++++D ++GRS+GY F+ +       +A+ +
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           LNG +L  R ++   +     
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDI 84

>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 = 73.4 bits (181), Expect = 3e-18
 Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          +++D +TGRS+G+AF+    +E   + + NL+G +   R L+  +S      
Sbjct: 34 MMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS-SNSDI 84

>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 =  109 bits (275), Expect = 3e-32
 Identities = 24/84 (28%), Positives = 47/84 (55%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           +    L V NL++  + +SL + F++YG V    +  +  +   RG+ FV +  + + + 
Sbjct: 11  DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQD 70

Query: 124 ALESLNGVELEGRAMRVSLAQGRR 147
           A  +++G EL+GR +RV +A+  R
Sbjct: 71  AEAAMDGAELDGRELRVQVARYGR 94

>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 = 74.6 bits (184), Expect = 1e-18
 Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 1/54 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
          +  +  T   RGFAFV      D       +DG E  GR LRV  + +   +  
Sbjct: 45 IPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA-RYGRRDL 97

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score =  108 bits (273), Expect = 6e-32
 Identities = 23/85 (27%), Positives = 46/85 (54%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
             D  ++VG L   V+   L + F + G VV   +  D  +G+ +GYGFV + ++ + + 
Sbjct: 13  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72

Query: 124 ALESLNGVELEGRAMRVSLAQGRRS 148
           A++ ++ ++L G+ +RV+ A     
Sbjct: 73  AIKIMDMIKLYGKPIRVNKASAHNK 97

>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 = 69.6 bits (171), Expect = 1e-16
 Identities = 16/54 (29%), Positives = 28/54 (51%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
           +  DR TG+ +G+ FV   + ED +  I+ +D  +  G+ +RVN +      L 
Sbjct: 47  MPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLS 100

>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 =  108 bits (273), Expect = 6e-32
 Identities = 23/85 (27%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A+   KLF+G L+     + L   F ++G +    ++ D  + +SRG+ F+ +   A+ +
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAK 62

Query: 123 TALESLNGVELEGRAMRVSLAQGRR 147
            A + +NG  L G+A++V  A+   
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAKKPS 87

>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 = 65.0 bits (159), Expect = 1e-14
 Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          ++ DR T +SRGFAF+T     D     ++++G+   G+ ++V  + KP  +
Sbjct: 39 LIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQ 89

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score =  108 bits (272), Expect = 6e-32
 Identities = 26/81 (32%), Positives = 38/81 (46%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           + LFV  +    T E +   F EYG +    +  D  +G  +GY  V Y T  E + A+E
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 127 SLNGVELEGRAMRVSLAQGRR 147
            LNG +L G+ + V     R 
Sbjct: 84  GLNGQDLMGQPISVDWCFVRG 104

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 74.6 bits (184), Expect = 2e-18
 Identities = 13/51 (25%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
           +  DR TG  +G+  V   T ++  A +E L+G++ +G+ + V++    + 
Sbjct: 55  LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC-FVRG 104

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score =  109 bits (274), Expect = 7e-32
 Identities = 26/81 (32%), Positives = 48/81 (59%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             L V NL++  + ++L + F++YG V    +  D  +  SRG+ FV +  K + E A++
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107

Query: 127 SLNGVELEGRAMRVSLAQGRR 147
           +++G  L+GR +RV +A+  R
Sbjct: 108 AMDGAVLDGRELRVQMARYGR 128

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 76.3 bits (188), Expect = 7e-19
 Identities = 19/52 (36%), Positives = 25/52 (48%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           +  DR T  SRGFAFV      D    ++ +DG    GR LRV  +   +P 
Sbjct: 79  IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 130

>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 =  108 bits (272), Expect = 8e-32
 Identities = 24/79 (30%), Positives = 44/79 (55%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            LF+ +L      + L Q F  +GNVV A+V  D ++  S+ +GFV Y      + A++S
Sbjct: 27  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86

Query: 128 LNGVELEGRAMRVSLAQGR 146
           +NG ++  + ++V L + +
Sbjct: 87  MNGFQIGMKRLKVQLKRSK 105

>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 = 62.3 bits (152), Expect = 1e-13
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
           V  D++T  S+ F FV+        A I++++G +   + L+V    + K
Sbjct: 57  VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK-RSK 105

>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 =  108 bits (271), Expect = 9e-32
 Identities = 29/93 (31%), Positives = 42/93 (45%), Gaps = 1/93 (1%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
           S       P   E D  +FVGNL   V  E L + F + G +    +  D   G+ + +G
Sbjct: 2   SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFG 60

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLAQ 144
           FVC+     +  A+  LNG+ L GR + VS   
Sbjct: 61  FVCFKHPESVSYAIALLNGIRLYGRPINVSGPS 93

>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 = 60.0 bits (146), Expect = 6e-13
 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
          T+  DRE G+ + F FV     E  +  I  L+G    GR + V+  
Sbjct: 47 TICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP 92

>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 =  108 bits (271), Expect = 1e-31
 Identities = 27/81 (33%), Positives = 48/81 (59%), Gaps = 4/81 (4%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L + NLS+S T E+L + F++   +     +   ++G+S+GY F+ +++  + + AL S
Sbjct: 17  TLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEALNS 72

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
            N  E+EGRA+R+ L   R S
Sbjct: 73  CNKREIEGRAIRLELQGPRGS 93

>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 = 71.2 bits (175), Expect = 3e-17
 Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           +   + G+S+G+AF+  ++ ED    + + + RE  GR +R+     P+  
Sbjct: 43 KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ-GPRGS 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 =  107 bits (269), Expect = 1e-31
 Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 2/82 (2%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYG--NVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
             L++GNL+W  T E LT+A    G  +++  +   +  +G+S+G+  V   ++A  +  
Sbjct: 2   IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61

Query: 125 LESLNGVELEGRAMRVSLAQGR 146
           ++ L   EL G+   V+ +   
Sbjct: 62  MDLLPKRELHGQNPVVTPSNKL 83

>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 = 73.0 bits (180), Expect = 4e-18
 Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLY 62
              +R  G+S+GFA V + +      +++ L  RE  G+   V  S         +
Sbjct: 34 KFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPS-NKLEHHHHH 89

>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 =  107 bits (269), Expect = 2e-31
 Identities = 25/84 (29%), Positives = 49/84 (58%), Gaps = 3/84 (3%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           ++    LFV  LS   T E+L ++F      V AR++ D E+G S+G+GFV ++++ + +
Sbjct: 12  SQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDAK 68

Query: 123 TALESLNGVELEGRAMRVSLAQGR 146
            A E++   E++G  + +  A+ +
Sbjct: 69  AAKEAMEDGEIDGNKVTLDWAKPK 92

>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 = 75.0 bits (185), Expect = 9e-19
 Identities = 19/52 (36%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          ++ DRETG S+GF FV  ++ ED  A  E ++  E  G  + ++++ KPK +
Sbjct: 44 IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA-KPKGE 94

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score =  107 bits (269), Expect = 2e-31
 Identities = 19/81 (23%), Positives = 45/81 (55%), Gaps = 1/81 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLF+  L +S T E L +  + +G V   R++ +  +G+ +G  +V Y  +++   A+  
Sbjct: 19  KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVMK 77

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           ++G+ ++   ++V+++    S
Sbjct: 78  MDGMTIKENIIKVAISNSGPS 98

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 70.0 bits (172), Expect = 7e-17
 Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 2/52 (3%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          ++ +R  G+ +G A+V        +  +  +DG      I++V  S    P 
Sbjct: 49 LVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS-NSGPS 98

>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 =  106 bits (268), Expect = 2e-31
 Identities = 25/81 (30%), Positives = 48/81 (59%), Gaps = 1/81 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            ++VGNL +S T+E + + F ++G V   +++YD E+ + +G+GFV       +  A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           L+  +  GR +RV+ A  ++S
Sbjct: 62  LDNTDFMGRTIRVTEANPKKS 82

>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 = 71.4 bits (176), Expect = 1e-17
 Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
          ++YDRET + +GF FV M   E  +  I  LD  +++GR +RV  +  PK  L 
Sbjct: 33 LIYDRETKKPKGFGFVEMQE-ESVSEAIAKLDNTDFMGRTIRVTEA-NPKKSLE 84

>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 =  106 bits (266), Expect = 4e-31
 Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYD-GESGRSRGYGFVCYSTKAEMETALE 126
           K+ +G L+ +VT + + + F  YG +    +  +      S+GY +V +    E E AL+
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 127 SLNGVELEGRAMRVSLAQGRR 147
            ++G +++G+ +  +      
Sbjct: 66  HMDGGQIDGQEITATAVLAPW 86

>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 = 68.7 bits (169), Expect = 2e-16
 Identities = 10/53 (18%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 7  VLYDR-ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          +  +R     S+G+A+V     ++    ++++DG +  G+ +       P P+
Sbjct: 36 MPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWPR 88

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score =  108 bits (272), Expect = 4e-31
 Identities = 30/85 (35%), Positives = 44/85 (51%), Gaps = 1/85 (1%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
            ET  KL V NL + V+   + + F E+G +  A V YD  SGRS G   V +  +A+  
Sbjct: 85  VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADAL 143

Query: 123 TALESLNGVELEGRAMRVSLAQGRR 147
            A++   GV L+GR M + L   + 
Sbjct: 144 KAMKQYKGVPLDGRPMDIQLVASQI 168

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 61.4 bits (149), Expect = 8e-13
 Identities = 16/56 (28%), Positives = 21/56 (37%), Gaps = 1/56 (1%)

Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
           L K  V YDR +GRS G A V      D    ++   G    GR + +        
Sbjct: 115 LKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 169

>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 =  106 bits (266), Expect = 6e-31
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYD---GESGRSRGYGFVCYSTKAEMETA 124
            LF+ NL++S T E+L   F + G +    +           S G+GFV Y    + + A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 125 LESLNGVELEGRAMRVSLAQGR 146
           L+ L G  ++G  + V +++  
Sbjct: 67  LKQLQGHTVDGHKLEVRISERA 88

>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 = 59.2 bits (144), Expect = 1e-12
 Identities = 14/56 (25%), Positives = 19/56 (33%), Gaps = 4/56 (7%)

Query: 6  TVLYDRETG---RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          T+   +       S GF FV     E     ++ L G    G  L V  S +   K
Sbjct: 36 TISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS-ERATK 90

>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 =  105 bits (265), Expect = 9e-31
 Identities = 25/98 (25%), Positives = 44/98 (44%)

Query: 50  NFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRG 109
           N  D      P  +   + LFV ++      + + + F +YG +    +  D  +G S+G
Sbjct: 10  NEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG 69

Query: 110 YGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
           Y  V Y T  +   A E+LNG E+ G+ ++V     + 
Sbjct: 70  YALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 107

>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 = 73.9 bits (182), Expect = 3e-18
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           +  DR TG S+G+A V   T +   A  E L+G E +G+ ++V++     PK
Sbjct: 58  LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK 109

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score =  105 bits (264), Expect = 1e-30
 Identities = 25/101 (24%), Positives = 48/101 (47%), Gaps = 6/101 (5%)

Query: 54  KPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFV 113
                LP        +F+ NLS+    E+L +  Q++G++   RV+   ++  S+G  F 
Sbjct: 3   SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 62

Query: 114 CYSTKAEMETALESLN------GVELEGRAMRVSLAQGRRS 148
            + T+   +  L + +      G++L+GR ++V LA  R  
Sbjct: 63  QFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 63.5 bits (155), Expect = 4e-14
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 7/57 (12%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLD------GREYLGRILRVNFSDKPKP 57
           V+   +T  S+G AF    T E     +          G +  GR L+V+ +   + 
Sbjct: 47  VVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA-VTRD 102

>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 =  104 bits (262), Expect = 2e-30
 Identities = 17/77 (22%), Positives = 37/77 (48%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L++  L    T + L +  Q YG +V  + + D  + + +GYGFV + + +  + A+ +
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 128 LNGVELEGRAMRVSLAQ 144
           L    ++ +  + S   
Sbjct: 67  LKASGVQAQMAKQSGPS 83

>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 = 64.9 bits (159), Expect = 5e-15
 Identities = 6/44 (13%), Positives = 17/44 (38%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
           + D+ T + +G+ FV   +       +  L       ++ + +
Sbjct: 37 AILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQS 80

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score =  108 bits (271), Expect = 2e-30
 Identities = 22/97 (22%), Positives = 44/97 (45%), Gaps = 2/97 (2%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYG--NVVGARVLYDGESGRSRG 109
                  +  Y      L++GNL+W  T E LT+A    G  +++  +   +  +G+S+G
Sbjct: 54  KGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG 113

Query: 110 YGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
           +  V   ++A  +  ++ L   EL G+   V+    +
Sbjct: 114 FALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ 150

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 69.4 bits (169), Expect = 2e-15
 Identities = 13/57 (22%), Positives = 26/57 (45%)

Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           + ++    +R  G+S+GFA V + +      +++ L  RE  G+   V   +K    
Sbjct: 97  ILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLS 153

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  104 bits (261), Expect = 3e-30
 Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 2/79 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +L V N+ +      L Q F ++G ++   ++++     S+G+GFV +   A+ + A E 
Sbjct: 31  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREK 88

Query: 128 LNGVELEGRAMRVSLAQGR 146
           L+G  +EGR + V+ A  R
Sbjct: 89  LHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 61.2 bits (149), Expect = 3e-13
 Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 3/51 (5%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
           ++++     S+GF FVT     D +   E L G    GR + VN +   + 
Sbjct: 61  IIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA-TARV 108

>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 =  103 bits (260), Expect = 4e-30
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 2/80 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +L V N+ +      L Q F ++G ++   ++++     S+G+GFV +   A+ + A E 
Sbjct: 17  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREK 74

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           L+G  +EGR + V+ A  R 
Sbjct: 75  LHGTVVEGRKIEVNNATARV 94

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 61.9 bits (151), Expect = 1e-13
 Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 3/52 (5%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          ++++     S+GF FVT     D +   E L G    GR + VN +   +  
Sbjct: 47 IIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA-TARVM 95

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score =  103 bits (259), Expect = 4e-30
 Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 2/79 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++FV NL +  T + L   F E G+V+ A +  +  +G+S+G G V + +    E A   
Sbjct: 10  QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRM 67

Query: 128 LNGVELEGRAMRVSLAQGR 146
           +NG++L GR + V + +  
Sbjct: 68  MNGMKLSGREIDVRIDRNA 86

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 59.9 bits (146), Expect = 4e-13
 Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 1/50 (2%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS-DKPKPK 58
            E G+S+G   V   + E        ++G +  GR + V    +   P 
Sbjct: 41 KMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGPS 90

>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 =  104 bits (262), Expect = 5e-30
 Identities = 29/96 (30%), Positives = 41/96 (42%), Gaps = 1/96 (1%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
            D  +P      E    LFV  +    T E +   F EYG +    +  D  +G  +GY 
Sbjct: 9   QDGDEPGPQRSVEGW-ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 67

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
            V Y T  E + A+E LNG +L G+ + V     R 
Sbjct: 68  LVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG 103

>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 = 72.0 bits (177), Expect = 2e-17
 Identities = 13/58 (22%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 3   SKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
             + +  DR TG  +G+  V   T ++  A +E L+G++ +G+ + V++    +    
Sbjct: 50  KNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC-FVRGPPK 106

>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 =  103 bits (258), Expect = 7e-30
 Identities = 18/80 (22%), Positives = 41/80 (51%), Gaps = 5/80 (6%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L   NLS+++T + L + F++   +         + G+S+G  ++ + ++A+ E  LE 
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 128 LNGVELEGRAMRVSLAQGRR 147
             G E++GR++ +     + 
Sbjct: 73  KQGAEIDGRSVSLYYTGEKG 92

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 68.1 bits (167), Expect = 3e-16
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          +    + G+S+G A++   +  D    +E   G E  GR + + ++   K  
Sbjct: 43 IRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT-GEKGG 93

>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 =  103 bits (258), Expect = 8e-30
 Identities = 20/80 (25%), Positives = 38/80 (47%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFV NLS++ + E L + F  YG +       D  + + +G+ FV +        A   
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           ++G   +GR + V  +  ++
Sbjct: 70  VDGQVFQGRMLHVLPSTIKK 89

>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 = 70.7 bits (174), Expect = 3e-17
 Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
          LS+L    D  T + +GFAFVT    E        +DG+ + GR+L V  S   K +  
Sbjct: 35 LSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS-TIKKEAS 92

>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 =  103 bits (259), Expect = 8e-30
 Identities = 21/80 (26%), Positives = 37/80 (46%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L++ NLS  VT   L   F  +    G  + +   +GR RG  F+ +  K     AL  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           +NG +L G+ + +   + ++
Sbjct: 87  VNGYKLYGKILVIEFGKNKK 106

>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 = 68.1 bits (167), Expect = 5e-16
 Identities = 15/54 (27%), Positives = 25/54 (46%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
           + +   TGR RG AF+T    E     +  ++G +  G+IL + F    K +  
Sbjct: 57  IQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSS 110

>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 =  102 bits (256), Expect = 2e-29
 Identities = 16/81 (19%), Positives = 37/81 (45%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             + V NLS       L + F+ +G++    +  D  +G+S+G+ F+ +  + +   A+ 
Sbjct: 16  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75

Query: 127 SLNGVELEGRAMRVSLAQGRR 147
            ++G   +   + V  A+   
Sbjct: 76  GVSGFGYDHLILNVEWAKPST 96

>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 = 77.3 bits (191), Expect = 1e-19
 Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 2  LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
          +S++ +  D+ TG+S+GFAF++    ED    I  + G  Y   IL V ++ KP  
Sbjct: 42 ISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA-KPST 96

>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 =  103 bits (259), Expect = 3e-29
 Identities = 24/96 (25%), Positives = 43/96 (44%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
            D      P  +   + LFV ++      + + + F +YG +    +  D  +G S+GY 
Sbjct: 58  DDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA 117

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
            V Y T  +   A E+LNG E+ G+ ++V     + 
Sbjct: 118 LVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 153

>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 = 72.9 bits (179), Expect = 3e-17
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           +  DR TG S+G+A V   T +   A  E L+G E +G+ ++V++     PK
Sbjct: 104 LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK 155

>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 =  102 bits (256), Expect = 3e-29
 Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 3/98 (3%)

Query: 47  LRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGR 106
           L+ +       K      T   L++ NL  S+  + L    + +G V+  R+L D  SG 
Sbjct: 8   LKASGVQAQMAKQQEQDPT--NLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGT 64

Query: 107 SRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ 144
           SRG GF    +  + E  +   NG  ++      +  +
Sbjct: 65  SRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 102

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 58.4 bits (142), Expect = 3e-12
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 1/46 (2%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
           +L D  +G SRG  F  M + E C AVI + +G+           +
Sbjct: 57  ILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT 101

>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 =  101 bits (254), Expect = 4e-29
 Identities = 26/80 (32%), Positives = 45/80 (56%), Gaps = 2/80 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            +F+ NL  S+  ++L   F  +GN++  +V+ D     S+GYGFV + T+   E A+E 
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 64

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           +NG+ L  R + V   + R+
Sbjct: 65  MNGMLLNDRKVFVGRFKSRK 84

>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 = 64.6 bits (158), Expect = 1e-14
 Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 3/77 (3%)

Query: 11  RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFK-- 68
            +   S+G+ FV   T E     IE ++G     R + V      K +         +  
Sbjct: 39  CDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFT 98

Query: 69  -LFVGNLSWSVTTESLT 84
            +++ N     T  + +
Sbjct: 99  NVYIKNFGPGSTRAAAS 115

>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 = 99.9 bits (250), Expect = 1e-28
 Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            ++VGN+ +  T E L   F   G+V    +L D  SG  +G+ ++ +S K  + T+L  
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA- 66

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           L+     GR ++V   +  R
Sbjct: 67  LDESLFRGRQIKVIPKRTNR 86

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 66.8 bits (164), Expect = 1e-15
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
          T+L D+ +G  +GFA++  S  E     +  LD   + GR ++V      +P
Sbjct: 37 TILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLFRGRQIKVIPKRTNRP 87

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 99.3 bits (248), Expect = 4e-28
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 3/83 (3%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLF+G +  ++  + L   F+E+G +    VL D  +G  +G  F+ Y  +     A  +
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74

Query: 128 LNG---VELEGRAMRVSLAQGRR 147
           L+    +    R ++V  A    
Sbjct: 75  LHEQKTLPGMNRPIQVKPADSES 97

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 66.2 bits (162), Expect = 2e-15
 Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 3/57 (5%)

Query: 5  LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL---GRILRVNFSDKPKPK 58
          LTVL DR TG  +G AF+T    E        L  ++ L    R ++V  +D     
Sbjct: 43 LTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRG 99

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 98.9 bits (247), Expect = 4e-28
 Identities = 29/85 (34%), Positives = 50/85 (58%), Gaps = 3/85 (3%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQE-YGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           ++ LFVG+L+  V    L + F + Y +  G +V+ D ++G S+GYGFV ++ + E + A
Sbjct: 9   EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRA 67

Query: 125 LESLNG-VELEGRAMRVSLAQGRRS 148
           L    G V L  + +R+S+A  + S
Sbjct: 68  LTECQGAVGLGSKPVRLSVAIPKAS 92

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 43.4 bits (103), Expect = 1e-06
 Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 2/53 (3%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG-RILRVNFSDKPKPK 58
          V+ D +TG S+G+ FV  +   +    +    G   LG + +R++ +     +
Sbjct: 42 VVLD-QTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASR 93

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 98.5 bits (246), Expect = 7e-28
 Identities = 22/97 (22%), Positives = 37/97 (38%), Gaps = 1/97 (1%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
             +P   L         +F   L+  +    L   F   G V   R++ D  S RS+G  
Sbjct: 11  VREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIA 70

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRRS 148
           +V +     +  A+  L G  L G  + V  +Q  ++
Sbjct: 71  YVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKN 106

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 65.0 bits (159), Expect = 8e-15
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 6   TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
            ++ DR + RS+G A+V    ++     I  L G+  LG  + V  S   K +L 
Sbjct: 56  RIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNRLS 109

>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 =   99 bits (249), Expect = 2e-27
 Identities = 31/163 (19%), Positives = 54/163 (33%), Gaps = 35/163 (21%)

Query: 15  RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFK------ 68
             +  A V M+        + +L+G +  G+ +R+  S     +LP   + D        
Sbjct: 39  NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYG 98

Query: 69  ------------------------LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGES 104
                                   L + N+  SV+ E L   F   G VV     +    
Sbjct: 99  NSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ--- 155

Query: 105 GRSRGYGFVCYSTKAEMETALESLNGVEL-EGRAMRVSLAQGR 146
            + R    +   +  E   AL  L+  +L E   +RVS ++  
Sbjct: 156 -KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197

>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 = 78.0 bits (192), Expect = 6e-19
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 69  LFVGNLS-WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           L V NL+   VT +SL   F  YG+V   ++L++      +    V  +   + + A+  
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60

Query: 128 LNGVELEGRAMRVSLA 143
           LNG +L G+ +R++L+
Sbjct: 61  LNGHKLHGKPIRITLS 76

>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 = 43.0 bits (101), Expect = 6e-06
 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 1/50 (2%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL-GRILRVNFSDKP 55
           V   +   + R  A + M +VE+    + +L   +      LRV+FS   
Sbjct: 148 VKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 97.4 bits (243), Expect = 2e-27
 Identities = 30/79 (37%), Positives = 47/79 (59%), Gaps = 1/79 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG L +  T  SL + F+ +G++  A V+ D ++G+SRGYGFV  + +A  E A + 
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78

Query: 128 LNGVELEGRAMRVSLAQGR 146
            N   ++GR   V+LA   
Sbjct: 79  PNP-IIDGRKANVNLAYLG 96

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 61.9 bits (151), Expect = 2e-13
 Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 6   TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF-SDKPKPKLPLYAE 64
            V+ DR+TG+SRG+ FVTM+         ++ +     GR   VN      KP+     +
Sbjct: 48  VVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPRSL---Q 103

Query: 65  TDFKLFVGNLS 75
           T F + V   S
Sbjct: 104 TGFAIGVSGPS 114

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 98.3 bits (245), Expect = 3e-27
 Identities = 24/81 (29%), Positives = 42/81 (51%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L+VGNLS+  T E + + F + G++    +  D     + G+ FV Y ++A+ E A+  
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           +NG  L+ R +R     G + 
Sbjct: 101 INGTRLDDRIIRTDWDAGFKE 121

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 61.0 bits (148), Expect = 7e-13
 Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
           + K+ +  D+    + GF FV   +  D    +  ++G     RI+R ++ D    
Sbjct: 66  IKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW-DAGFK 120

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 96.2 bits (240), Expect = 4e-27
 Identities = 21/96 (21%), Positives = 46/96 (47%), Gaps = 2/96 (2%)

Query: 53  DKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGF 112
                   L  E  +  +VGNL ++     +   F++   +   R++ D ++ + +G+ +
Sbjct: 2   SSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCY 60

Query: 113 VCYSTKAEMETALESLNGVELEGRAMRVSLAQGRRS 148
           V +     ++ AL   +G  L  R++RV +A+GR+ 
Sbjct: 61  VEFDEVDSLKEALT-YDGALLGDRSLRVDIAEGRKQ 95

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 63.4 bits (155), Expect = 3e-14
 Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
          ++ D++T + +GF +V    V+     +   DG     R LRV+ ++  K 
Sbjct: 46 LVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQ 95

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 97.1 bits (242), Expect = 4e-27
 Identities = 17/80 (21%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            ++VGN+ +  T + L   F   G++    +L D  SG  +GY ++ ++ +  ++ A+  
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA- 96

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           ++     GR ++V   +   
Sbjct: 97  MDETVFRGRTIKVLPKRTNM 116

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 64.7 bits (158), Expect = 2e-14
 Identities = 14/65 (21%), Positives = 35/65 (53%), Gaps = 4/65 (6%)

Query: 2   LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPL 61
           ++++T+L D+ +G  +G+A++  +     +A +  +D   + GR ++V      +  +P 
Sbjct: 63  INRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVL---PKRTNMPG 118

Query: 62  YAETD 66
            + TD
Sbjct: 119 ISSTD 123

>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 = 95.8 bits (239), Expect = 6e-27
 Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 8/84 (9%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGA--------RVLYDGESGRSRGYGFVCYSTKA 119
            +FV  L  +VT ES+   F++ G +            +  D E+G+ +G   V +    
Sbjct: 15  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 120 EMETALESLNGVELEGRAMRVSLA 143
             + A++  +G E  G  ++VS A
Sbjct: 75  SAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 68.9 bits (169), Expect = 2e-16
 Identities = 16/48 (33%), Positives = 27/48 (56%)

Query: 4  KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
           + +  DRETG+ +G A V+        A I+  DG+E+ G  ++V+F
Sbjct: 50 MINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 95.5 bits (238), Expect = 1e-26
 Identities = 12/81 (14%), Positives = 32/81 (39%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++    L+ +V    L    ++YG V    +L    + +  G   V +++    +  +++
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           L+   + G  +   L    + 
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQ 88

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 70.9 bits (174), Expect = 5e-17
 Identities = 11/59 (18%), Positives = 24/59 (40%)

Query: 4  KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLY 62
          ++ +L    T +  G A V  ++       ++NL     +G I+      K + ++  Y
Sbjct: 35 EVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQQRMKYY 93

>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 = 94.7 bits (236), Expect = 2e-26
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGE-SGRSRGYGFVCYSTKAEMETALE 126
           K+ V N+ +      + + F  +G +   R+      +G  RG+GFV + TK + + A  
Sbjct: 17  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76

Query: 127 SL-NGVELEGRAMRVSLAQGRRS 148
           +L +   L GR + +  A    +
Sbjct: 77  ALCHSTHLYGRRLVLEWADSEVT 99

>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 = 57.7 bits (140), Expect = 5e-12
 Identities = 14/59 (23%), Positives = 21/59 (35%), Gaps = 3/59 (5%)

Query: 2  LSKLTVLYDRE-TGRSRGFAFVTMSTVEDCNAVIENL-DGREYLGRILRVNFSDKPKPK 58
          L  + +      TG  RGF FV   T +D       L       GR L + ++   +  
Sbjct: 42 LKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWA-DSEVT 99

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 94.8 bits (236), Expect = 2e-26
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 8/87 (9%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNV--------VGARVLYDGESGRSRGYGFVCYSTKA 119
            +FV  L  +VT ES+   F++ G +            +  D E+G+ +G   V +    
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 120 EMETALESLNGVELEGRAMRVSLAQGR 146
             + A++  +G E  G  ++VS A  R
Sbjct: 69  SAKAAIDWFDGKEFSGNPIKVSFATRR 95

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 67.8 bits (166), Expect = 9e-16
 Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 4  KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           + +  DRETG+ +G A V+        A I+  DG+E+ G  ++V+F+   +  
Sbjct: 44 MINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA-TRRAD 97

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 94.2 bits (235), Expect = 3e-26
 Identities = 23/97 (23%), Positives = 42/97 (43%), Gaps = 3/97 (3%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGE-SGRSRGY 110
                 +  L     +  F+GNL + VT ES+ + F+    +   R+  +     R +G+
Sbjct: 5   HHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF 63

Query: 111 GFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
           G+  +     + +AL  LN   L  R +RV +A   +
Sbjct: 64  GYAEFEDLDSLLSALS-LNEESLGNRRIRVDVADQAQ 99

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 56.1 bits (136), Expect = 2e-11
 Identities = 8/47 (17%), Positives = 20/47 (42%), Gaps = 1/47 (2%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
               R +GF +     ++   + +  L+      R +RV+ +D+ +
Sbjct: 54 PSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNRRIRVDVADQAQ 99

>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 = 96.2 bits (239), Expect = 1e-25
 Identities = 31/161 (19%), Positives = 54/161 (33%), Gaps = 35/161 (21%)

Query: 15  RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFK------ 68
             +  A V M+        + +L+G +  G+ +R+  S     +LP   + D        
Sbjct: 70  NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYG 129

Query: 69  ------------------------LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGES 104
                                   L + N+  SV+ E L   F   G VV     +    
Sbjct: 130 NSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ--- 186

Query: 105 GRSRGYGFVCYSTKAEMETALESLNGVEL-EGRAMRVSLAQ 144
            + R    +   +  E   AL  L+  +L E   +RVS ++
Sbjct: 187 -KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK 226

>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 = 74.6 bits (183), Expect = 2e-17
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 6/77 (7%)

Query: 69  LFVGNLS-WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           L V NL+   VT +SL   F  YG+V   ++L++      +    V  +   + + A+  
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 91

Query: 128 LNGVELEGRAMRVSLAQ 144
           LNG +L G+ +R++L++
Sbjct: 92  LNGHKLHGKPIRITLSK 108

>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 = 43.4 bits (102), Expect = 5e-06
 Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 1/46 (2%)

Query: 11  RETGRSRGFAFVTMSTVEDCNAVIENLDGREYL-GRILRVNFSDKP 55
           +   + R  A + M +VE+    + +L   +      LRV+FS   
Sbjct: 183 KFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>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 = 92.9 bits (231), Expect = 1e-25
 Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 8/87 (9%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNV--------VGARVLYDGESGRSRGYGFVCYSTKA 119
            ++V  L+ SVT + L   F++ G V            +  D E+G+ +G   V Y    
Sbjct: 17  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76

Query: 120 EMETALESLNGVELEGRAMRVSLAQGR 146
             + A+E  +G + +G  ++VSLA+ +
Sbjct: 77  TAKAAVEWFDGKDFQGSKLKVSLARKK 103

>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 = 68.2 bits (167), Expect = 6e-16
 Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 4   KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
            + +  D+ETG+ +G A V+        A +E  DG+++ G  L+V+   + KP 
Sbjct: 52  MIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSL-ARKKPP 105

>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 = 92.3 bits (230), Expect = 1e-25
 Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
               L+VGNLS  VT   + Q F + G     +++ +  S     Y FV +    +   A
Sbjct: 14  QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAA 71

Query: 125 LESLNGVELEGRAMRVSLAQGRRS 148
           L ++NG ++ G+ ++V+ A    S
Sbjct: 72  LAAMNGRKILGKEVKVNWATTPSS 95

>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 = 50.7 bits (122), Expect = 2e-09
 Identities = 11/52 (21%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          ++ +  +     + FV      D  A +  ++GR+ LG+ ++VN++  P  +
Sbjct: 47 MITEHTSNDP--YCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ 96

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 91.6 bits (228), Expect = 2e-25
 Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 6/84 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGN--VVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
            + + N++     +S+  A   Y +  V   R++ D ++ ++RG+ FV  S+  +    L
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 126 ESLNGVE----LEGRAMRVSLAQG 145
           + L  +     ++G+ + V  A+ 
Sbjct: 71  QILQSLHPPLKIDGKTIGVDFAKS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 63.9 bits (156), Expect = 2e-14
 Identities = 14/54 (25%), Positives = 32/54 (59%), Gaps = 4/54 (7%)

Query: 3  SKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL----GRILRVNFS 52
          + + ++ D++T ++RGFAFV +S+  D + +++ L          G+ + V+F+
Sbjct: 39 NNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 91.9 bits (229), Expect = 2e-25
 Identities = 22/90 (24%), Positives = 41/90 (45%), Gaps = 3/90 (3%)

Query: 60  PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYD-GESGRSRGYGFVCYSTK 118
            L     +  F+GNL + VT ES+ + F+    +   R+  +     R +G+G+  +   
Sbjct: 9   RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDL 67

Query: 119 AEMETALESLNGVELEGRAMRVSLAQGRRS 148
             + +AL  LN   L  + +RV +A   + 
Sbjct: 68  DSLLSALS-LNEESLGNKRIRVDVADQAQD 96

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 59.2 bits (144), Expect = 1e-12
 Identities = 8/52 (15%), Positives = 22/52 (42%), Gaps = 1/52 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
                  R +GF +     ++   + + +L+      + +RV+ +D+ + K
Sbjct: 47 PREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDK 97

>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 = 91.5 bits (228), Expect = 3e-25
 Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 7/82 (8%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KL++GNLS +VT + L Q F +    +       G+     GY FV Y  +     A+E+
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIET 63

Query: 128 LNG-VELEGRAMRVSLAQGRRS 148
           L+G VEL G+ M V  +  ++ 
Sbjct: 64  LSGKVELHGKIMEVDYSVSKKL 85

>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 = 59.2 bits (144), Expect = 1e-12
 Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGR-EYLGRILRVNFSDKPKPK 58
             +     G+AFV           IE L G+ E  G+I+ V++S   K +
Sbjct: 36 LAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR 86

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 91.1 bits (227), Expect = 4e-25
 Identities = 21/83 (25%), Positives = 44/83 (53%), Gaps = 1/83 (1%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
               K+FVG +  +     L + F+++G V    ++YD E  R RG+GF+ +  +  ++ 
Sbjct: 8   SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQ 67

Query: 124 ALESLNGVELEGRAMRVSLAQGR 146
           A+  ++  ++ G+ + V  A+ R
Sbjct: 68  AVN-MHFHDIMGKKVEVKRAEPR 89

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 54.1 bits (131), Expect = 8e-11
 Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 4/53 (7%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           ++YD E  R RGF F+T    +  +  +      + +G+ + V    + +P+
Sbjct: 41 VMIYDAEKQRPRGFGFITFEDEQSVDQAVNM-HFHDIMGKKVEVK---RAEPR 89

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 91.1 bits (227), Expect = 4e-25
 Identities = 18/79 (22%), Positives = 40/79 (50%), Gaps = 3/79 (3%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            +FVG +   +    +   F  YG+V   +++ D  +G S+GYGFV +    +++  +E 
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE- 68

Query: 128 LNGVELEGRAMRVSLAQGR 146
            + +   G+ +++  A  +
Sbjct: 69  -SQINFHGKKLKLGPAIRK 86

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 50.7 bits (122), Expect = 2e-09
 Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 3/45 (6%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
           ++ DR TG S+G+ FV+     D   ++E+     + G+ L++ 
Sbjct: 40 KIITDR-TGVSKGYGFVSFYNDVDVQKIVES--QINFHGKKLKLG 81

>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 = 90.8 bits (226), Expect = 5e-25
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFVGNL   +T E + + F++YG      +       + +G+GF+   T+   E A   
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETRTLAEIAKVE 70

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           L+ + L G+ +RV  A    S
Sbjct: 71  LDNMPLRGKQLRVRFACHSAS 91

>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 = 55.3 bits (134), Expect = 4e-11
 Identities = 11/44 (25%), Positives = 17/44 (38%)

Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          + +GF F+ + T          LD     G+ LRV F+      
Sbjct: 49 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASL 92

>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 = 90.4 bits (225), Expect = 7e-25
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 6/80 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L+V NL  S + E + + F         RV       + R Y FV +S + +   A+++
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKA 70

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           LNG  L+G  + V+LA+   
Sbjct: 71  LNGKVLDGSPIEVTLAKPVD 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 = 54.6 bits (132), Expect = 6e-11
 Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 3  SKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          + +         + R +AFV  S  ED    ++ L+G+   G  + V  + KP  K
Sbjct: 37 NNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA-KPVDK 91

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 88.9 bits (221), Expect = 4e-24
 Identities = 30/99 (30%), Positives = 51/99 (51%), Gaps = 1/99 (1%)

Query: 50  NFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRG 109
           + S    P+      +  K+F+G LSW  T E L + F ++G V    V+ D  + RSRG
Sbjct: 9   HHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG 68

Query: 110 YGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRRS 148
           +GFV +  +A ++  L   +  EL+ + +   +A  RR+
Sbjct: 69  FGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPKVAFPRRA 106

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 54.2 bits (131), Expect = 1e-10
 Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 4/40 (10%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIEN----LDGRE 41
           V+ D  T RSRGF FVT       + V+      LD + 
Sbjct: 56 LVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKT 95

>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 = 89.9 bits (223), Expect = 5e-24
 Identities = 28/111 (25%), Positives = 46/111 (41%), Gaps = 5/111 (4%)

Query: 42  YLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNV--VGARVL 99
             GRI R         +     E + +++V NL+  V  + L   F  Y +      R++
Sbjct: 21  EKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIM 80

Query: 100 YD---GESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
           +D    + GR +G  F+    +     AL+  NG  L G+ M V  A+  R
Sbjct: 81  FDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSAR 131

>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 = 54.1 bits (130), Expect = 3e-10
 Identities = 11/49 (22%), Positives = 23/49 (46%)

Query: 10  DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
             + GR +G AF+ +   +     ++  +G    G+ + V F+   +PK
Sbjct: 85  LMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPK 133

>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 = 91.3 bits (226), Expect = 5e-24
 Identities = 23/159 (14%), Positives = 41/159 (25%), Gaps = 32/159 (20%)

Query: 16  SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFK------- 68
             G A V M+     +  I +L+     G+ + V  S +P          +         
Sbjct: 41  KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDF 100

Query: 69  -------------------------LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGE 103
                                    L   N    VT E+  +   E G      V     
Sbjct: 101 SESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSG 160

Query: 104 SGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL 142
                  G + + +K++    L  LN  +++        
Sbjct: 161 KSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 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 = 62.4 bits (151), Expect = 5e-13
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 6/76 (7%)

Query: 69  LFVGNLSWS-VTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           L V  L  S +  + +   F  YGNV   + +         G   V  +    ++ A+  
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITH 61

Query: 128 LNGVELEGRAMRVSLA 143
           LN   + G+ M V ++
Sbjct: 62  LNNNFMFGQKMNVCVS 77

>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 = 40.1 bits (93), Expect = 7e-05
 Identities = 4/51 (7%), Positives = 12/51 (23%)

Query: 4   KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
             +V              +   +  D    +  L+  +         ++ K
Sbjct: 152 PTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLK 202

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 88.5 bits (220), Expect = 6e-24
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 4/83 (4%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLFVG L+   + E + + FQ +G +    VL     G S+G  FV +S+  E + A+ +
Sbjct: 17  KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQAAIHA 75

Query: 128 LNG---VELEGRAMRVSLAQGRR 147
           L+G   +     ++ V  A   +
Sbjct: 76  LHGSQTMPGASSSLVVKFADTDK 98

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 55.8 bits (135), Expect = 3e-11
 Identities = 20/59 (33%), Positives = 26/59 (44%), Gaps = 4/59 (6%)

Query: 5   LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL---GRILRVNFSDKPKPKLP 60
            TVL     G S+G AFV  S+  +  A I  L G + +      L V F+D  K   P
Sbjct: 45  CTVLRG-PDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESGP 102

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 88.1 bits (219), Expect = 9e-24
 Identities = 21/93 (22%), Positives = 40/93 (43%), Gaps = 2/93 (2%)

Query: 56  KPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCY 115
              +    +    L V  L W  T + L + F  +G V+  +V  D ++G S+G+GFV +
Sbjct: 5   SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64

Query: 116 STKAEMETALESLNGVELEGRAMRVSLAQGRRS 148
           +        +   +   ++GR     L   ++S
Sbjct: 65  TEYETQVKVMSQRH--MIDGRWCDCKLPNSKQS 95

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 52.6 bits (127), Expect = 4e-10
 Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 3/39 (7%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIEN---LDGRE 41
           V  D +TG S+GF FV  +  E    V+     +DGR 
Sbjct: 46 QVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRW 84

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 87.1 bits (217), Expect = 9e-24
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG LS + T E +   F+++G V  A +++D  + R RG+GFV + ++  +E   E 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 128 LNGVELEGRAMRVSLA 143
            +  E+  + +    A
Sbjct: 61  -HFHEINNKMVECKKA 75

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 52.1 bits (126), Expect = 3e-10
 Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 4/40 (10%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIEN----LDGRE 41
           +++D+ T R RGF FVT  + +    V E     ++ + 
Sbjct: 30 MLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKM 69

>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 = 87.3 bits (217), Expect = 1e-23
 Identities = 24/81 (29%), Positives = 44/81 (54%), Gaps = 8/81 (9%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           +K+FVGN+S + T++ L   F+  G V+   V+        + Y FV    +A+ + A+ 
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIA 61

Query: 127 SLNGVELEGRAMRVSLAQGRR 147
            LNG E++G+ + V L+   +
Sbjct: 62  QLNGKEVKGKRINVELSTKGQ 82

>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 = 53.4 bits (129), Expect = 1e-10
 Identities = 15/42 (35%), Positives = 22/42 (52%)

Query: 17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          + +AFV M    D  A I  L+G+E  G+ + V  S K + K
Sbjct: 43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKK 84

>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 = 87.3 bits (217), Expect = 1e-23
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 8/79 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            LFV NL+ +VT E L +AF ++G +   + L        + Y F+ +  +     A+E 
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEE 64

Query: 128 LNGVELEGRAMRVSLAQGR 146
           +NG +LEG  + +  A+  
Sbjct: 65  MNGKDLEGENIEIVFAKPP 83

>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 = 47.7 bits (114), Expect = 4e-08
 Identities = 8/43 (18%), Positives = 20/43 (46%)

Query: 16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           + +AF+     +     +E ++G++  G  + + F+  P  K
Sbjct: 44 LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK 86

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 87.3 bits (217), Expect = 2e-23
 Identities = 31/86 (36%), Positives = 43/86 (50%), Gaps = 1/86 (1%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A+   KLFVG L WS T E+L   F +YG VV   ++ D  + +SRG+GFV +     + 
Sbjct: 13  ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVG 72

Query: 123 TALESLNGVELEGRAMRVSLAQGRRS 148
           T L S     L+GR +       R  
Sbjct: 73  TVLAS-RPHTLDGRNIDPKPCTPRGM 97

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 4/39 (10%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIEN----LDGR 40
           ++ D+ T +SRGF FV          V+ +    LDGR
Sbjct: 47 VIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGR 85

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 86.5 bits (215), Expect = 2e-23
 Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           E   K+FVG LSW  + + L   F ++G VV   +  D  +GRSRG+GF+ +   A +E 
Sbjct: 9   EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEK 68

Query: 124 ALESLNGVELEGRAMRVSLA 143
            L+      L+GR +    A
Sbjct: 69  VLDQKEH-RLDGRVIDPKKA 87

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 52.6 bits (127), Expect = 3e-10
 Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 4/40 (10%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIEN----LDGRE 41
          T+  D  TGRSRGF F+          V++     LDGR 
Sbjct: 42 TIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRV 81

>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 = 86.7 bits (215), Expect = 3e-23
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 3/80 (3%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++ NL + +T E +   F +YG +   RV        +RG  +V Y    + + A++ L
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNAVDHL 67

Query: 129 NGVELEGRAMRVSLAQGRRS 148
           +G  +  R + V      R+
Sbjct: 68  SGFNVSNRYLVVLYYNANRA 87

>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 = 55.8 bits (135), Expect = 4e-11
 Identities = 11/45 (24%), Positives = 20/45 (44%)

Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
           T  +RG A+V    + D    +++L G     R L V + +  +
Sbjct: 42 NTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANR 86

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 85.6 bits (213), Expect = 4e-23
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+F+G LSW  T E L + F ++G V    V+ D  + RSRG+GFV +  +A ++  L  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 128 LNGVELEGRAMRVSLA 143
            +  EL+ + +   +A
Sbjct: 62  -SRHELDSKTIDPKVA 76

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 53.6 bits (130), Expect = 8e-11
 Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 4/40 (10%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIEN----LDGRE 41
           V+ D  T RSRGF FVT       + V+      LD + 
Sbjct: 31 LVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKT 70

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 86.6 bits (215), Expect = 4e-23
 Identities = 31/92 (33%), Positives = 50/92 (54%), Gaps = 1/92 (1%)

Query: 55  PKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVC 114
           P  +     E   KLF+G LS+  T ESL   ++++G +    V+ D  S RSRG+GFV 
Sbjct: 16  PLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 75

Query: 115 YSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
           +S+ AE++ A+ +     ++GR +    A  R
Sbjct: 76  FSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAR 106

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 4/39 (10%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIEN----LDGR 40
           V+ D  + RSRGF FVT S++ + +A +      +DGR
Sbjct: 58 VVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGR 96

>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 = 85.1 bits (211), Expect = 1e-22
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           ++ G ++  +T + + Q F  +G ++  RV  +      +GY FV +ST      A+ S+
Sbjct: 28  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81

Query: 129 NGVELEGRAMRVSLAQ 144
           NG  +EG  ++    +
Sbjct: 82  NGTTIEGHVVKCYWGK 97

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 15  RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
             +G++FV  ST E     I +++G    G +++  +  K  P
Sbjct: 59  PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG-KESP 100

>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 = 84.2 bits (209), Expect = 2e-22
 Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 8/84 (9%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           +   KL VGN+S + T + L   F+EYG V+   ++        + Y FV      +   
Sbjct: 8   KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVE 59

Query: 124 ALESLNGVELEGRAMRVSLAQGRR 147
           A+  L+  E +G+ M V L+  R 
Sbjct: 60  AIRGLDNTEFQGKRMHVQLSTSRL 83

>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 = 52.6 bits (127), Expect = 4e-10
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          + +AFV M   ED    I  LD  E+ G+ + V  S   + +
Sbjct: 44 KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS-TSRLR 84

>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 = 83.9 bits (208), Expect = 2e-22
 Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 5/89 (5%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYG-NVVGARVLYDGESGRSRGYGFVCYSTKAEM 121
           +     L++G+L   +    +++AF   G  V+  +++ +  +G   GY FV ++  A  
Sbjct: 6   SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATA 65

Query: 122 ETALESLNGVELEG----RAMRVSLAQGR 146
           E  L  +NG  L G    +  +++ A   
Sbjct: 66  EKCLHKINGKPLPGATPAKRFKLNYATYS 94

>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 = 51.6 bits (124), Expect = 9e-10
 Identities = 10/55 (18%), Positives = 25/55 (45%), Gaps = 4/55 (7%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG----RILRVNFSDKPKP 57
          ++ +R TG   G+ FV  + +      +  ++G+   G    +  ++N++    P
Sbjct: 42 IIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGP 96

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 83.7 bits (207), Expect = 3e-22
 Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 5/84 (5%)

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
               ++VGNL        L +A +E G  V  R+ + G     R   F+ Y   A  + A
Sbjct: 18  LAADVYVGNLPRDARVSDLKRALRELG-SVPLRLTWQG----PRRRAFLHYPDSAAAQQA 72

Query: 125 LESLNGVELEGRAMRVSLAQGRRS 148
           +  L G+ L    +RV+LA+ +R 
Sbjct: 73  VSCLQGLRLGTDTLRVALARQQRD 96

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 47.5 bits (113), Expect = 4e-08
 Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 1/58 (1%)

Query: 2  LSKLTVLYDRETGR-SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          L +L  +  R T +  R  AF+           +  L G       LRV  + + + K
Sbjct: 40 LRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRDK 97

>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 = 83.0 bits (206), Expect = 4e-22
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 8/80 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLF+GNL    T + +   F++YG V+   ++        + YGFV    K   E A+ +
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           L+  +L G  + V  ++ + 
Sbjct: 62  LHHYKLHGVNINVEASKNKS 81

>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 = 52.2 bits (126), Expect = 4e-10
 Identities = 11/44 (25%), Positives = 16/44 (36%), Gaps = 1/44 (2%)

Query: 17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
          + + FV +         I NL   +  G  + V  S K K K  
Sbjct: 42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS-KNKSKAS 84

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 82.4 bits (204), Expect = 1e-21
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
            ++GN+    T   L   FQ +G ++  +          +G  F+ Y T  +    + +L
Sbjct: 30  AYIGNIPHFATEADLIPLFQNFGFILDFKH------YPEKGCCFIKYDTHEQAAVCIVAL 83

Query: 129 NGVELEGRAMRVSLAQGR 146
                +GR +R    + R
Sbjct: 84  ANFPFQGRNLRTGWGKER 101

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 44.2 bits (105), Expect = 5e-07
 Identities = 10/39 (25%), Positives = 14/39 (35%)

Query: 13 TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
              +G  F+   T E     I  L    + GR LR  +
Sbjct: 59 HYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW 97

>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 = 81.6 bits (202), Expect = 2e-21
 Identities = 19/85 (22%), Positives = 36/85 (42%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
                + V N+ ++V+ + +   F  Y  + G+  L   E G   G   V + ++ E   
Sbjct: 13  PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72

Query: 124 ALESLNGVELEGRAMRVSLAQGRRS 148
           A+  LN   +  R +++ L  G  S
Sbjct: 73  AVIDLNDRPIGSRKVKLVLGSGPSS 97

>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 = 56.2 bits (136), Expect = 1e-11
 Identities = 11/49 (22%), Positives = 20/49 (40%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP 55
           L   E G   G A V   + ++  A + +L+ R    R +++     P
Sbjct: 47 CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP 95

>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 = 82.6 bits (204), Expect = 4e-21
 Identities = 29/135 (21%), Positives = 48/135 (35%), Gaps = 13/135 (9%)

Query: 21  FVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLY--------AETDFKLFVG 72
            V  +T E       N +G +          +         +           D K++VG
Sbjct: 20  AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVG 79

Query: 73  NLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVE 132
           NL  +     L +AF  YG +    V     +    G+ FV +    +   A+  L+G  
Sbjct: 80  NLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRELDGRT 134

Query: 133 LEGRAMRVSLAQGRR 147
           L G  +RV L+ G +
Sbjct: 135 LCGCRVRVELSNGEK 149

>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 = 49.5 bits (118), Expect = 2e-08
 Identities = 15/42 (35%), Positives = 18/42 (42%)

Query: 15  RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
              GFAFV      D    +  LDGR   G  +RV  S+  K
Sbjct: 108 NPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK 149

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 81.2 bits (201), Expect = 4e-21
 Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 8/80 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFV      V    L + F  +G +   ++L         G+ FV +        A+E 
Sbjct: 33  RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEE 84

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           ++G     + + V  ++   
Sbjct: 85  VHGKSFANQPLEVVYSKLPA 104

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 51.1 bits (123), Expect = 2e-09
 Identities = 13/42 (30%), Positives = 19/42 (45%)

Query: 17  RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
            GFAFV     E     IE + G+ +  + L V +S  P  +
Sbjct: 65  NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR 106

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 80.8 bits (200), Expect = 5e-21
 Identities = 17/80 (21%), Positives = 34/80 (42%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
                + V N+ ++V+ + +   F  Y  + G+  L   E G   G   V + ++ E   
Sbjct: 13  PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72

Query: 124 ALESLNGVELEGRAMRVSLA 143
           A+  LN   +  R +++S  
Sbjct: 73  AVIDLNDRPIGSRKVKLSGP 92

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 54.6 bits (132), Expect = 5e-11
 Identities = 10/48 (20%), Positives = 20/48 (41%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
           L   E G   G A V   + ++  A + +L+ R    R ++++    
Sbjct: 47 CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS 94

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 79.5 bits (197), Expect = 7e-21
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG LS     E + + F  +G V    +  D ++ + RG+ F+ +  +  ++  +E 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 128 LNGVELEGRAMRVSLA 143
                +      + +A
Sbjct: 61  -KYHNVGLSKCEIKVA 75

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 48.3 bits (116), Expect = 9e-09
 Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 4/40 (10%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIEN----LDGRE 41
           +  D +T + RGF F+T    E    ++E     +   +
Sbjct: 30 ELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSK 69

>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 = 79.6 bits (197), Expect = 1e-20
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 7/82 (8%)

Query: 69  LFVGNLSWSVTTESLTQA----FQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           +++ NL+  +  + L ++    F  +G ++   V     S + RG  FV +   +    A
Sbjct: 11  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFKEVSSATNA 67

Query: 125 LESLNGVELEGRAMRVSLAQGR 146
           L S+ G     + MR+  A+  
Sbjct: 68  LRSMQGFPFYDKPMRIQYAKTD 89

>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 = 50.7 bits (122), Expect = 2e-09
 Identities = 8/41 (19%), Positives = 19/41 (46%)

Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
           + + RG AFV    V      + ++ G  +  + +R+ ++
Sbjct: 46 RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86

>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 = 79.5 bits (196), Expect = 2e-20
 Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 7/83 (8%)

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           ++ ++ V  L  S + + L    +E G+V  A V          G G V +  K +M  A
Sbjct: 14  SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGVVEFVRKEDMTYA 66

Query: 125 LESLNGVELEGRAMRVSLAQGRR 147
           +  L+  +        +  + + 
Sbjct: 67  VRKLDNTKFRSHEGETAYIRVKV 89

>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 = 39.8 bits (93), Expect = 3e-05
 Identities = 6/37 (16%), Positives = 10/37 (27%)

Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
             G   V     ED    +  LD  ++        +
Sbjct: 48 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY 84

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 79.0 bits (195), Expect = 2e-20
 Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KL + N+   +  E L     +YG V     +             V YS+K +   AL+ 
Sbjct: 17  KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQALDK 73

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           LNG +LE   ++V+      +
Sbjct: 74  LNGFQLENFTLKVAYIPDEMA 94

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 46.7 bits (111), Expect = 6e-08
 Identities = 8/44 (18%), Positives = 16/44 (36%)

Query: 13 TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
          T        VT S+ +     ++ L+G +     L+V +     
Sbjct: 50 TDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM 93

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

 Score = 78.9 bits (195), Expect = 3e-20
 Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 5/80 (6%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K++VGNL        L +AF  YG +    +  +       G+ FV +    + E A+  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           L+G  + G  +RV L+ G  
Sbjct: 57  LDGKVICGSRVRVELSTGMP 76

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

 Score = 50.0 bits (120), Expect = 4e-09
 Identities = 13/44 (29%), Positives = 17/44 (38%)

Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
             GFAFV      D    +  LDG+   G  +RV  S     +
Sbjct: 35 NPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRR 78

>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 = 78.5 bits (194), Expect = 4e-20
 Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 3/86 (3%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
              D +++VGNL   + T+ +   F +YG +    +           + FV +    + E
Sbjct: 19  GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAE 75

Query: 123 TALESLNGVELEGRAMRVSLAQGRRS 148
            A+   +G + +G  +RV   +  R 
Sbjct: 76  DAVYGRDGYDYDGYRLRVEFPRSGRG 101

>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 = 53.9 bits (130), Expect = 2e-10
 Identities = 13/46 (28%), Positives = 16/46 (34%)

Query: 13  TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
                 FAFV      D    +   DG +Y G  LRV F    +  
Sbjct: 57  RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 102

>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 = 81.8 bits (201), Expect = 8e-20
 Identities = 18/82 (21%), Positives = 37/82 (45%), Gaps = 7/82 (8%)

Query: 69  LFVGNLSWSVTTESLTQA----FQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           +++ NL+  +  + L ++    F ++G ++   V     S + RG  FV +   +    A
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQAFVIFKEVSSATNA 68

Query: 125 LESLNGVELEGRAMRVSLAQGR 146
           L S+ G     + MR+  A+  
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTD 90

>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 = 66.4 bits (161), Expect = 4e-14
 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
           F+ NL        L+  F ++      R++            FV +  + +   A ++L 
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARDALQ 265

Query: 130 GVEL-EGRAMRVSLAQ 144
           G ++ +  AM++S A+
Sbjct: 266 GFKITQNNAMKISFAK 281

>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 = 52.2 bits (124), Expect = 5e-09
 Identities = 15/104 (14%), Positives = 31/104 (29%), Gaps = 3/104 (2%)

Query: 12  ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP---KPKLPLYAETDFK 68
            + + RG AFV    V      + ++ G  +  + +R+ ++        K+        +
Sbjct: 47  RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDR 106

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGF 112
                   S  T +  +A Q  G       +     G       
Sbjct: 107 KREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQA 150

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 77.9 bits (192), Expect = 9e-20
 Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 4/85 (4%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLY--DGESGRSRGYGFVCYSTKAEMETAL 125
           +LF+G +      E + +   +    V   ++Y    +  ++RG+ FV Y +      A 
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 126 ESLN--GVELEGRAMRVSLAQGRRS 148
             L    ++L G  + V  A+    
Sbjct: 70  RKLMPGRIQLWGHQIAVDWAEPEID 94

>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 = 42.5 bits (100), Expect = 4e-06
 Identities = 10/50 (20%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL--GRILRVNFSDKPKP 57
            +  ++RGFAFV   +          L        G  + V++++ P+ 
Sbjct: 45 AADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAE-PEI 93

>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 = 77.3 bits (191), Expect = 1e-19
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 8/80 (10%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L+V      +T   L  AF  +GN++   +         R   FV Y      + A+  L
Sbjct: 18  LYVYGED--MTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAEL 69

Query: 129 NGVELEGRAMRVSLAQGRRS 148
           NG ++E   ++V++A+ +  
Sbjct: 70  NGTQVESVQLKVNIARKQPM 89

>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 = 50.0 bits (120), Expect = 4e-09
 Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
          D      R  AFVT   +E  +  +  L+G +     L+VN + + +P
Sbjct: 42 DLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA-RKQP 88

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 76.5 bits (188), Expect = 6e-19
 Identities = 12/83 (14%), Positives = 34/83 (40%), Gaps = 7/83 (8%)

Query: 68  KLFVGNLSWSVTTESLTQA----FQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
            + + N++  V  E L           G+++   V     S  + G  ++ ++T+   + 
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDILDIVV---DLSDDNSGKAYIVFATQESAQA 87

Query: 124 ALESLNGVELEGRAMRVSLAQGR 146
            +E+  G   +G  + ++ ++  
Sbjct: 88  FVEAFQGYPFQGNPLVITFSETP 110

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 49.1 bits (117), Expect = 1e-08
 Identities = 12/46 (26%), Positives = 22/46 (47%)

Query: 11  RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
             +  + G A++  +T E   A +E   G  + G  L + FS+ P+
Sbjct: 66  DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ 111

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 74.9 bits (184), Expect = 1e-18
 Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 7/83 (8%)

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           ++ ++ V  L  S + + L    +E G+V  A V          G G V +  K +M  A
Sbjct: 15  SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGVVEFVRKEDMTYA 67

Query: 125 LESLNGVELEGRAMRVSLAQGRR 147
           +  L+  +        +  + + 
Sbjct: 68  VRKLDNTKFRSHEGETAYIRVKV 90

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 6/37 (16%), Positives = 10/37 (27%)

Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
             G   V     ED    +  LD  ++        +
Sbjct: 49 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY 85

>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 = 74.3 bits (183), Expect = 2e-18
 Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 9/82 (10%)

Query: 68  KLFVGNLSWSVTTES-LTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           ++F+GNL+ ++  +S +   F +YG V G  V         +GY FV YS +     A+ 
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80

Query: 127 SLNGVELEGRAMRVSLAQGRRS 148
             NG  L G+ + +++A   + 
Sbjct: 81  GENGRVLAGQTLDINMAGEPKP 102

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 55.1 bits (133), Expect = 6e-11
 Identities = 14/43 (32%), Positives = 22/43 (51%)

Query: 16  SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
            +G+AFV  S      A +   +GR   G+ L +N + +PKP 
Sbjct: 61  HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPD 103

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 73.7 bits (181), Expect = 4e-18
 Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 3/76 (3%)

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
             +++ + NL    + + L    +E              +    G G + + ++  +  A
Sbjct: 27  KRYRITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTGALEFPSEEILVEA 83

Query: 125 LESLNGVELEGRAMRV 140
           LE LN +E  G  + V
Sbjct: 84  LERLNNIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 48.7 bits (116), Expect = 2e-08
 Identities = 11/48 (22%), Positives = 18/48 (37%)

Query: 10  DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
              T    G   +   + E     +E L+  E+ G ++ V   D P P
Sbjct: 60  SVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPPP 107

>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 = 72.7 bits (179), Expect = 5e-18
 Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +L+VG L  + +  +L + F  +G++     +      +   + ++ Y +    + A   
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACAK 72

Query: 128 LNGVELEG--RAMRVSLAQGRRS 148
           + G  L G  R +RV  A+   S
Sbjct: 73  MRGFPLGGPDRRLRVDFAKSGPS 95

>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 = 44.5 bits (106), Expect = 4e-07
 Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 2/45 (4%)

Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGREYLG--RILRVNFSDKPKP 57
          +   FA++   +++   A    + G    G  R LRV+F+     
Sbjct: 51 KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS 95

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 72.5 bits (178), Expect = 9e-18
 Identities = 15/76 (19%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 70  FVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN 129
            + +    V  ++LT  F + G VV      D  +G+++G+ FV   +  + +  ++S +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 130 GVELEGR-AMRVSLAQ 144
           G  L+ +  + +   +
Sbjct: 76  GKRLDLKHRLFLYTMK 91

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 55.5 bits (134), Expect = 3e-11
 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGR-ILRVN-FSDKPK 56
           D  TG+++GF FV   ++ D   +I++  G+    +  L +    D  +
Sbjct: 46 IDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVER 95

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 72.6 bits (178), Expect = 2e-17
 Identities = 17/95 (17%), Positives = 42/95 (44%), Gaps = 1/95 (1%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
           S + + +     E  F +++  L +    + +   F++   V  +  +  G +G++ G G
Sbjct: 11  SGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEG 70

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
           FV +  +A+ + AL   +   +  R ++V     +
Sbjct: 71  FVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKK 104

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 1/48 (2%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
            +     G++ G  FV      D  A +     +    R ++V+   K
Sbjct: 57  YIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITK 103

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 69.6 bits (171), Expect = 8e-17
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 7/75 (9%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE- 126
            L+VG L  ++T   L   F ++G +    V+        +   F+ ++T+   E A E 
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEK 67

Query: 127 SLNGVELEGRAMRVS 141
           S N + + GR + V 
Sbjct: 68  SFNKLIVNGRRLNVK 82

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 70.7 bits (173), Expect = 8e-17
 Identities = 17/92 (18%), Positives = 32/92 (34%), Gaps = 1/92 (1%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
               +      +  D  + +  L +  T E + Q F     V     L     G+  G  
Sbjct: 28  QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEA 87

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
           FV ++++   E AL   +   +  R + V  +
Sbjct: 88  FVQFASQELAEKALG-KHKERIGHRYIEVFKS 118

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 36.8 bits (85), Expect = 5e-04
 Identities = 10/47 (21%), Positives = 15/47 (31%), Gaps = 1/47 (2%)

Query: 6   TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
             L     G+  G AFV  ++ E     +          R + V  S
Sbjct: 73  ITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKS 118

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 70.2 bits (172), Expect = 9e-17
 Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 1/80 (1%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
                  + N+ +S+T   + Q  +       A  +    +G+  G   V +  + +   
Sbjct: 13  SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 72

Query: 124 ALESLNGVELEGRAMRVSLA 143
           +   L+  +L GR   V + 
Sbjct: 73  SER-LHRKKLNGREAFVHVV 91

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 41.6 bits (98), Expect = 7e-06
 Identities = 12/53 (22%), Positives = 18/53 (33%), Gaps = 2/53 (3%)

Query: 6  TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           VL D   G+  G A V     +D       L  ++  GR   V+       +
Sbjct: 47 HVLVDN-NGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTLEDMR 97

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 68.4 bits (168), Expect = 2e-16
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG  +  +T E L Q F +YG VV   +         R + FV ++     ++    
Sbjct: 13  KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG- 66

Query: 128 LNGVELEGRAMRVSLAQGR 146
              + ++G ++ +S A+ +
Sbjct: 67  -EDLIIKGISVHISNAEPK 84

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 68.2 bits (167), Expect = 3e-16
 Identities = 13/78 (16%), Positives = 38/78 (48%), Gaps = 6/78 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARV-----LYDGESGRSRGYGFVCYSTKAEME 122
           +L+VGN+ + +T E++   F     + G        +   +  + + + F+ + +  E  
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 123 TALESLNGVELEGRAMRV 140
            A+   +G+  +G+++++
Sbjct: 68  QAMA-FDGIIFQGQSLKI 84

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 49.4 bits (118), Expect = 5e-09
 Identities = 8/44 (18%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
           +   +  + + FAF+   +V++    +   DG  + G+ L++ 
Sbjct: 43 PVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR 85

>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 = 67.8 bits (166), Expect = 4e-16
 Identities = 11/77 (14%), Positives = 25/77 (32%), Gaps = 7/77 (9%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            + V NL      + +    ++Y               R++   FV      + + A++ 
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLKYC-------YVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 128 LNGVELEGRAMRVSLAQ 144
            +     G+ + V L  
Sbjct: 60  FHQYSFRGKDLIVQLQP 76

>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 = 47.0 bits (112), Expect = 4e-08
 Identities = 10/43 (23%), Positives = 16/43 (37%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
               R++  AFVT+   E     I+      + G+ L V   
Sbjct: 33 YCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ 75

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 68.6 bits (168), Expect = 4e-16
 Identities = 25/95 (26%), Positives = 38/95 (40%), Gaps = 7/95 (7%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
           S KP P  P     D  + V  + +S     +   F     V    +L D   GR+ G G
Sbjct: 6   SGKPLPINP----DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKD-HVGRNNGNG 59

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
            V + +  +   AL+  N + +  R + VS A  R
Sbjct: 60  LVKFLSPQDTFEALK-RNRMLMIQRYVEVSPATER 93

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 37.4 bits (87), Expect = 2e-04
 Identities = 7/43 (16%), Positives = 18/43 (41%), Gaps = 1/43 (2%)

Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
            GR+ G   V   + +D    ++  +    + R + V+ + +
Sbjct: 51 HVGRNNGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPATE 92

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 67.2 bits (165), Expect = 6e-16
 Identities = 15/79 (18%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            +FVG  +  +T + L + F +YG+V+   +         R + FV ++     ++    
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQSLCG- 60

Query: 128 LNGVELEGRAMRVSLAQGR 146
              + ++G ++ +S A+ +
Sbjct: 61  -EDLIIKGISVHISNAEPK 78

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

 Score = 67.6 bits (166), Expect = 7e-16
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 9/81 (11%)

Query: 68  KLFVGNLSW-SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           +LF+GNL   +V+ E L + F  YG+++   +           +GF+ +     +  A+E
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 63

Query: 127 SLNGVELEGRAMRVSLAQGRR 147
             +     G+ + + ++    
Sbjct: 64  CESQEMNFGKKLILEVSSSNA 84

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

 Score = 52.2 bits (126), Expect = 4e-10
 Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 1/44 (2%)

Query: 16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS-DKPKPK 58
             F F+     +     IE        G+ L +  S    +P+
Sbjct: 44 KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQ 87

>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 = 67.0 bits (164), Expect = 1e-15
 Identities = 17/97 (17%), Positives = 39/97 (40%), Gaps = 9/97 (9%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSW-SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGY 110
                  +P  +    +LF+GNL   +V+ E L + F  YG+++   +           +
Sbjct: 8   HHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAF 59

Query: 111 GFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
           GF+ +     +  A+E  +     G+ + + ++    
Sbjct: 60  GFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA 96

>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 = 51.2 bits (123), Expect = 1e-09
 Identities = 7/42 (16%), Positives = 12/42 (28%), Gaps = 1/42 (2%)

Query: 17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
            F F+     +     IE        G+ L +  S     +
Sbjct: 57 NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVS-SSNAR 97

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 67.1 bits (164), Expect = 1e-15
 Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
              D  + +  L +  + E + Q F     V     L     GRS G  FV ++++   E
Sbjct: 12  TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAE 71

Query: 123 TALESLNGVELEGRAMRVSLA 143
            AL+  +   +  R + +  +
Sbjct: 72  KALK-KHKERIGHRYIEIFKS 91

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 35.9 bits (83), Expect = 8e-04
 Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 1/48 (2%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
           L     GRS G AFV  ++ E     ++         R + +  S +
Sbjct: 47 TLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSR 93

>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 = 65.7 bits (160), Expect = 6e-15
 Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 6/81 (7%)

Query: 69  LFVGNLSWSVTTESL---TQAFQEYGNVVGARVLYD---GESGRSRGYGFVCYSTKAEME 122
           +FV  LS  +    +    + F ++G +    +        S       +V Y    +  
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 123 TALESLNGVELEGRAMRVSLA 143
            A++ +N V ++GR ++ SL 
Sbjct: 78  RAIQCVNNVVVDGRTLKASLG 98

>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 = 50.2 bits (120), Expect = 4e-09
 Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 3/53 (5%)

Query: 3  SKLTVLYDRETGRSR---GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
           K+ +        S+     A+VT    ED    I+ ++     GR L+ +  
Sbjct: 46 HKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLG 98

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 64.8 bits (158), Expect = 1e-14
 Identities = 21/98 (21%), Positives = 43/98 (43%), Gaps = 9/98 (9%)

Query: 53  DKPKPKLPLYAETDFKLFVGNL------SWSVTTESLTQAFQEYGNVVGARVLYDGESGR 106
           D  K +       D  + V N+              + + F ++G +      Y  E G+
Sbjct: 2   DVLKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGK 59

Query: 107 SRGYGFVCYSTKAEMETALESLNGVELEGR-AMRVSLA 143
           ++GY F+ Y++ A    A+++ +G +L+ +   RV+L 
Sbjct: 60  TKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLF 97

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 53.2 bits (128), Expect = 3e-10
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 2/49 (4%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGR-ILRVN-FSD 53
            Y  E G+++G+ F+  ++       ++N DG +   +   RVN F+D
Sbjct: 51 DFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTD 99

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 63.5 bits (155), Expect = 2e-14
 Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
             T   + +    ++VT +++ +        V  R++ +   G   GY FV +S + E++
Sbjct: 7   GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVK 64

Query: 123 TALESLNGVELEGRAMRVSLA 143
            AL+  N   + GR + V   
Sbjct: 65  QALK-CNREYMGGRYIEVFRE 84

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 64.9 bits (158), Expect = 2e-14
 Identities = 14/92 (15%), Positives = 30/92 (32%), Gaps = 3/92 (3%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
                 +  + + T   + +  L +  T   +   F      V   +      GR  G  
Sbjct: 32  RGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIG-PDGRVTGEA 89

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
            V ++T  E   A+   +   ++ R + + L 
Sbjct: 90  DVEFATHEEAVAAMS-KDRANMQHRYIELFLN 120

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 62.3 bits (152), Expect = 6e-14
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 6/79 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            +FV      V +  L++ F  +G V  A V+ D + G    +  V        E  L  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPV--ASVVMDKDKGV---FAIVEMGDVGAREAVLS- 63

Query: 128 LNGVELEGRAMRVSLAQGR 146
            +   L G  +RV   + +
Sbjct: 64  QSQHSLGGHRLRVRPREQK 82

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 61.7 bits (150), Expect = 1e-13
 Identities = 8/77 (10%), Positives = 28/77 (36%), Gaps = 2/77 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            +++       T + + +  ++ G V+  ++         +G  FV + +    +  +E 
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE- 70

Query: 128 LNGVELEGRAMRVSLAQ 144
             G + +   + +    
Sbjct: 71  TPGQKYKETDLLILFKD 87

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 38.9 bits (91), Expect = 7e-05
 Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 1/38 (2%)

Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
               +G  FV   ++E     +E   G++Y    L +
Sbjct: 47 LHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLI 83

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 65.6 bits (159), Expect = 2e-13
 Identities = 24/79 (30%), Positives = 45/79 (56%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           LFV  +++  T   L + F+ YG +    ++Y   SG+ RGY F+ Y  + +M +A +  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 129 NGVELEGRAMRVSLAQGRR 147
           +G +++GR + V + +GR 
Sbjct: 165 DGKKIDGRRVLVDVERGRT 183

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 38.7 bits (89), Expect = 3e-04
 Identities = 13/52 (25%), Positives = 28/52 (53%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           ++Y + +G+ RG+AF+      D ++  ++ DG++  GR + V+       K
Sbjct: 134 MVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVK 185

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 60.9 bits (148), Expect = 3e-13
 Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 3/80 (3%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
            T   + +  L +  T   +   F    N +   +      GR  G   V ++T  +   
Sbjct: 13  TTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIG-PDGRVTGEADVEFATHEDAVA 70

Query: 124 ALESLNGVELEGRAMRVSLA 143
           A+   +   ++ R + + L 
Sbjct: 71  AMA-KDKANMQHRYVELFLN 89

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 59.2 bits (143), Expect = 2e-12
 Identities = 14/87 (16%), Positives = 36/87 (41%), Gaps = 8/87 (9%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGES--GRSRGYGFVCYSTKAEMETAL 125
           K+FVG L   +  + +T +F+ +G +V               +GY F+ +  ++ ++  +
Sbjct: 10  KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69

Query: 126 ESL------NGVELEGRAMRVSLAQGR 146
           ++         + +    ++    Q R
Sbjct: 70  DACLEEDGKLYLCVSSPTIKDKPVQIR 96

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 58.2 bits (141), Expect = 2e-12
 Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 8/74 (10%)

Query: 69  LFVGNL------SWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           + V N+              + + F ++G +      Y  E G+++GY F+ Y++ A   
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASPAHAV 61

Query: 123 TALESLNGVELEGR 136
            A+++ +G +L+ +
Sbjct: 62  DAVKNADGYKLDKQ 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 47.4 bits (113), Expect = 2e-08
 Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGR-ILRVN 50
            Y  E G+++G+ F+  ++       ++N DG +   +   RVN
Sbjct: 37 DFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN 81

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 58.8 bits (142), Expect = 3e-12
 Identities = 11/81 (13%), Positives = 28/81 (34%), Gaps = 8/81 (9%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE-- 126
           + +  L   VT   +      +G V    +L      + +   F+  +T+    T +   
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYY 87

Query: 127 SLNGVELEGRAMRVSLAQGRR 147
           +     L G+ + +  +  + 
Sbjct: 88  TSVTPVLRGQPIYIQFSNHKE 108

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 58.2 bits (141), Expect = 3e-12
 Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 8/81 (9%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           + +  L   V    L +A QE+G +    V+        +    V +        A+   
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVNYA 77

Query: 129 --NGVELEGRAMRVSLAQGRR 147
             N + + G    V+ +  ++
Sbjct: 78  ADNQIYIAGHPAFVNYSTSQK 98

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 36.3 bits (84), Expect = 5e-04
 Identities = 7/40 (17%), Positives = 11/40 (27%), Gaps = 2/40 (5%)

Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGREYL--GRILRVNFS 52
            +  A V    V      +      +    G    VN+S
Sbjct: 55 PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYS 94

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 58.7 bits (142), Expect = 3e-12
 Identities = 16/92 (17%), Positives = 35/92 (38%), Gaps = 4/92 (4%)

Query: 55  PKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGAR---VLYDGESGRSRGYG 111
            +    L  E    + +  L ++ T E +   F ++  + G +   +      GR  G  
Sbjct: 12  NEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDA 71

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
           FV ++ +   + AL   +   L  R + +  +
Sbjct: 72  FVLFACEEYAQNALR-KHKDLLGKRYIELFRS 102

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 57.9 bits (140), Expect = 5e-12
 Identities = 12/75 (16%), Positives = 22/75 (29%), Gaps = 6/75 (8%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +   NL        + + F  +G++   RVL             V +    E   A   L
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLG--RVLLP----EGGITAIVEFLEPLEARKAFRHL 66

Query: 129 NGVELEGRAMRVSLA 143
              +     + +  A
Sbjct: 67  AYSKFHHVPLYLEWA 81

>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 = 39.8 bits (93), Expect = 4e-05
 Identities = 4/37 (10%), Positives = 10/37 (27%)

Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
               A V      +      +L   ++    L + +
Sbjct: 44 EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEW 80

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 56.7 bits (137), Expect = 1e-11
 Identities = 11/81 (13%), Positives = 28/81 (34%), Gaps = 8/81 (9%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE-- 126
           + V  L  SV    L +A +++G +    +         +    V +      +  +   
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFENIDSAKECVTFA 71

Query: 127 SLNGVELEGRAMRVSLAQGRR 147
           +   V + G+    + +  +R
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKR 92

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 56.8 bits (137), Expect = 1e-11
 Identities = 11/81 (13%), Positives = 28/81 (34%), Gaps = 8/81 (9%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE-- 126
           + +  L   VT   +      +G V    +L      + +   F+  +T+    T +   
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYY 72

Query: 127 SLNGVELEGRAMRVSLAQGRR 147
           +     L G+ + +  +  + 
Sbjct: 73  TSVTPVLRGQPIYIQFSNHKE 93

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 57.3 bits (138), Expect = 1e-11
 Identities = 17/95 (17%), Positives = 34/95 (35%), Gaps = 5/95 (5%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEY---GNVVGARVLYDGESGRSR 108
             +    L       F + +  L WS + E +     +        G   +Y    GR  
Sbjct: 30  MGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYT-REGRQS 88

Query: 109 GYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
           G  FV   ++ +++ AL+  +   +  R + V  +
Sbjct: 89  GEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKS 122

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 56.1 bits (135), Expect = 3e-11
 Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 5/95 (5%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEY---GNVVGARVLYDGESGRSR 108
           S      L       + + +  L WS + E +     +      V G   +Y    GR  
Sbjct: 3   SGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYT-REGRQS 61

Query: 109 GYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA 143
           G  FV   ++ +++ AL+  +   +  R + V  +
Sbjct: 62  GEAFVELESEDDVKLALK-KDRESMGHRYIEVFKS 95

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 54.9 bits (132), Expect = 6e-11
 Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 3/82 (3%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARV--LYDGESGRSRGYGFVCYSTKAEM 121
           +  F +    L WS T E +   F +     G           G+ RG   +   ++ ++
Sbjct: 9   DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDV 68

Query: 122 ETALESLNGVELEGRAMRVSLA 143
           + ALE  + + +  R + V   
Sbjct: 69  QKALE-KHRMYMGQRYVEVYEI 89

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 54.1 bits (130), Expect = 1e-10
 Identities = 12/78 (15%), Positives = 26/78 (33%), Gaps = 8/78 (10%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE-- 126
           L +  L   VT   +      +G V    +L      + +   F+  +T+    T +   
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELATEEAAITMVNYY 71

Query: 127 SLNGVELEGRAMRVSLAQ 144
           S     L  + + +  + 
Sbjct: 72  SAVTPHLRNQPIYIQYSN 89

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 51.1 bits (122), Expect = 2e-09
 Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 6/65 (9%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +  G L   V+   L    ++ G V    +        ++ Y F  Y T  E + A  +L
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMP------PNKPYSFARYRTTEESKRAYVTL 83

Query: 129 NGVEL 133
           NG E+
Sbjct: 84  NGKEV 88

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 50.9 bits (121), Expect = 1e-08
 Identities = 19/131 (14%), Positives = 48/131 (36%), Gaps = 16/131 (12%)

Query: 24  MSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT--- 80
           +   ED   +    +  +  GR    ++ +     +  + + +  L+VG +  ++ +   
Sbjct: 93  IPDEEDIGKLALRTEVLDCFGREKFADYREDMGG-IGSFRKKNKTLYVGGIDGALNSKHL 151

Query: 81  ------ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELE 134
                   +   F   G++   R +       S+  GFV +  +A  E A E+++   L 
Sbjct: 152 KPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQANAEFAKEAMSNQTLL 205

Query: 135 GRAMRVSLAQG 145
             + +    + 
Sbjct: 206 LPSDKEWDDRR 216

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 49.1 bits (116), Expect = 4e-08
 Identities = 8/83 (9%), Positives = 29/83 (34%), Gaps = 2/83 (2%)

Query: 62  YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEM 121
               +  +++       T + + +  ++ G V+  ++         +G  FV + +    
Sbjct: 105 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESA 163

Query: 122 ETALESLNGVELEGRAMRVSLAQ 144
           +  +E   G + +   + +    
Sbjct: 164 KKFVE-TPGQKYKETDLLILFKD 185

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 47.4 bits (112), Expect = 1e-07
 Identities = 18/122 (14%), Positives = 43/122 (35%), Gaps = 6/122 (4%)

Query: 25  STVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLT 84
                  A ++ ++  +     L  + +               ++ V NL + VT + L 
Sbjct: 5   HHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLH 64

Query: 85  QAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL--EGRAMRVSL 142
           Q F ++G V+            ++    + Y+     + A  SL+G  +      +R+  
Sbjct: 65  QIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 120

Query: 143 AQ 144
           ++
Sbjct: 121 SK 122

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 45.8 bits (108), Expect = 1e-07
 Identities = 16/90 (17%), Positives = 34/90 (37%), Gaps = 7/90 (7%)

Query: 63  AETDFKLFVGNLSWSVTT----ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTK 118
           +     + V N+ + ++     + L +AF  +G V    +         +    V     
Sbjct: 6   SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENL 62

Query: 119 AEMETALESLNGVELEGRAMRVSLAQGRRS 148
            +   A+ SL+  ++  + + VSLA G   
Sbjct: 63  QDAIGAVNSLHRYKIGSKKILVSLATGASG 92

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 46.1 bits (109), Expect = 2e-07
 Identities = 19/78 (24%), Positives = 28/78 (35%), Gaps = 7/78 (8%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           +     + V  L  +V  E LT  F+      G  VL      R    G + +   A+ E
Sbjct: 5   SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVL---SWQRLGCGGVLTFREPADAE 61

Query: 123 TALE----SLNGVELEGR 136
             L      L+G +L  R
Sbjct: 62  RVLAQADHELHGAQLSLR 79

>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 = 42.9 bits (101), Expect = 2e-06
 Identities = 9/46 (19%), Positives = 17/46 (36%)

Query: 7   VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
            + D       G  +V     ED    + +L+ R + G+ +    S
Sbjct: 58  NVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103

>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 = 36.8 bits (85), Expect = 3e-04
 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 81  ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV 140
           E  T+  ++YG V    V  D       G  +V +  + + E A+  LN     G+ +  
Sbjct: 42  EVFTEMEEKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100

Query: 141 SL 142
            L
Sbjct: 101 EL 102

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 42.7 bits (100), Expect = 4e-06
 Identities = 16/78 (20%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           + V NL + VT + L Q F ++G V+            ++    + Y+     + A  SL
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSL 86

Query: 129 NGVEL--EGRAMRVSLAQ 144
           +G  +      +R+  ++
Sbjct: 87  DGQNIYNACCTLRIDFSK 104

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 40.3 bits (94), Expect = 3e-05
 Identities = 17/96 (17%), Positives = 38/96 (39%), Gaps = 9/96 (9%)

Query: 51  FSDKPKPKLPLYAETDFKLFVGNLSWSVTTES-LTQAFQEYGNVVGARVLYDGESGRSRG 109
              KP  K     E    + + NL  S  ++S + +  + YG +    ++      R + 
Sbjct: 10  PEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM------RMKS 63

Query: 110 YGFVCYSTKAEMETALE--SLNGVELEGRAMRVSLA 143
             F+   T+ +    ++      +  +GR ++V L+
Sbjct: 64  QAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS 99

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 37.5 bits (87), Expect = 2e-04
 Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 9/79 (11%)

Query: 69  LFVGNLSWSVTTES-LTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE- 126
           + + +          L Q  + +G +    +L            F+  +T  + + A++ 
Sbjct: 18  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKINEAFIEMATTEDAQAAVDY 71

Query: 127 -SLNGVELEGRAMRVSLAQ 144
            +     + G+ +RV L+Q
Sbjct: 72  YTTTPALVFGKPVRVHLSQ 90

>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 = 37.4 bits (87), Expect = 3e-04
 Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 9/55 (16%)

Query: 16  SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLF 70
             G A V+    E+ +  I+ LDGR + GR +     D           TD++  
Sbjct: 63  PDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWD---------GTTDYQSG 108

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 36.2 bits (83), Expect = 8e-04
 Identities = 13/78 (16%), Positives = 29/78 (37%), Gaps = 7/78 (8%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L + N  + +T + L       G V    +       R+     V + +    + A  +L
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKVQRIVIF-----KRNGIQAMVEFESVLCAQKAKAAL 82

Query: 129 NGVELEGRA--MRVSLAQ 144
           NG ++      +++  A+
Sbjct: 83  NGADIYAGCCTLKIEYAR 100

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	148
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.98
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.98
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.98
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.98
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.97
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.97
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.96
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.96
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.95
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.95
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.93
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.92
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.91
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.91
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.91
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.91
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.91
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.9
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.9
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.9
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.9
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.9
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.9
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.9
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.9
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.9
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.9
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.9
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.89
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.89
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.89
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.89
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.89
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.89
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.89
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.89
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.89
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.89
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.89
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.89
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.89
2div_A	99	TRNA selenocysteine associated protein; structural	99.89
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.89
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.89
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.89
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.89
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.88
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.88
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.88
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.88
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.88
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.88
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.88
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.88
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.88
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.88
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.88
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.88
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.88
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.88
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.88
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.88
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.88
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.88
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.88
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.87
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.87
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.87
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.87
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.87
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.87
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.87
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.87
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.87
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.87
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.87
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.87
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.87
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.87
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.87
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.86
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.86
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.86
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.86
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.86
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.86
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.86
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.86
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.86
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.86
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.86
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.86
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.86
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.86
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.86
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.85
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.85
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.85
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.85
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.85
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.85
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.85
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.85
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.85
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.85
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.85
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.85
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.85
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.85
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.85
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.85
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.84
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.84
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.84
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.84
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.84
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.84
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.84
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.84
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.84
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.84
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.84
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.84
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.84
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.84
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.84
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.84
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.84
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.84
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.83
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.83
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.83
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.83
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.83
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.83
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.83
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.83
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.83
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.83
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.83
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.82
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.82
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.82
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.82
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.82
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.82
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.82
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.82
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.71
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.82
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.81
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.81
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.81
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.81
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.81
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.81
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.81
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.8
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.8
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.8
1x5p_A	97	Negative elongation factor E; structure genomics,	99.8
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.79
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.79
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.79
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.79
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.79
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.79
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.78
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.77
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.77
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.76
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.76
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.76
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.75
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.75
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.74
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.74
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.74
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.72
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.72
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.71
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.7
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.69
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.69
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.69
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.68
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.67
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.65
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.63
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.61
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.61
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.57
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.56
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.54
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.52
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.51
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.5
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.46
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.45
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.45
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.45
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.44
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.44
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.44
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.44
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.44
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.43
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.43
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.43
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.42
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.42
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.41
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.41
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.4
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.4
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.4
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.39
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.39
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.39
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.39
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.39
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.39
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.38
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.38
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.38
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.38
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.38
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.38
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.37
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.37
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.37
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.37
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.37
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.37
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.36
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.36
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.36
2div_A	99	TRNA selenocysteine associated protein; structural	99.36
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.36
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.36
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.35
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.35
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.35
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.35
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.35
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.35
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.34
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.34
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.34
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.33
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.33
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.33
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.33
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.32
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.32
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.31
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.31
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.31
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.31
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.31
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.31
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.3
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.3
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.29
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.29
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.29
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.29
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.28
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.28
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.28
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.28
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.28
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.28
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.27
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.27
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.27
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.27
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.27
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.26
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.26
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.26
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.25
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.25
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.25
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.24
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.24
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.24
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.24
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.24
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.23
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.22
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.22
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.22
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.22
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.21
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.19
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.19
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.17
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.17
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.17
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.16
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.16
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.15
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.15
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.75
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.13
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.12
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	99.11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.11
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.11
1x5p_A	97	Negative elongation factor E; structure genomics,	99.09
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.09
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.08
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.07
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.06
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.06
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.05
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.05
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.05
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.04
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.03
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.03
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.02
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.02
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.01
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.0
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.0
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.0
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.99
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.98
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.98
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.97
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.97
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.97
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.96
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.96
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.96
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.94
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.93
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.93
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.93
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.9
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.9
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.89
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.89
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	98.86
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.85
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	98.85
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.81
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.8
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	98.68
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	98.61
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.59
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	98.53
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.45
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.42
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.31
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.16
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.1
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	98.1
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.98
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.95
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.82
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.37
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.27
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	97.09
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.73
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.7
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	94.63
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	93.63
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	91.82
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	81.71

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.1e-33  Score=177.64  Aligned_cols=141  Identities=28%  Similarity=0.648  Sum_probs=129.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      .|.+|++++++ +++++|||||+|.+.++|..|+..+++..+.|+++.+.++.....   ....+..+|+|+|||..+++
T Consensus        26 ~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~---~~~~~~~~l~v~nl~~~~t~  101 (166)
T 3md3_A           26 PIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQ---SSSDDTFNLFVGDLNVNVDD  101 (166)
T ss_dssp             CEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCC---CCCTTCEEEEEESCCTTCCH
T ss_pred             CeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCC---CCCCCCceEEECCCCCCCCH
Confidence            47889999996 688999999999999999999999999999999999999876544   23446779999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      ++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|.+|+..|||..++|+.|+|.++++
T Consensus       102 ~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          102 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             HHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            99999999999999999999988899999999999999999999999999999999999999864

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=4.3e-33  Score=176.65  Aligned_cols=138  Identities=32%  Similarity=0.537  Sum_probs=128.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|..|+..+++..+.|+++.+.++.+...     ....++|+|+|||..+++
T Consensus        29 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~-----~~~~~~l~v~nl~~~~t~  103 (168)
T 1b7f_A           29 PINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGE-----SIKDTNLYVTNLPRTITD  103 (168)
T ss_dssp             CEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCSS-----TTTTCEEEEESCCTTCCH
T ss_pred             CeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCCcc-----cCCCCCEEEeCCCCCCCH
Confidence            378999999999999999999999999999999999999999999999999876543     235679999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEec
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG--RAMRVSLA  143 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g--~~l~v~~~  143 (148)
                      ++|+++|++||.|..+.+..+..++.++|+|||+|.+.++|.+|+..|||..++|  ++|+|++|
T Consensus       104 ~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          104 DQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            9999999999999999999998789999999999999999999999999999988  99999986

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=1.5e-32  Score=173.86  Aligned_cols=138  Identities=29%  Similarity=0.551  Sum_probs=126.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      .|.++++++++.+|+++|||||+|.+.++|..|+..+++..+.|+++.+.++.+...     .....+|+|+|||..+++
T Consensus        28 ~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~-----~~~~~~l~v~nl~~~~t~  102 (167)
T 1fxl_A           28 EIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSA-----SIRDANLYVSGLPKTMTQ  102 (167)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCG-----GGTTCEEEEESCCTTCCH
T ss_pred             CeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCCcc-----cCCCCcEEECCCCCcCCH
Confidence            378999999998999999999999999999999999999999999999999875432     235578999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeE--EEEEec
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRA--MRVSLA  143 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~--l~v~~~  143 (148)
                      ++|+++|++||.|..+.+..+..++.++|+|||+|.+.++|.+|+..|||..++|+.  |+|.||
T Consensus       103 ~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          103 KELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            999999999999999999999888999999999999999999999999999999964  888875

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=1.6e-32  Score=177.99  Aligned_cols=145  Identities=26%  Similarity=0.424  Sum_probs=124.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC-CCCCCCcceEEEcCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL-PLYAETDFKLFVGNLSWSVT   79 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~-~~~~~~~~~l~i~nlp~~~~   79 (148)
                      .|.+|++++++.+|.++|||||+|.+.++|.+|+.. ++..+.|+.+.+.++....... +......++|+|+|||++++
T Consensus        39 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t  117 (196)
T 1l3k_A           39 TLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTE  117 (196)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC-----------CCSEEEEECCTTTCC
T ss_pred             CEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecccCcccccccccCCCcceEEEeCCCCCCC
Confidence            478999999999999999999999999999999984 8999999999999987654332 22334568999999999999


Q ss_pred             HHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           80 TESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        80 ~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      +++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|.+|+.. +|..++|+.|.|.++.++.
T Consensus       118 ~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~  184 (196)
T 1l3k_A          118 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQ  184 (196)
T ss_dssp             HHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC---
T ss_pred             HHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChh
Confidence            999999999999999999999988899999999999999999999995 8999999999999998764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=2.7e-33  Score=184.15  Aligned_cols=147  Identities=22%  Similarity=0.416  Sum_probs=128.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC------CCCCCcceEEEcCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP------LYAETDFKLFVGNL   74 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~------~~~~~~~~l~i~nl   74 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|.+|+..+++..+.|++|.|.++.......+      ......++|+|+||
T Consensus        54 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl  133 (216)
T 2qfj_A           54 PIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASV  133 (216)
T ss_dssp             CEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECC
T ss_pred             CEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCccccchhhhhhhcccCCCcEEEEeCC
Confidence            478999999998999999999999999999999999999999999999988764432110      11235579999999


Q ss_pred             CCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           75 SWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        75 p~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      |.++++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|.+|+..|||..++|+.|.|.++.++.
T Consensus       134 p~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          134 HQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             CTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             CCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            9999999999999999999999999998889999999999999999999999999999999999999998763

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=6.2e-33  Score=182.38  Aligned_cols=141  Identities=27%  Similarity=0.465  Sum_probs=126.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      .|++|+|++++.+|+++|||||+|.+.++|.+|+..+++..+.|+.+.+.++......   ......+|+|+|||+.+++
T Consensus        41 ~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~~~---~~~~~~~l~v~nl~~~~t~  117 (213)
T 4f02_A           41 PILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSL---RKSGVGNIFIKNLDKSIDN  117 (213)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCTHH---HHHCTTEEEEESCCTTCCH
T ss_pred             CEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccccccccc---cccccccceECCcccccHH
Confidence            4789999999999999999999999999999999999999999999999987644321   1123458999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ++|+++|++||.|..+.++.+.  +.++|+|||+|.+.++|++|+..|||..|+|+.|.|.++.++
T Consensus       118 ~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          118 KALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             HHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             HHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            9999999999999999999874  447999999999999999999999999999999999998765

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.98  E-value=7e-31  Score=179.21  Aligned_cols=144  Identities=21%  Similarity=0.309  Sum_probs=131.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCC-C
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSV-T   79 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~-~   79 (148)
                      .|.++++++++.+|.++|||||+|.+.++|..|+..+++..+.|++|.|.++.+.....  .....++|+|+|||.++ +
T Consensus       121 ~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~--~~~~~~~l~v~nlp~~~~~  198 (284)
T 3smz_A          121 SLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTP--ALLHSRCLCVDRLPPGFND  198 (284)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGCCT--TTTSCSEEEEECCCTTCCC
T ss_pred             CeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCCc--ccCCccEEEEecCCcccCC
Confidence            36789999999999999999999999999999999999999999999999987654432  23466799999999995 9


Q ss_pred             HHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           80 TESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        80 ~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      +++|+++|++||.|..+.+..++ ++.++|+|||+|.+.++|.+|+..|||..++|+.|+|.++.++.
T Consensus       199 ~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  265 (284)
T 3smz_A          199 VDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP  265 (284)
T ss_dssp             HHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSS
T ss_pred             HHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCC
Confidence            99999999999999999999885 68899999999999999999999999999999999999998764

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.98  E-value=1.2e-32  Score=174.50  Aligned_cols=139  Identities=23%  Similarity=0.511  Sum_probs=125.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|..|+.  ++..+.|+.+.+.++.+...     .....+|+|+|||.++++
T Consensus        29 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~~~~~-----~~~~~~l~V~nlp~~~t~  101 (167)
T 2cjk_A           29 TVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAIPRDE-----QDKTGKIFVGGIGPDVRP  101 (167)
T ss_dssp             CEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECCCHHH-----HHHCEEEEEEEECTTCCH
T ss_pred             CEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEcccccccchhh-----ccCCCeEEECCCCCCCCH
Confidence            47899999999999999999999999999999998  46789999999988754321     234568999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      ++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|++|+. ++|..++|+.|.|.++.++.
T Consensus       102 ~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk~  167 (167)
T 2cjk_A          102 KEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPRH  167 (167)
T ss_dssp             HHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCCC
T ss_pred             HHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCCC
Confidence            9999999999999999999888889999999999999999999998 89999999999999998873

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.98  E-value=4.9e-31  Score=171.26  Aligned_cols=138  Identities=21%  Similarity=0.438  Sum_probs=121.7

Q ss_pred             ecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC---------------CCCCCCcceEEEcC
Q 032044            9 YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL---------------PLYAETDFKLFVGN   73 (148)
Q Consensus         9 ~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~---------------~~~~~~~~~l~i~n   73 (148)
                      .+...++++|||||+|.+.++|++|+ .+++..+.|++|.|.++.......               .......++|+|+|
T Consensus        43 ~~~~~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~n  121 (198)
T 2yh0_A           43 LAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG  121 (198)
T ss_dssp             EEEEEETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEEC
T ss_pred             EEeEecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeC
Confidence            33345678999999999999999999 799999999999999876543221               11124668999999


Q ss_pred             CCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           74 LSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        74 lp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      ||.++++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|..|+..|||..++|+.|+|.++.++.
T Consensus       122 l~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             CCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            99999999999999999999999999998889999999999999999999999999999999999999998764

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.98  E-value=5.5e-31  Score=167.58  Aligned_cols=126  Identities=23%  Similarity=0.484  Sum_probs=115.7

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCC
Q 032044           13 TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGN   92 (148)
Q Consensus        13 ~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~   92 (148)
                      .++++|||||+|.+.++|+.|+ .+++..+.|+++.+.++.....     .....+|+|+|||.++++++|+++|++||.
T Consensus        47 ~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~~~~~~~-----~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~  120 (172)
T 2g4b_A           47 INQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQP-----LPGAHKLFIGGLPNYLNDDQVKELLTSFGP  120 (172)
T ss_dssp             EETTTTEEEEEESSHHHHHHHG-GGTTCEETTEECEEECCSSCCC-----CTTTTCEEEECCCTTCCHHHHHHHHHTTSC
T ss_pred             ecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCceeeecCCcccCC-----CCCCCEEEEEcCCCcCCHHHHHHHHHhcCC
Confidence            4567899999999999999999 7999999999999998765432     234679999999999999999999999999


Q ss_pred             eeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           93 VVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        93 v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      |..+.+..++.++.++|+|||+|.+.++|.+|+..|||..++|+.|.|++|.
T Consensus       121 v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          121 LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             EEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            9999999998889999999999999999999999999999999999999974

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.97  E-value=6.8e-31  Score=179.90  Aligned_cols=144  Identities=22%  Similarity=0.306  Sum_probs=120.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC--CCCCCcceEEEcCCCCC-
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP--LYAETDFKLFVGNLSWS-   77 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~--~~~~~~~~l~i~nlp~~-   77 (148)
                      .|.+|++++++. |.++|||||+|.+.++|..|+..+++..+.|++|.|.++.+......  ......++|+|+|||.. 
T Consensus       144 ~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~  222 (292)
T 2ghp_A          144 VALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTEL  222 (292)
T ss_dssp             CCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC---------CCTTTEEEEEEECTTT
T ss_pred             CeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccccccCCCCceEEEECCCccc
Confidence            377899999864 88999999999999999999999999999999999999876554332  24456789999999999 


Q ss_pred             CCHHHHHHHHhhcCCeeEEEEEEcCC-CCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           78 VTTESLTQAFQEYGNVVGARVLYDGE-SGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        78 ~~~~~l~~~f~~~g~v~~~~~~~~~~-~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      +++++|+++|++||.|..+.++.+.. ++.++|+|||+|.+.++|.+|+ .|||..++|+.|.|.++.++
T Consensus       223 ~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          223 LDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             CCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             CCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            99999999999999999999988755 4889999999999999999999 99999999999999999886

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.97  E-value=1.3e-30  Score=166.16  Aligned_cols=139  Identities=28%  Similarity=0.434  Sum_probs=122.6

Q ss_pred             CcceeEeeecCCCC--CcccEEEEEeCCHHHHHHHHHHhCCCeec---CcEEEEeecCCCCCCCCCCCCCcceEEEcCCC
Q 032044            1 MLSKLTVLYDRETG--RSRGFAFVTMSTVEDCNAVIENLDGREYL---GRILRVNFSDKPKPKLPLYAETDFKLFVGNLS   75 (148)
Q Consensus         1 ~i~~i~~~~~~~~~--~~~g~afv~f~~~~~a~~a~~~l~~~~~~---~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp   75 (148)
                      .|.+|++++++.+|  +++|||||+|.+.++|+.|+..+++..+.   +..+.+.++......    ....++|+|+|||
T Consensus        29 ~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~l~v~nl~  104 (175)
T 3nmr_A           29 AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNN----AVEDRKLFIGMIS  104 (175)
T ss_dssp             CEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGCCS----CGGGSEEEEESCC
T ss_pred             CEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEccccccccc----cCCCCeEEEcCCC
Confidence            47899999998877  89999999999999999999999998775   677888876544332    3356799999999


Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC---CeEEEEEecc
Q 032044           76 WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELE---GRAMRVSLAQ  144 (148)
Q Consensus        76 ~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~---g~~l~v~~~~  144 (148)
                      +++++++|+++|++||.|..+.++.++ ++.++|+|||+|.+.++|.+|+..|||..+.   |++|+|.|++
T Consensus       105 ~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          105 KKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             TTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             CcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            999999999999999999999999884 5889999999999999999999999998776   4999999974

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.97  E-value=5.8e-31  Score=167.98  Aligned_cols=131  Identities=24%  Similarity=0.476  Sum_probs=116.7

Q ss_pred             eeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHH
Q 032044            7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQA   86 (148)
Q Consensus         7 ~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~   86 (148)
                      ++++..+|.++|||||+|.+.++|++|++ +++..+.|++|.|.++......   .....++|+|+|||..+++++|+++
T Consensus        44 ~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~~~~~~~---~~~~~~~l~v~nlp~~~t~~~l~~~  119 (175)
T 1fje_B           44 AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSK---KVRAARTLLAKNLSFNITEDELKEV  119 (175)
T ss_dssp             CCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCSSCS---TTGGGGEEEEESCCSSCCHHHHHHH
T ss_pred             EEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecCCCcccc---ccccCCEEEEeCCCCCCCHHHHHHH
Confidence            45555688999999999999999999995 9999999999999998765432   3446789999999999999999999


Q ss_pred             HhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           87 FQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        87 f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      |++||.|..+     ..++.++|+|||+|.+.++|.+|+..|||..++|+.|+|+++.++
T Consensus       120 F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          120 FEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             CTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            9999987655     466788999999999999999999999999999999999999886

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.97  E-value=1.3e-29  Score=159.41  Aligned_cols=142  Identities=20%  Similarity=0.363  Sum_probs=115.4

Q ss_pred             eeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEE-------eecC-CCCCCCCCCCCCcceEEEcCCC
Q 032044            4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV-------NFSD-KPKPKLPLYAETDFKLFVGNLS   75 (148)
Q Consensus         4 ~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v-------~~~~-~~~~~~~~~~~~~~~l~i~nlp   75 (148)
                      +++++++..  +++|||||+|.+.++|++|+..+++....+.....       .... .............++|||+|||
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~   79 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT   79 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCC
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCC
Confidence            578888864  69999999999999999999877653222222221       1111 1122223334567899999999


Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           76 WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        76 ~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      +++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+..|||..++|+.|+|.++.+++
T Consensus        80 ~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             TTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             CCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            999999999999999999999999988889999999999999999999999999999999999999998764

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.97  E-value=6.5e-29  Score=169.31  Aligned_cols=135  Identities=19%  Similarity=0.337  Sum_probs=116.5

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC-----------------------
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK-----------------------   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~-----------------------   58 (148)
                      |.+|++++   +|+++|||||+|.+.++|..|+..+++..+.|+.|.|.++......                       
T Consensus        40 i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (282)
T 3pgw_A           40 ILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQ  116 (282)
T ss_pred             eEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhcccc
Confidence            66777765   7789999999999999999999999999999999999987543310                       


Q ss_pred             --------------------------------------------------------------------------------
Q 032044           59 --------------------------------------------------------------------------------   58 (148)
Q Consensus        59 --------------------------------------------------------------------------------   58 (148)
                                                                                                      
T Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  196 (282)
T 3pgw_A          117 ETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMP  196 (282)
T ss_pred             chhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccC
Confidence                                                                                            


Q ss_pred             ---CCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC-
Q 032044           59 ---LPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELE-  134 (148)
Q Consensus        59 ---~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~-  134 (148)
                         ........++|||+|||..+++++|+++|++||.|..+.+..++     +|+|||+|.+.++|.+|+..|||..++ 
T Consensus       197 ~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~  271 (282)
T 3pgw_A          197 PAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQ  271 (282)
T ss_pred             ccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCC
Confidence               00112245789999999999999999999999999999988552     579999999999999999999999999 


Q ss_pred             CeEEEEEecc
Q 032044          135 GRAMRVSLAQ  144 (148)
Q Consensus       135 g~~l~v~~~~  144 (148)
                      |+.|+|.|++
T Consensus       272 g~~l~v~~ak  281 (282)
T 3pgw_A          272 NNAMKISFAK  281 (282)
T ss_pred             CCEEEEEEec
Confidence            9999999986

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.97  E-value=4.1e-29  Score=163.08  Aligned_cols=136  Identities=18%  Similarity=0.230  Sum_probs=112.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC--------------------
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP--------------------   60 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~--------------------   60 (148)
                      .|.+|+++++     .+|||||+|.+.++|+.|++.||+..+.|++|.|.++........                    
T Consensus        31 ~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~  105 (205)
T 3tyt_A           31 NVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRN  105 (205)
T ss_dssp             CEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTT
T ss_pred             CeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCccCCCcccccccCCccccccCCCcc
Confidence            4778888876     369999999999999999999999999999999999864321000                    


Q ss_pred             ------------CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCe--eEEEEEEcCCCCCceeEEEEEecCHHHHHHHHH
Q 032044           61 ------------LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNV--VGARVLYDGESGRSRGYGFVCYSTKAEMETALE  126 (148)
Q Consensus        61 ------------~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v--~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~  126 (148)
                                  ....+..+|||+|||+++++++|+++|++||.|  ..+.+..+.  +..+|+|||+|.+.++|.+|+.
T Consensus       106 ~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~  183 (205)
T 3tyt_A          106 NRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLG  183 (205)
T ss_dssp             CSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHH
T ss_pred             ccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHH
Confidence                        001245689999999999999999999999998  788877553  4456999999999999999999


Q ss_pred             HhCCceeCCe----EEEEEec
Q 032044          127 SLNGVELEGR----AMRVSLA  143 (148)
Q Consensus       127 ~l~~~~i~g~----~l~v~~~  143 (148)
                      .|||..+.|.    ++.|++|
T Consensus       184 ~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          184 FLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             HHTTCEECCSSSSSCEECEEE
T ss_pred             HhCCCCccCCCCCcceEEEec
Confidence            9999999886    5777665

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.96  E-value=3.6e-28  Score=165.80  Aligned_cols=122  Identities=29%  Similarity=0.426  Sum_probs=114.8

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCe
Q 032044           14 GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNV   93 (148)
Q Consensus        14 ~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v   93 (148)
                      +.++|||||+|.+.++|..|+..+++..+.|+++.+.++.           ..++|+|+|||+++++++|+++|++||.|
T Consensus        54 ~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~-----------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i  122 (284)
T 3smz_A           54 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP-----------TDALLCVANLPPSLTQQQFEELVRPFGSL  122 (284)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC-----------CSCEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC-----------CCCEEEEcCCCCcCCHHHHHHHHHhcCCe
Confidence            5678999999999999999999999999999999999854           34689999999999999999999999999


Q ss_pred             eEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           94 VGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ..+.++.++.++.++|+|||+|.+.++|..|+..|+|..++|+.|.|.++.++
T Consensus       123 ~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~  175 (284)
T 3smz_A          123 ERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAG  175 (284)
T ss_dssp             EEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGG
T ss_pred             eEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            99999999888999999999999999999999999999999999999998765

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.96  E-value=2e-28  Score=162.49  Aligned_cols=136  Identities=22%  Similarity=0.382  Sum_probs=117.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC--------------------
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP--------------------   60 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~--------------------   60 (148)
                      .|.+|++++++     +|||||+|.+.++|++|++.+++..+.|++|.|.++.......+                    
T Consensus        61 ~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (229)
T 2adc_A           61 DVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHR  135 (229)
T ss_dssp             CEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCC
T ss_pred             CeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCccccCccccccccccccccccCcccc
Confidence            37788998875     78999999999999999999999999999999998865421110                    


Q ss_pred             ----------CCCCCcceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 032044           61 ----------LYAETDFKLFVGNLSWSVTTESLTQAFQEYG-NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN  129 (148)
Q Consensus        61 ----------~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  129 (148)
                                ....+.++|+|+|||..+++++|+++|++|| .|..+.+...     .+|+|||+|.+.++|.+|+..||
T Consensus       136 ~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~  210 (229)
T 2adc_A          136 FKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLH  210 (229)
T ss_dssp             CCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHT
T ss_pred             cCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHC
Confidence                      0122468899999999999999999999999 9999988642     36799999999999999999999


Q ss_pred             CceeC-CeEEEEEeccCC
Q 032044          130 GVELE-GRAMRVSLAQGR  146 (148)
Q Consensus       130 ~~~i~-g~~l~v~~~~~~  146 (148)
                      |..++ |+.|+|.|++++
T Consensus       211 g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          211 NHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             TCBSSSSCBCEEEECSSC
T ss_pred             CCccCCCCeEEEEEecCC
Confidence            99999 999999999875

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.96  E-value=1.1e-28  Score=160.34  Aligned_cols=136  Identities=22%  Similarity=0.382  Sum_probs=117.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC--------------------
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP--------------------   60 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~--------------------   60 (148)
                      .|.+|++++++     +|||||+|.+.++|+.|+..+++..+.|++|.|.++.......+                    
T Consensus        30 ~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r  104 (198)
T 1qm9_A           30 DVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHR  104 (198)
T ss_dssp             CCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSCCCSSSSSSSSSCEEESSCCCTTS
T ss_pred             CEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCcCCCCcCCccccccccccCCchhh
Confidence            36788888875     68999999999999999999999999999999998865421110                    


Q ss_pred             ----------CCCCCcceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 032044           61 ----------LYAETDFKLFVGNLSWSVTTESLTQAFQEYG-NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN  129 (148)
Q Consensus        61 ----------~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  129 (148)
                                ....+.++|+|+|||..+++++|+++|++|| .|..+.+..+     .+|+|||+|.+.++|.+|+..||
T Consensus       105 ~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~  179 (198)
T 1qm9_A          105 FKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLH  179 (198)
T ss_dssp             SSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHT
T ss_pred             ccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhc
Confidence                      0123478899999999999999999999999 9999988643     26899999999999999999999


Q ss_pred             CceeC-CeEEEEEeccCC
Q 032044          130 GVELE-GRAMRVSLAQGR  146 (148)
Q Consensus       130 ~~~i~-g~~l~v~~~~~~  146 (148)
                      |..++ |+.|+|.|++++
T Consensus       180 g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          180 NHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             SSCCSSCCSCCEEEECCC
T ss_pred             CCccCCCCeEEEEeeccc
Confidence            99999 999999999875

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.96  E-value=1.8e-27  Score=162.90  Aligned_cols=130  Identities=17%  Similarity=0.217  Sum_probs=114.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      .|.+|++++++.+  ++|||||+|.+.++|..|+. +++..+.|+++.+.++            ..++|+|+|||+.+++
T Consensus        67 ~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~~------------~~~~l~v~nlp~~~t~  131 (292)
T 2ghp_A           67 PIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL------------TECTLWMTNFPPSYTQ  131 (292)
T ss_dssp             CEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC------------CSCEEEEECCCTTCCH
T ss_pred             CeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEEC------------CCCEEEEECCCCCCCH
Confidence            4788999998633  58999999999999999995 9999999999999986            3568999999999999


Q ss_pred             HHHHHHHhhcC-CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           81 ESLTQAFQEYG-NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        81 ~~l~~~f~~~g-~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ++|+++|.+|| .|..+.++.++. +.++|+|||+|.+.++|..|+..|+|..++|+.|.|.++.++
T Consensus       132 ~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  197 (292)
T 2ghp_A          132 RNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPL  197 (292)
T ss_dssp             HHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             HHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            99999999999 999999988754 678999999999999999999999999999999999998765

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

Probab=99.95  E-value=1.9e-27  Score=148.37  Aligned_cols=129  Identities=22%  Similarity=0.295  Sum_probs=113.6

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHh-CCCeecCcEEEEeecCCCC-----------CCCCCCCCCcceEEEcCCCCCCCH
Q 032044           13 TGRSRGFAFVTMSTVEDCNAVIENL-DGREYLGRILRVNFSDKPK-----------PKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus        13 ~~~~~g~afv~f~~~~~a~~a~~~l-~~~~~~~~~i~v~~~~~~~-----------~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      ....+|+++++|.+.++|++|+..+ ++..+.| ++.+.++....           ..........++|||+|||+++++
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~   87 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNK   87 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSC
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCH
Confidence            3478999999999999999999999 9999999 99998775421           122334456789999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      ++|+++|++||.|..+.++.+     ++|+|||+|.+.++|..|+..|||..++|+.|+|+++.+++
T Consensus        88 ~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           88 TELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            999999999999999999765     58899999999999999999999999999999999998875

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.95  E-value=9.1e-27  Score=157.23  Aligned_cols=127  Identities=33%  Similarity=0.438  Sum_probs=114.0

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHH
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTE   81 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~   81 (148)
                      |.+|++.+      ++|||||+|.+.++|..|+..+++..+.|++|.|.++.+           ..+|+|+|||+.++++
T Consensus        49 i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~-----------~~~l~v~nl~~~~t~~  111 (261)
T 3sde_A           49 PSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH-----------GAALTVKNLSPVVSNE  111 (261)
T ss_dssp             CSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC-----------SSEEEEESCCTTCCHH
T ss_pred             EEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc-----------CCcccccCCCCCCCHH
Confidence            66777754      469999999999999999999999999999999999863           4589999999999999


Q ss_pred             HHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhC-CceeC---CeEEEEEeccCC
Q 032044           82 SLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN-GVELE---GRAMRVSLAQGR  146 (148)
Q Consensus        82 ~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~-~~~i~---g~~l~v~~~~~~  146 (148)
                      +|+++|.+||.|..+.++.+ .++.++|+|||+|.+.++|..|+..|| +..+.   |++|.|.++.+.
T Consensus       112 ~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          112 LLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             HHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             HHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            99999999999999999998 678899999999999999999999995 55554   899999998654

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.93  E-value=3.4e-25  Score=128.86  Aligned_cols=81  Identities=35%  Similarity=0.588  Sum_probs=78.0

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||+++++++|+++|++||.|..+.+++++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|++++
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 032044          145 G  145 (148)
Q Consensus       145 ~  145 (148)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            6

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.92  E-value=5.3e-25  Score=134.83  Aligned_cols=125  Identities=26%  Similarity=0.449  Sum_probs=82.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEE
Q 032044           17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGA   96 (148)
Q Consensus        17 ~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~   96 (148)
                      .-|+|+++.+...+..|+..+++....+.. ...+.     ..+......++|||+|||+++++++|+++|++||.|..+
T Consensus         4 ~~~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~-----~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v   77 (135)
T 2lea_A            4 SHHHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYG-----RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV   77 (135)
T ss_dssp             --------------------------------CCSC-----CSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEE
T ss_pred             cccccccccCCCchhhhhhhccCCCCCCCC-CCCcC-----CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEE
Confidence            357899999999999999988887655543 11221     123334567899999999999999999999999999999


Q ss_pred             EEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           97 RVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        97 ~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      .++.++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|+++++++
T Consensus        78 ~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A           78 YIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             ECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCC
T ss_pred             EEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            999888888999999999999999999999999999999999999998763

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.91  E-value=1.4e-24  Score=124.46  Aligned_cols=82  Identities=18%  Similarity=0.343  Sum_probs=76.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhC-CceeCCeEEEEEec
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYG-NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN-GVELEGRAMRVSLA  143 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~-~~~i~g~~l~v~~~  143 (148)
                      +++|+|+|||+++++++|+++|++|| .|..+.+++++.++.++|||||+|.+.++|++|+..++ +..++|++|+|+++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 79999999998999999999999999999999999874 57899999999999


Q ss_pred             cCCC
Q 032044          144 QGRR  147 (148)
Q Consensus       144 ~~~~  147 (148)
                      .++.
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            8764

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.91  E-value=1.2e-23  Score=124.46  Aligned_cols=83  Identities=14%  Similarity=0.202  Sum_probs=79.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .++++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 032044          144 QGR  146 (148)
Q Consensus       144 ~~~  146 (148)
                      ..+
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            654

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.91  E-value=2.2e-23  Score=131.78  Aligned_cols=125  Identities=23%  Similarity=0.358  Sum_probs=79.7

Q ss_pred             EEeCCHHHHHHHHHHhCCCeec--CcEEEEeecCCC---------------CCCCCCCCCCcceEEEcCCCCCCCHHHHH
Q 032044           22 VTMSTVEDCNAVIENLDGREYL--GRILRVNFSDKP---------------KPKLPLYAETDFKLFVGNLSWSVTTESLT   84 (148)
Q Consensus        22 v~f~~~~~a~~a~~~l~~~~~~--~~~i~v~~~~~~---------------~~~~~~~~~~~~~l~i~nlp~~~~~~~l~   84 (148)
                      .+|.+.++|..|+..+++....  |+.....+....               ....+....+.++|||+|||+.+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            6899999999999988876554  444444332110               11112234456789999999999999999


Q ss_pred             HHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           85 QAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        85 ~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ++|.+||.|..+.++.++.++.++|||||+|.+.++|+.|+..|||..|+|+.|.|.++.++
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  152 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK  152 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            99999999999999999889999999999999999999999999999999999999998765

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.91  E-value=3.5e-23  Score=117.68  Aligned_cols=83  Identities=37%  Similarity=0.685  Sum_probs=76.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .+.++|||+|||.++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+..|||..++|+.|+|+++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            35679999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             cCC
Q 032044          144 QGR  146 (148)
Q Consensus       144 ~~~  146 (148)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            875

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.91  E-value=5.1e-23  Score=116.02  Aligned_cols=81  Identities=36%  Similarity=0.775  Sum_probs=78.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      .+|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+..|||..++|+.|+|+++.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            58999999999999999999999999999999999889999999999999999999999999999999999999999887


Q ss_pred             C
Q 032044          147 R  147 (148)
Q Consensus       147 ~  147 (148)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.90  E-value=9.5e-23  Score=118.78  Aligned_cols=86  Identities=21%  Similarity=0.454  Sum_probs=80.2

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ....+.++|||+|||+++++++|+++|.+||.|..+.+..++ ++.++|+|||+|.+.++|++|+..|||..++|+.|+|
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   90 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKV   90 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            334567899999999999999999999999999999999986 8889999999999999999999999999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      ++++++.
T Consensus        91 ~~a~~~~   97 (100)
T 2do4_A           91 AISNSGP   97 (100)
T ss_dssp             EECCCCS
T ss_pred             EECCCCC
Confidence            9998875

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.90  E-value=6.7e-23  Score=120.96  Aligned_cols=89  Identities=35%  Similarity=0.676  Sum_probs=83.2

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           60 PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        60 ~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      +....++++|||+|||.++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+..|+|..++|+.|+
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~   99 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK   99 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34455778999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 032044          140 VSLAQGRRS  148 (148)
Q Consensus       140 v~~~~~~~~  148 (148)
                      |+++.++.+
T Consensus       100 V~~a~~k~d  108 (108)
T 2jrs_A          100 VGHVTERTD  108 (108)
T ss_dssp             EECSCSSCC
T ss_pred             EEEcccCCC
Confidence            999998864

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.90  E-value=1.6e-22  Score=116.80  Aligned_cols=85  Identities=34%  Similarity=0.545  Sum_probs=80.0

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34556789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EeccC
Q 032044          141 SLAQG  145 (148)
Q Consensus       141 ~~~~~  145 (148)
                      +++++
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99875

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.90  E-value=1.4e-22  Score=118.66  Aligned_cols=86  Identities=20%  Similarity=0.403  Sum_probs=81.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ...+.++|||+|||.++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus        91 ~a~~~~   96 (103)
T 2cq0_A           91 WAKPST   96 (103)
T ss_dssp             ESSCCC
T ss_pred             ECCCCC
Confidence            998764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.90  E-value=1.5e-23  Score=120.72  Aligned_cols=82  Identities=21%  Similarity=0.424  Sum_probs=75.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCC--eeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCc----eeCCeE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGN--VVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV----ELEGRA  137 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~--v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~----~i~g~~  137 (148)
                      ..-.+|||+|||+++++++|+++|++||.  +..+++++++.++.++|||||+|.+.++|++|++.|||.    .++|++
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            34568999999999999999999999995  678999999999999999999999999999999999986    599999


Q ss_pred             EEEEeccC
Q 032044          138 MRVSLAQG  145 (148)
Q Consensus       138 l~v~~~~~  145 (148)
                      |.|++|++
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999875

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.90  E-value=7e-23  Score=118.52  Aligned_cols=83  Identities=22%  Similarity=0.521  Sum_probs=78.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ++++|||+|||.++++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|+.|+..|||..++|+.|+|+++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            35789999999999999999999999999999999998889999999999999999999999999999999999999998


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      +++
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            764

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.90  E-value=8.2e-23  Score=115.65  Aligned_cols=82  Identities=33%  Similarity=0.571  Sum_probs=77.6

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+..|||..++|+.|+|++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34677999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             cc
Q 032044          143 AQ  144 (148)
Q Consensus       143 ~~  144 (148)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.90  E-value=3.5e-22  Score=119.18  Aligned_cols=87  Identities=37%  Similarity=0.643  Sum_probs=81.4

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ......++|||+|||..+++++|+++|.+||.|..+.++.++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34557789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      .++.++.
T Consensus        90 ~~a~~~~   96 (115)
T 2dgo_A           90 NWATRKP   96 (115)
T ss_dssp             EESSCCC
T ss_pred             EEccCCC
Confidence            9997763

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.90  E-value=7.5e-23  Score=118.14  Aligned_cols=84  Identities=37%  Similarity=0.676  Sum_probs=79.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .++++|||+|||.++++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|+++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            45679999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 032044          144 QGRR  147 (148)
Q Consensus       144 ~~~~  147 (148)
                      .++.
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            8774

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.90  E-value=2.4e-22  Score=119.93  Aligned_cols=86  Identities=28%  Similarity=0.526  Sum_probs=80.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||.++++++|+++|.+||.|..+.++.++.++.++++|||+|.+.++|++|+..||+..++|+.|+|+
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34466899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      +++++.
T Consensus       101 ~a~~~~  106 (115)
T 2cpz_A          101 LKRSKN  106 (115)
T ss_dssp             CCCCSC
T ss_pred             EcCCCC
Confidence            998764

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.90  E-value=1.2e-22  Score=118.17  Aligned_cols=85  Identities=24%  Similarity=0.432  Sum_probs=80.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+..|||..++|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34678999999999999999999999999999999999888899999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +.++.
T Consensus        85 a~~~~   89 (99)
T 1whw_A           85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            98764

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=1.2e-22  Score=119.32  Aligned_cols=87  Identities=26%  Similarity=0.458  Sum_probs=81.3

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ......++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..||+..++|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34457789999999999999999999999999999999998888999999999999999999999999999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      +++.++.
T Consensus        90 ~~a~~~~   96 (105)
T 1x5u_A           90 NKASAHN   96 (105)
T ss_dssp             EETTTTS
T ss_pred             EECCCCC
Confidence            9998764

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.89  E-value=2.2e-22  Score=117.08  Aligned_cols=85  Identities=25%  Similarity=0.414  Sum_probs=79.5

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeE--------EEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCc
Q 032044           60 PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVG--------ARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV  131 (148)
Q Consensus        60 ~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~--------~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~  131 (148)
                      ..+....++|||+|||.++++++|+++|++||.|..        +.++.++.++.++|+|||+|.+.++|++|+..|||.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            445567789999999999999999999999999999        999999888999999999999999999999999999


Q ss_pred             eeCCeEEEEEecc
Q 032044          132 ELEGRAMRVSLAQ  144 (148)
Q Consensus       132 ~i~g~~l~v~~~~  144 (148)
                      .++|+.|+|++++
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999974

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=9e-23  Score=118.03  Aligned_cols=84  Identities=26%  Similarity=0.536  Sum_probs=79.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEE-EEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGA-RVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~-~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      .+.++|||+|||+++++++|+++|++||.|..+ .++.++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            356799999999999999999999999999999 9998888899999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +.++.
T Consensus        83 a~~~~   87 (96)
T 1x5t_A           83 AFKKD   87 (96)
T ss_dssp             SCCCC
T ss_pred             ecccC
Confidence            98764

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=1.9e-22  Score=118.73  Aligned_cols=86  Identities=30%  Similarity=0.484  Sum_probs=80.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||.++++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|+.|+..|||..++|+.|.|+
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            998764

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.89  E-value=1.8e-22  Score=117.14  Aligned_cols=87  Identities=22%  Similarity=0.342  Sum_probs=80.4

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34567899999999999999999999999999888888888889999999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 032044          142 LAQGRRS  148 (148)
Q Consensus       142 ~~~~~~~  148 (148)
                      ++..+.+
T Consensus        91 ~a~~~~s   97 (98)
T 2cqp_A           91 LGSGPSS   97 (98)
T ss_dssp             ESSCSSC
T ss_pred             EcCCCCC
Confidence            9987754

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.89  E-value=5.3e-22  Score=116.21  Aligned_cols=87  Identities=24%  Similarity=0.551  Sum_probs=80.3

Q ss_pred             CCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 032044           59 LPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAM  138 (148)
Q Consensus        59 ~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l  138 (148)
                      .+.+..+.++|||+|||+++++++|+++|.+|| |..+.++.++.++.++|+|||+|.+.++|+.|+ .||+..++|+.|
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   85 (103)
T 2dng_A            8 KELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSL   85 (103)
T ss_dssp             CCCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEE
Confidence            344556788999999999999999999999996 999999999888999999999999999999999 899999999999


Q ss_pred             EEEeccCCC
Q 032044          139 RVSLAQGRR  147 (148)
Q Consensus       139 ~v~~~~~~~  147 (148)
                      +|.++.++.
T Consensus        86 ~V~~a~~~~   94 (103)
T 2dng_A           86 RVDIAEGRK   94 (103)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEecCCC
Confidence            999998764

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.89  E-value=2e-22  Score=117.17  Aligned_cols=85  Identities=25%  Similarity=0.543  Sum_probs=79.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||.++++++|+++|.+||.|..+.++.++.++.++|+|||+|.+.++|++|+. +++..++|+.|+|+
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999 99999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus        85 ~a~~~~   90 (99)
T 2dgs_A           85 RAEPRD   90 (99)
T ss_dssp             ECCCCC
T ss_pred             ECCCCc
Confidence            998764

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.89  E-value=3e-22  Score=115.39  Aligned_cols=83  Identities=28%  Similarity=0.541  Sum_probs=78.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++++|||+|.+.++|++|+..|||..++|+.|+|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34567899999999999999999999999999999999988888899999999999999999999999999999999999


Q ss_pred             ecc
Q 032044          142 LAQ  144 (148)
Q Consensus       142 ~~~  144 (148)
                      +++
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            974

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.89  E-value=2.5e-22  Score=119.81  Aligned_cols=81  Identities=32%  Similarity=0.604  Sum_probs=74.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ...+|||+|||+++++++|+++|++||.|..+.++.+.  +.++|||||+|.+.++|++|+..|+|..++|+.|+|.++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35689999999999999999999999999999999884  4478999999999999999999999999999999999987


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      ++.
T Consensus        82 ~~~   84 (115)
T 4f25_A           82 SRK   84 (115)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            653

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.89  E-value=2.1e-22  Score=119.23  Aligned_cols=86  Identities=26%  Similarity=0.460  Sum_probs=80.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ...+.++|||+|||..+++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+..|||..++|+.|+|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            997764

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.89  E-value=3.6e-22  Score=118.41  Aligned_cols=87  Identities=26%  Similarity=0.497  Sum_probs=81.2

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhC------CceeC
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN------GVELE  134 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~------~~~i~  134 (148)
                      ....+.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|+|||+|.+.++|++|+..+|      +..++
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            344567899999999999999999999999999999999998889999999999999999999999999      99999


Q ss_pred             CeEEEEEeccCCC
Q 032044          135 GRAMRVSLAQGRR  147 (148)
Q Consensus       135 g~~l~v~~~~~~~  147 (148)
                      |+.|+|+++.++.
T Consensus        90 g~~l~v~~a~~~~  102 (111)
T 1x4h_A           90 GRQLKVDLAVTRD  102 (111)
T ss_dssp             SCEEEEECCCCCC
T ss_pred             CEEEEEEECCCCc
Confidence            9999999998764

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=1.7e-22  Score=118.15  Aligned_cols=85  Identities=33%  Similarity=0.556  Sum_probs=80.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..+.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|+|||+|.+.++|+.|+..||+..++|+.|+|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            44678999999999999999999999999999999999888889999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +.+++
T Consensus        89 a~~~~   93 (102)
T 2cqb_A           89 AKPMR   93 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98764

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.89  E-value=3e-22  Score=117.99  Aligned_cols=88  Identities=24%  Similarity=0.448  Sum_probs=81.1

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEc-CCCCCceeEEEEEecCHHHHHHHHHHh-CCceeCCeE
Q 032044           60 PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYD-GESGRSRGYGFVCYSTKAEMETALESL-NGVELEGRA  137 (148)
Q Consensus        60 ~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~~~~~fv~f~~~~~a~~a~~~l-~~~~i~g~~  137 (148)
                      .......++|||+|||..+++++|+++|.+||.|..+.++.+ +.++.++|+|||+|.+.++|++|+..| |+..++|+.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~   88 (107)
T 2cph_A            9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR   88 (107)
T ss_dssp             SCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCB
T ss_pred             cccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCE
Confidence            344557789999999999999999999999999999999988 678899999999999999999999999 999999999


Q ss_pred             EEEEeccCCC
Q 032044          138 MRVSLAQGRR  147 (148)
Q Consensus       138 l~v~~~~~~~  147 (148)
                      |+|+++.++.
T Consensus        89 l~v~~a~~~~   98 (107)
T 2cph_A           89 LVLEWADSEV   98 (107)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEeCCCCC
Confidence            9999998764

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.89  E-value=3.1e-22  Score=116.37  Aligned_cols=85  Identities=24%  Similarity=0.426  Sum_probs=80.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCee-EEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeE----
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVV-GARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRA----  137 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~-~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~----  137 (148)
                      ..++++|||+|||+++++++|+++|++||.|. .+.++.++.++.++|+|||+|.+.++|++|+..|||..++|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            45678999999999999999999999999999 9999999888999999999999999999999999999999999    


Q ss_pred             EEEEeccCCC
Q 032044          138 MRVSLAQGRR  147 (148)
Q Consensus       138 l~v~~~~~~~  147 (148)
                      |+|.++++.+
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999998753

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.89  E-value=2.6e-22  Score=116.49  Aligned_cols=83  Identities=27%  Similarity=0.466  Sum_probs=77.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCC---CCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGE---SGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ++++|||+|||+++++++|+++|++||.|..+.+..++.   ++.++++|||+|.+.++|+.|+..|||..++|+.|.|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            567899999999999999999999999999999998765   55889999999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus        84 ~a~~~~   89 (98)
T 2cpf_A           84 ISERAT   89 (98)
T ss_dssp             CSSCSS
T ss_pred             EccCCC
Confidence            998764

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=1.8e-22  Score=117.96  Aligned_cols=86  Identities=37%  Similarity=0.648  Sum_probs=80.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++++|||+|.+.++|+.|+..||+..++|+.|+|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34467899999999999999999999999999999999988888899999999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus        88 ~a~~~~   93 (102)
T 1x5s_A           88 QAGKSS   93 (102)
T ss_dssp             EEECCC
T ss_pred             ECCCCC
Confidence            987764

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.89  E-value=3.6e-23  Score=118.37  Aligned_cols=81  Identities=26%  Similarity=0.506  Sum_probs=72.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYG--NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      .+|||+|||+++++++|+++|++||  .|..+.++.++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999998899999999999999999999999999999999999999988


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      ++.
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            763

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.89  E-value=1.5e-22  Score=118.59  Aligned_cols=86  Identities=28%  Similarity=0.529  Sum_probs=80.4

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ...+.++|||+|||.++++++|+++|.+||.|..+.+..++.++.++|+|||+|.+.++|++|+..|||..++|+.|.|+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++++++
T Consensus        89 ~a~~~~   94 (103)
T 2dnm_A           89 VARYGR   94 (103)
T ss_dssp             ECSSCC
T ss_pred             ECCcCC
Confidence            998653

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.88  E-value=4e-22  Score=113.75  Aligned_cols=82  Identities=28%  Similarity=0.536  Sum_probs=77.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||+++++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|++|+ .+||..++|+.|+|++++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            3568999999999999999999999999999999999888999999999999999999999 899999999999999998


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      +++
T Consensus        84 ~~~   86 (89)
T 3ucg_A           84 TNR   86 (89)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            764

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=6.9e-22  Score=115.71  Aligned_cols=85  Identities=33%  Similarity=0.636  Sum_probs=78.9

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ....+.++|||+|||+++++++|+++|.+||.|..+.+..+  ++.++++|||+|.+.++|+.|+..|||..++|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV   87 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            34557789999999999999999999999999999999887  7889999999999999999999999999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      .++.++.
T Consensus        88 ~~a~~~~   94 (103)
T 2d9p_A           88 ALAQRKE   94 (103)
T ss_dssp             EECSSCC
T ss_pred             EEecccc
Confidence            9998764

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.88  E-value=2.6e-22  Score=114.27  Aligned_cols=83  Identities=22%  Similarity=0.448  Sum_probs=77.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCC-ceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGR-SRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~-~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .+++|||+|||.++++++|+++|++||.|..+.++.+..++. ++|+|||+|.+.++|+.|+..|||..++|+.|+|+++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            457899999999999999999999999999999998876655 8899999999999999999999999999999999999


Q ss_pred             cCCC
Q 032044          144 QGRR  147 (148)
Q Consensus       144 ~~~~  147 (148)
                      .+++
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.88  E-value=2e-22  Score=122.43  Aligned_cols=87  Identities=33%  Similarity=0.568  Sum_probs=81.4

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            33456789999999999999999999999999999999999888899999999999999999999999999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      +++.+++
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9998775

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=6.4e-22  Score=116.04  Aligned_cols=86  Identities=27%  Similarity=0.489  Sum_probs=79.3

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCC-CCceeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 032044           60 PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGES-GRSRGYGFVCYSTKAEMETALESLNGVELEGRAM  138 (148)
Q Consensus        60 ~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~-~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l  138 (148)
                      +.+..+.++|||+|||+++++++|+++|.+|| |..+.++.++.+ +.++|+|||+|.+.++|++|+ .||+..++|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   86 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRI   86 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEE
Confidence            34455778999999999999999999999999 999999998877 889999999999999999999 899999999999


Q ss_pred             EEEeccCCC
Q 032044          139 RVSLAQGRR  147 (148)
Q Consensus       139 ~v~~~~~~~  147 (148)
                      +|+++.++.
T Consensus        87 ~V~~a~~~~   95 (104)
T 1wi8_A           87 RVDVADQAQ   95 (104)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCCC
Confidence            999998764

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.88  E-value=5.6e-23  Score=119.74  Aligned_cols=82  Identities=21%  Similarity=0.339  Sum_probs=78.2

Q ss_pred             CcceEEEcCCCC------CCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC-eE
Q 032044           65 TDFKLFVGNLSW------SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG-RA  137 (148)
Q Consensus        65 ~~~~l~i~nlp~------~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g-~~  137 (148)
                      .+++|||+|||+      ++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..|||..++| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            467999999999      99999999999999999999999999989999999999999999999999999999999 99


Q ss_pred             EEEEeccCC
Q 032044          138 MRVSLAQGR  146 (148)
Q Consensus       138 l~v~~~~~~  146 (148)
                      |+|.++.++
T Consensus        85 l~V~~a~~~   93 (100)
T 3ns6_A           85 LFLYTMKDV   93 (100)
T ss_dssp             CEEEESHHH
T ss_pred             EEEEECchh
Confidence            999998764

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.88  E-value=1.2e-21  Score=115.03  Aligned_cols=84  Identities=30%  Similarity=0.474  Sum_probs=78.3

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC---eEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG---RAMR  139 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g---~~l~  139 (148)
                      ...+++|||+|||+++++++|+++|++||.|..+.+..++ ++.++|+|||+|.+.++|++|+..|||..+.|   +.|+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3467899999999999999999999999999999999986 68899999999999999999999999999988   9999


Q ss_pred             EEeccCCC
Q 032044          140 VSLAQGRR  147 (148)
Q Consensus       140 v~~~~~~~  147 (148)
                      |.++.++.
T Consensus        91 V~~a~~~~   98 (105)
T 2dnh_A           91 VKFADTDK   98 (105)
T ss_dssp             EEESCSSC
T ss_pred             EEECccCc
Confidence            99998764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.88  E-value=1.5e-21  Score=120.07  Aligned_cols=86  Identities=28%  Similarity=0.520  Sum_probs=80.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||.++++++|+++|+.||.|..+.++.++.++.++|+|||+|.+.++|.+|+..|||..++|+.|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34466899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus       118 ~a~~~~  123 (139)
T 1u6f_A          118 LAASGH  123 (139)
T ss_dssp             ESSCCC
T ss_pred             ECCCCC
Confidence            998763

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.88  E-value=8.4e-22  Score=113.71  Aligned_cols=83  Identities=34%  Similarity=0.572  Sum_probs=77.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||+.+++++|+++|++||.|..+.++.++. +.++|+|||+|.+.++|++|+..|||..++|+.|+|+
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            345678999999999999999999999999999999999865 8899999999999999999999999999999999999


Q ss_pred             eccC
Q 032044          142 LAQG  145 (148)
Q Consensus       142 ~~~~  145 (148)
                      +++.
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9864

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.88  E-value=5.3e-22  Score=116.78  Aligned_cols=87  Identities=23%  Similarity=0.434  Sum_probs=80.5

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee---CCeE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL---EGRA  137 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i---~g~~  137 (148)
                      ......++|||+|||.++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..||+..+   .|+.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            3445678999999999999999999999999999999999888899999999999999999999999999988   8999


Q ss_pred             EEEEeccCCC
Q 032044          138 MRVSLAQGRR  147 (148)
Q Consensus       138 l~v~~~~~~~  147 (148)
                      |+|+++.+++
T Consensus        88 l~v~~a~~~~   97 (106)
T 2dgp_A           88 IQVKPADSES   97 (106)
T ss_dssp             CEEEECCCCS
T ss_pred             EEEEECCccc
Confidence            9999997764

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=1.2e-21  Score=113.25  Aligned_cols=82  Identities=20%  Similarity=0.265  Sum_probs=75.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLT----QAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAM  138 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l  138 (148)
                      ....++|||+|||+++++++|+    ++|++||.|..+.++.++.+   +++|||+|.+.++|++|+..|||..++|+.|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            3456799999999999999999    99999999999999887654   7899999999999999999999999999999


Q ss_pred             EEEeccCCC
Q 032044          139 RVSLAQGRR  147 (148)
Q Consensus       139 ~v~~~~~~~  147 (148)
                      +|++++++.
T Consensus        83 ~V~~a~~~~   91 (96)
T 2dgx_A           83 LVSLATGAS   91 (96)
T ss_dssp             EEEECCCSS
T ss_pred             EEEEcCCCC
Confidence            999998764

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=3e-21  Score=112.97  Aligned_cols=85  Identities=28%  Similarity=0.563  Sum_probs=77.6

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ......++|||+|||+++++++|+++|.+||.|..+.++.+..  .++++|||+|.+.++|++|+..||+..++|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4455678999999999999999999999999999999987754  37899999999999999999999999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      +++.++.
T Consensus        88 ~~a~~~~   94 (103)
T 2cq3_A           88 NNATARV   94 (103)
T ss_dssp             EECCSSC
T ss_pred             EEcccCC
Confidence            9998764

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=3.5e-21  Score=112.71  Aligned_cols=85  Identities=26%  Similarity=0.390  Sum_probs=77.1

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ......++|||+|||+.+++++|+++|++||.|..+.++.++.+  ++++|||+|.+.++|++|+..||+..++|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            34456789999999999999999999999999999999887443  6899999999999999999999999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      +++.++.
T Consensus        88 ~~a~~~~   94 (103)
T 2cqi_A           88 NWATTPS   94 (103)
T ss_dssp             EECCCTT
T ss_pred             EECCCCc
Confidence            9998764

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.88  E-value=1.6e-21  Score=114.86  Aligned_cols=83  Identities=39%  Similarity=0.580  Sum_probs=77.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ...+.++|||+|||+.+++++|+++|.+||.|..+.++.++ ++.++|+|||+|.+.++|++|+..|||..++|+.|+|+
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34567899999999999999999999999999999999997 88899999999999999999999999999999999999


Q ss_pred             eccC
Q 032044          142 LAQG  145 (148)
Q Consensus       142 ~~~~  145 (148)
                      ++.+
T Consensus       104 ~a~s  107 (107)
T 3ulh_A          104 LVTS  107 (107)
T ss_dssp             EECC
T ss_pred             EeCC
Confidence            9863

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=2.3e-22  Score=117.92  Aligned_cols=84  Identities=39%  Similarity=0.706  Sum_probs=79.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||+|||..+++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|+.|+..|||..++|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            35678999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 032044          144 QGRR  147 (148)
Q Consensus       144 ~~~~  147 (148)
                      .++.
T Consensus        86 ~~~~   89 (104)
T 1p1t_A           86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCcc
Confidence            8764

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.88  E-value=9.9e-22  Score=112.76  Aligned_cols=83  Identities=30%  Similarity=0.526  Sum_probs=77.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..+.++|||+|||.++++++|+++|++||.|..+.+..  +++.++++|||+|.+.++|+.|+..|||..++|+.|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~--~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEE--SSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEc--cCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45678999999999999999999999999999999886  3678899999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      ++++.
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            98764

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=1.1e-21  Score=116.61  Aligned_cols=86  Identities=27%  Similarity=0.451  Sum_probs=79.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCee--------EEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVV--------GARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL  133 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~--------~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i  133 (148)
                      .....++|||+|||+++++++|+++|.+||.|.        .+.++.++.++.++|+|||+|.+.++|++|+..|||..+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345678999999999999999999999999998        689998888899999999999999999999999999999


Q ss_pred             CCeEEEEEeccCCC
Q 032044          134 EGRAMRVSLAQGRR  147 (148)
Q Consensus       134 ~g~~l~v~~~~~~~  147 (148)
                      +|+.|+|++++++.
T Consensus        91 ~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           91 QGSKLKVSLARKKP  104 (113)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCCEEEEEECCCCC
Confidence            99999999998764

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.88  E-value=7.7e-22  Score=117.81  Aligned_cols=84  Identities=27%  Similarity=0.521  Sum_probs=78.4

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ...+++|||+|||.++++++|+++|++||.|..+.+..+. ++.++|+|||+|.+.++|+.|+..|||..++|+.|+|++
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999999886 888999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      ++++.
T Consensus        83 a~~~~   87 (116)
T 2fy1_A           83 AKKPS   87 (116)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            97653

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.88  E-value=2.2e-21  Score=110.25  Aligned_cols=80  Identities=35%  Similarity=0.680  Sum_probs=75.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+. +++..++|+.|.|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            4467799999999999999999999999999999999998889999999999999999999997 688899999999987


Q ss_pred             c
Q 032044          143 A  143 (148)
Q Consensus       143 ~  143 (148)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.87  E-value=8.4e-22  Score=115.52  Aligned_cols=84  Identities=32%  Similarity=0.579  Sum_probs=78.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhh-cCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCce-eCCeEEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQE-YGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVE-LEGRAMRV  140 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~-~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~-i~g~~l~v  140 (148)
                      ..+.++|||+|||+++++++|+++|.+ ||.|..+.++.++ ++.++|+|||+|.+.++|+.|+..||+.. ++|+.|+|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            456789999999999999999999999 9999999999997 88999999999999999999999999999 99999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      .++.++.
T Consensus        85 ~~a~~~~   91 (104)
T 2dhg_A           85 SVAIPKA   91 (104)
T ss_dssp             CBCCCCC
T ss_pred             EEccCCC
Confidence            9987653

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.87  E-value=9.1e-22  Score=123.07  Aligned_cols=82  Identities=28%  Similarity=0.472  Sum_probs=77.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYG--NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..++|||+|||+++++++|+++|++||  .|..+.++.++.++.++|||||+|.+.++|++|+..|||..++|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            457999999999999999999999999  899999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 032044          143 AQGR  146 (148)
Q Consensus       143 ~~~~  146 (148)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8754

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.87  E-value=7e-22  Score=118.39  Aligned_cols=83  Identities=25%  Similarity=0.528  Sum_probs=77.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999988888999999999999999999999999999999999999


Q ss_pred             ecc
Q 032044          142 LAQ  144 (148)
Q Consensus       142 ~~~  144 (148)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            874

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=1.5e-21  Score=114.61  Aligned_cols=86  Identities=36%  Similarity=0.558  Sum_probs=80.3

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ......++|||+|||+.+++++|+++|.+||.|..+.++.++.++.++|+|||+|.+.++|++|+.. ++..++|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V   89 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP   89 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEE
Confidence            3455778999999999999999999999999999999999988899999999999999999999998 999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      +++.++.
T Consensus        90 ~~a~~~~   96 (105)
T 2dh8_A           90 KPCTPRG   96 (105)
T ss_dssp             CCSCCSS
T ss_pred             EEccCCC
Confidence            9998764

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.87  E-value=5.4e-22  Score=114.50  Aligned_cols=82  Identities=21%  Similarity=0.330  Sum_probs=75.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ..+++|||+|||+++++++|+++|.+||.|..+.++.++.++.++++|||+|.+.++|++|+..||+..++|+.|+|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            35689999999999999999999999999998888888888899999999999999999999999999999999999998


Q ss_pred             cC
Q 032044          144 QG  145 (148)
Q Consensus       144 ~~  145 (148)
                      .+
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            64

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=4.4e-21  Score=109.83  Aligned_cols=82  Identities=22%  Similarity=0.330  Sum_probs=76.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ....++|||+|||+++++++|+++|++| .|..+.++.+ .++.++|+|||+|.+.++|++|+. +||..++|+.|.|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            4467899999999999999999999999 8999999998 778999999999999999999999 999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +.++.
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98763

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.87  E-value=1.2e-21  Score=112.98  Aligned_cols=78  Identities=15%  Similarity=0.199  Sum_probs=70.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCce--eCCeEEEEE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVE--LEGRAMRVS  141 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~--i~g~~l~v~  141 (148)
                      .++++|||+|||+++++++|+++|++||.|.++.+++      .+|+|||+|.+.++|..|+..+++..  ++|++|+|+
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            4677999999999999999999999999999998873      36799999999999999999999864  889999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      +++++.
T Consensus        93 ~S~~k~   98 (100)
T 3r27_A           93 YSTSQK   98 (100)
T ss_dssp             ECSCSC
T ss_pred             eccccc
Confidence            998864

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.87  E-value=3.8e-21  Score=120.49  Aligned_cols=84  Identities=29%  Similarity=0.480  Sum_probs=79.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ....++|||.|||.++++++|+++|++||.|..+.++.++.++.++++|||+|.+.++|++|+..||+..|+|+.|+|++
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34678999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ccCC
Q 032044          143 AQGR  146 (148)
Q Consensus       143 ~~~~  146 (148)
                      +.++
T Consensus       116 a~~~  119 (156)
T 1h2v_Z          116 DAGF  119 (156)
T ss_dssp             ESCC
T ss_pred             CCCC
Confidence            9765

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=8.9e-22  Score=114.57  Aligned_cols=79  Identities=14%  Similarity=0.220  Sum_probs=71.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhC--CceeCCeEEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN--GVELEGRAMRV  140 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~--~~~i~g~~l~v  140 (148)
                      +.+.++|||+|||+++++++|+++|++||.|..+.++.+      +|+|||+|.+.++|+.|+..++  +..++|+.|+|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            346679999999999999999999999999999998854      6899999999999999999886  47899999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      .+++++.
T Consensus        87 ~~A~~~~   93 (105)
T 1sjq_A           87 QFSNHKE   93 (105)
T ss_dssp             CCCSSSS
T ss_pred             EEcCCCC
Confidence            9998764

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=1.1e-20  Score=110.53  Aligned_cols=85  Identities=24%  Similarity=0.441  Sum_probs=78.2

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ....+.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|+|||+|.+.++|++|+.  ++..++|+.|.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v   87 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDC   87 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEE
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEE
Confidence            344567899999999999999999999999999999999998889999999999999999999999  578999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      +++.++.
T Consensus        88 ~~a~~~~   94 (103)
T 2cqg_A           88 KLPNSKQ   94 (103)
T ss_dssp             ECCCTTC
T ss_pred             EecCCCC
Confidence            9998763

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=3.5e-21  Score=115.00  Aligned_cols=85  Identities=36%  Similarity=0.550  Sum_probs=78.8

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ......++|||.|||+++++++|+++|.+||.|..+.++.++.++.++++|||+|.+.++|++|+..+++ .++|+.|+|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            3445678999999999999999999999999999999999988899999999999999999999999998 899999999


Q ss_pred             EeccCC
Q 032044          141 SLAQGR  146 (148)
Q Consensus       141 ~~~~~~  146 (148)
                      +++.++
T Consensus        91 ~~a~~~   96 (116)
T 2cqd_A           91 NLAYLG   96 (116)
T ss_dssp             EESTTT
T ss_pred             EEcccC
Confidence            998653

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.87  E-value=1.9e-21  Score=115.28  Aligned_cols=86  Identities=17%  Similarity=0.288  Sum_probs=77.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHH---HHHhhcCCeeEEEEEEcCCC---CCceeEEEEEecCHHHHHHHHHHhCCceeCC
Q 032044           62 YAETDFKLFVGNLSWSVTTESLT---QAFQEYGNVVGARVLYDGES---GRSRGYGFVCYSTKAEMETALESLNGVELEG  135 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~---~~f~~~g~v~~~~~~~~~~~---~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g  135 (148)
                      .....++|||+|||+++++++|+   ++|.+||.|..+.++.+..+   +.++|+|||+|.+.++|++|+..|||..++|
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            34467799999999999999999   99999999999999877653   3566999999999999999999999999999


Q ss_pred             eEEEEEeccCCC
Q 032044          136 RAMRVSLAQGRR  147 (148)
Q Consensus       136 ~~l~v~~~~~~~  147 (148)
                      +.|+|.++.++.
T Consensus        91 r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 RTLKASLGTTKY  102 (111)
T ss_dssp             EEEEEESCCCCS
T ss_pred             EEEEEEeccccc
Confidence            999999998764

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.87  E-value=1.4e-21  Score=118.32  Aligned_cols=85  Identities=31%  Similarity=0.494  Sum_probs=79.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|+|||+|.+.++|+.|+..|||..++|+.|.|+
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34467899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.++
T Consensus        98 ~a~~~  102 (126)
T 3ex7_B           98 WCFVR  102 (126)
T ss_dssp             ESEES
T ss_pred             EecCC
Confidence            99765

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.87  E-value=1.8e-21  Score=115.05  Aligned_cols=85  Identities=33%  Similarity=0.602  Sum_probs=75.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||.++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..+ +..++|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            3456789999999999999999999999999999999999888999999999999999999999976 599999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus       100 ~a~~~~  105 (109)
T 2rs2_A          100 VAFPRR  105 (109)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            998764

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.87  E-value=2.9e-22  Score=116.70  Aligned_cols=85  Identities=28%  Similarity=0.507  Sum_probs=75.3

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcC-CCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDG-ESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~-~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      ......++|||+|||.++++++|+++|++|| |..+.+..++ .++.++|+|||+|.+.++|++|+ .|||..++|+.|+
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~   91 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIR   91 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEE
Confidence            3445678999999999999999999999999 9999999887 57889999999999999999999 8999999999999


Q ss_pred             EEeccCCC
Q 032044          140 VSLAQGRR  147 (148)
Q Consensus       140 v~~~~~~~  147 (148)
                      |++++++.
T Consensus        92 V~~a~~~~   99 (100)
T 2j76_E           92 VDVADQAQ   99 (100)
T ss_dssp             CEECCCSC
T ss_pred             EEeccCCC
Confidence            99998875

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=8.1e-21  Score=112.22  Aligned_cols=84  Identities=21%  Similarity=0.436  Sum_probs=75.6

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ......++|||.|||+++++++|+++|++||.|..+.+..+   +.++++|||+|.+.++|+.|+..||+..++|+.|+|
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   93 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   93 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            34456789999999999999999999999999999988643   457899999999999999999999999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      +++++++
T Consensus        94 ~~a~~~~  100 (109)
T 1x4a_A           94 EFPRSGR  100 (109)
T ss_dssp             ECCCCCC
T ss_pred             EEcccCC
Confidence            9998764

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=1e-20  Score=112.61  Aligned_cols=84  Identities=32%  Similarity=0.450  Sum_probs=77.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||.++++++|+++|.+||.|..+.++.++ ++.++++|||+|.+.++|+.|+..||+..++|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34467899999999999999999999999999999999886 58899999999999999999999999999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      +++..
T Consensus        90 ~a~~~   94 (114)
T 2do0_A           90 MDERA   94 (114)
T ss_dssp             ECSCC
T ss_pred             EcccC
Confidence            98643

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=6.3e-22  Score=117.90  Aligned_cols=81  Identities=25%  Similarity=0.384  Sum_probs=76.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||.++++++|+++|.+||.|..+.++.++.++.++|+|||+|.+.++|++|+ .|||..++|+.|+|+++.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            4579999999999999999999999999999999999888899999999999999999999 899999999999999987


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      ++
T Consensus       103 ~~  104 (114)
T 2cq4_A          103 AE  104 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.86  E-value=4.2e-21  Score=107.22  Aligned_cols=75  Identities=19%  Similarity=0.215  Sum_probs=69.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      +.+.-|+|+||++.+++++|+++|.+||+|..+.+..      ++|||||+|.++++|++|++.||+..++|+.|+|+++
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            3566799999999999999999999999999998853      5899999999999999999999999999999999998


Q ss_pred             c
Q 032044          144 Q  144 (148)
Q Consensus       144 ~  144 (148)
                      .
T Consensus        79 ~   79 (89)
T 2wbr_A           79 S   79 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.86  E-value=6.2e-22  Score=120.67  Aligned_cols=86  Identities=24%  Similarity=0.430  Sum_probs=79.4

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeE--EEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCc----eeC
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVG--ARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV----ELE  134 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~--~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~----~i~  134 (148)
                      ......++|||+|||+++++++|+++|.+||.|..  +.+++++.++.++|||||+|.+. +|.+|+..|||.    .++
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~   96 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTID   96 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGG
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCC
Confidence            33456789999999999999999999999999976  99999988999999999999999 999999999999    999


Q ss_pred             CeEEEEEeccCCC
Q 032044          135 GRAMRVSLAQGRR  147 (148)
Q Consensus       135 g~~l~v~~~~~~~  147 (148)
                      |+.|+|+++.+++
T Consensus        97 gr~l~V~~a~~~~  109 (131)
T 2m2b_A           97 GKTINVEFAKGSK  109 (131)
T ss_dssp             GCCCCCEECCCSC
T ss_pred             CEEEEEEECCCCC
Confidence            9999999998763

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1e-21  Score=114.74  Aligned_cols=80  Identities=10%  Similarity=0.206  Sum_probs=74.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||+|||+++++++|+++|++||.|..+.++.++. +.++|+|||+|.+.++|+.|+. +++..++|+.|.|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3567999999999999999999999999999999999876 8899999999999999999999 9999999999999986


Q ss_pred             cC
Q 032044          144 QG  145 (148)
Q Consensus       144 ~~  145 (148)
                      .+
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            43

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=2.6e-21  Score=114.34  Aligned_cols=84  Identities=27%  Similarity=0.564  Sum_probs=76.8

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ......++|||+|||.++++++|+++|++||.|..+.+..+.  +.++|+|||+|.+.++|++|+..|||..++|+.|+|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            334567899999999999999999999999999999998774  347899999999999999999999999999999999


Q ss_pred             EeccCC
Q 032044          141 SLAQGR  146 (148)
Q Consensus       141 ~~~~~~  146 (148)
                      +++.++
T Consensus       102 ~~a~~~  107 (109)
T 2err_A          102 NNATAR  107 (109)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            999876

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=2.3e-22  Score=113.84  Aligned_cols=82  Identities=21%  Similarity=0.432  Sum_probs=76.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .++++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+..|||..++|+.++++++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            45679999999999999999999999999999999999888999999999999999999999999999999999998876


Q ss_pred             cC
Q 032044          144 QG  145 (148)
Q Consensus       144 ~~  145 (148)
                      ++
T Consensus        83 ~s   84 (85)
T 1x4e_A           83 SS   84 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.9e-21  Score=116.16  Aligned_cols=83  Identities=36%  Similarity=0.613  Sum_probs=78.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|+|||+|.+.++|+.|+.. ++..++|+.|+|.++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            3568999999999999999999999999999999999988899999999999999999999997 999999999999999


Q ss_pred             cCCC
Q 032044          144 QGRR  147 (148)
Q Consensus       144 ~~~~  147 (148)
                      .++.
T Consensus       104 ~~~~  107 (116)
T 1x4b_A          104 VARE  107 (116)
T ss_dssp             SSCC
T ss_pred             CCCc
Confidence            8764

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.86  E-value=1.1e-20  Score=114.13  Aligned_cols=84  Identities=36%  Similarity=0.566  Sum_probs=79.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||..+++++|+++|++||.|..+.+..++ ++.++|+|||+|.+.++|+.|+..|||..++|+.|+|+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            45577899999999999999999999999999999999887 88899999999999999999999999999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.+.
T Consensus       110 ~a~~~  114 (124)
T 2kt5_A          110 LVASQ  114 (124)
T ss_dssp             EECCT
T ss_pred             EeCCC
Confidence            98765

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.86  E-value=4.2e-21  Score=115.93  Aligned_cols=82  Identities=21%  Similarity=0.499  Sum_probs=77.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||.++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+ .|||..++|+.|+|.+++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4579999999999999999999999999999999999888999999999999999999999 799999999999999997


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      +++
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.1e-20  Score=112.56  Aligned_cols=84  Identities=24%  Similarity=0.466  Sum_probs=78.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee--------C
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL--------E  134 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i--------~  134 (148)
                      ....++|||+|||+++++++|+++|.+||.|..+.++.++ ++.++|+|||+|.+.++|+.|+..|||..+        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            4467899999999999999999999999999999999997 888999999999999999999999999999        5


Q ss_pred             CeEEEEEeccCCC
Q 032044          135 GRAMRVSLAQGRR  147 (148)
Q Consensus       135 g~~l~v~~~~~~~  147 (148)
                      +++|.|.++.++.
T Consensus       101 ~~~l~v~~a~p~~  113 (114)
T 1x5o_A          101 TEPLLCKFSGPSS  113 (114)
T ss_dssp             SSCBEEEECCCSC
T ss_pred             CCceeEEccCCCC
Confidence            7889999998764

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.2e-20  Score=109.76  Aligned_cols=81  Identities=14%  Similarity=0.167  Sum_probs=71.9

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHh--CCceeCCeEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL--NGVELEGRAM  138 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l--~~~~i~g~~l  138 (148)
                      ....++++|||+|||+.+++++|+++|++||.|..+.++.+      +|+|||+|.+.++|+.|+..+  ++..++|+.|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   83 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   83 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEE
Confidence            33456789999999999999999999999999999988743      789999999999999999977  5688999999


Q ss_pred             EEEeccCCC
Q 032044          139 RVSLAQGRR  147 (148)
Q Consensus       139 ~v~~~~~~~  147 (148)
                      +|.+++++.
T Consensus        84 ~V~~a~~~~   92 (101)
T 2cq1_A           84 YIQYSNHKE   92 (101)
T ss_dssp             EEEECSCSS
T ss_pred             EEEEcCccc
Confidence            999998763

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=3.8e-21  Score=113.65  Aligned_cols=84  Identities=20%  Similarity=0.347  Sum_probs=77.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEE-EcCCCCCceeEEEEEecCHHHHHHHHHHhC--CceeCCeEEE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGN-VVGARVL-YDGESGRSRGYGFVCYSTKAEMETALESLN--GVELEGRAMR  139 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~-v~~~~~~-~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~--~~~i~g~~l~  139 (148)
                      .+.++|||+|||+++++++|+++|.+||. |..+.++ .+..++.++|+|||+|.+.++|+.|+..|+  +..++|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            35679999999999999999999999998 9999888 677778899999999999999999999996  5899999999


Q ss_pred             EEeccCCC
Q 032044          140 VSLAQGRR  147 (148)
Q Consensus       140 v~~~~~~~  147 (148)
                      |.++.++.
T Consensus        86 V~~a~~~~   93 (109)
T 2dis_A           86 VDWAEPEI   93 (109)
T ss_dssp             EEESCSSC
T ss_pred             EEEcCCCC
Confidence            99998764

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.86  E-value=9.6e-22  Score=108.70  Aligned_cols=75  Identities=31%  Similarity=0.594  Sum_probs=71.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        68 ~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      +|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+. +++..++|+.|+|+++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            48999999999999999999999999999999988889999999999999999999998 9999999999999875

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.85  E-value=1e-20  Score=116.40  Aligned_cols=82  Identities=33%  Similarity=0.557  Sum_probs=76.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ...+.++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..|||..++|+.|+|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999988889999999999999999999999999999999999999


Q ss_pred             ec
Q 032044          142 LA  143 (148)
Q Consensus       142 ~~  143 (148)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            85

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=3.4e-21  Score=111.96  Aligned_cols=78  Identities=18%  Similarity=0.233  Sum_probs=70.4

Q ss_pred             CCCcceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCC--ceeCCeEEE
Q 032044           63 AETDFKLFVGNLSW-SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNG--VELEGRAMR  139 (148)
Q Consensus        63 ~~~~~~l~i~nlp~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~--~~i~g~~l~  139 (148)
                      ..++++|||+|||+ .+++++|+++|++||.|..+.++++      +++|||+|.+.++|+.|+..|++  ..++|++|+
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            34678999999999 9999999999999999999998754      47999999999999999999986  469999999


Q ss_pred             EEeccCC
Q 032044          140 VSLAQGR  146 (148)
Q Consensus       140 v~~~~~~  146 (148)
                      |.+++.+
T Consensus        86 V~~a~~~   92 (102)
T 1x4d_A           86 VHLSQKY   92 (102)
T ss_dssp             EEEECCC
T ss_pred             EEECCCC
Confidence            9999864

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.85  E-value=5.1e-22  Score=113.55  Aligned_cols=80  Identities=30%  Similarity=0.689  Sum_probs=73.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ++|||+|||.++++++|+++|++||.|..+.+..++.++.++|+|||+|.+.+ |++|+..|||..++|+.|+|+++.++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            57999999999999999999999999999999999888999999999999999 99999999999999999999999765


Q ss_pred             C
Q 032044          147 R  147 (148)
Q Consensus       147 ~  147 (148)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=2.4e-20  Score=110.05  Aligned_cols=79  Identities=25%  Similarity=0.348  Sum_probs=72.7

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC-----e
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG-----R  136 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g-----~  136 (148)
                      +....++|||.|||+++++++|+++|.+||.|..+.++.+       ++|||+|.+.++|+.|+..||+..++|     +
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~   83 (108)
T 1x4c_A           11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   83 (108)
T ss_dssp             CCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcce
Confidence            3456789999999999999999999999999999988754       799999999999999999999999999     9


Q ss_pred             EEEEEeccCCC
Q 032044          137 AMRVSLAQGRR  147 (148)
Q Consensus       137 ~l~v~~~~~~~  147 (148)
                      .|+|+++.++.
T Consensus        84 ~i~V~~a~~~~   94 (108)
T 1x4c_A           84 YIRVKVDGPRS   94 (108)
T ss_dssp             EEEEEESSCCS
T ss_pred             EEEEEeCCCCC
Confidence            99999998763

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=1.7e-21  Score=108.24  Aligned_cols=76  Identities=34%  Similarity=0.647  Sum_probs=72.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ++|+|+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..++ ..++|+.|.|+++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999998889999999999999999999999999 9999999999986

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=8.7e-21  Score=112.93  Aligned_cols=80  Identities=14%  Similarity=0.215  Sum_probs=72.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCC--ceeCCeEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNG--VELEGRAMR  139 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~--~~i~g~~l~  139 (148)
                      ...++++|||+|||+++++++|+++|++||.|..+.++.+      +|+|||+|.+.++|+.|+..+++  ..++|+.|+
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            3446789999999999999999999999999999998854      68999999999999999998874  689999999


Q ss_pred             EEeccCCC
Q 032044          140 VSLAQGRR  147 (148)
Q Consensus       140 v~~~~~~~  147 (148)
                      |.+++++.
T Consensus       101 V~~a~~k~  108 (119)
T 2ad9_A          101 IQFSNHKE  108 (119)
T ss_dssp             EEECSSSS
T ss_pred             EEEccCCC
Confidence            99998763

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.85  E-value=1.2e-20  Score=113.95  Aligned_cols=82  Identities=16%  Similarity=0.340  Sum_probs=73.3

Q ss_pred             CCCcceEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLT----QAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAM  138 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l  138 (148)
                      ..+.++|||+|||+.+++++|+    ++|++||.|..+.+.   .++.++|+|||+|.+.++|+.|+..|||..+.|+.|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~---~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            3456799999999999999876    699999999988775   356789999999999999999999999999999999


Q ss_pred             EEEeccCCC
Q 032044          139 RVSLAQGRR  147 (148)
Q Consensus       139 ~v~~~~~~~  147 (148)
                      +|.++.++.
T Consensus       103 ~V~~a~~~~  111 (127)
T 2a3j_A          103 VITFSETPQ  111 (127)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCcc
Confidence            999998764

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.85  E-value=6.1e-21  Score=112.02  Aligned_cols=82  Identities=22%  Similarity=0.394  Sum_probs=74.6

Q ss_pred             CCCcceEEEcCCCCCC------CHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCe
Q 032044           63 AETDFKLFVGNLSWSV------TTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR  136 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~------~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~  136 (148)
                      ...+++|||+|||+.+      ++++|+++|++||.|..+.++  +.++.++|+|||+|.+.++|+.|+..|||..++|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3456799999999999      779999999999999999887  46788999999999999999999999999999998


Q ss_pred             -EEEEEeccCC
Q 032044          137 -AMRVSLAQGR  146 (148)
Q Consensus       137 -~l~v~~~~~~  146 (148)
                       .|+|.++.+.
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             9999998653

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.85  E-value=8.6e-21  Score=113.58  Aligned_cols=81  Identities=21%  Similarity=0.388  Sum_probs=75.4

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCC---eeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGN---VVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~---v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      ....++|||+|||+++++++|+++|++||.   |..+.++.++. +.++|+|||+|.+.++|++|+. +|+..|+|+.|+
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            446789999999999999999999999998   89999999866 8899999999999999999999 999999999999


Q ss_pred             EEeccC
Q 032044          140 VSLAQG  145 (148)
Q Consensus       140 v~~~~~  145 (148)
                      |.++.+
T Consensus        92 V~~a~~   97 (118)
T 2db1_A           92 VFKSHR   97 (118)
T ss_dssp             EEEECH
T ss_pred             EEECCH
Confidence            998754

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

Probab=99.85  E-value=1.9e-20  Score=106.97  Aligned_cols=77  Identities=29%  Similarity=0.575  Sum_probs=71.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..+.++|||+|||.++++++|+++|++||.|..+.+.        +++|||+|.+.++|+.|+..||+..++|+.|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            4567899999999999999999999999999999886        56999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +.++.
T Consensus        77 a~~~~   81 (90)
T 2dnq_A           77 SKNKS   81 (90)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            97764

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=2.3e-20  Score=108.04  Aligned_cols=79  Identities=20%  Similarity=0.427  Sum_probs=72.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC--CeEEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELE--GRAMRV  140 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~--g~~l~v  140 (148)
                      ..++++|||+|||+++++++|+++|++||.|..+.+..+      +++|||+|.+.++|++|+..||+..++  |+.|+|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            345679999999999999999999999999999988643      679999999999999999999999999  999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      ++++++.
T Consensus        88 ~~a~~~~   94 (97)
T 1why_A           88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9998875

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=3.3e-20  Score=108.35  Aligned_cols=84  Identities=29%  Similarity=0.497  Sum_probs=75.9

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           61 LYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ....+.++|||+|||.++++++|+++|++|+   .+.++.++.++.++++|||+|.+.++|++|+..||+..++|+.|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            3455678999999999999999999999873   6777888788899999999999999999999999999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      +++.++.
T Consensus        87 ~~a~~~~   93 (102)
T 2fc8_A           87 DWAKPKG   93 (102)
T ss_dssp             EECCCCC
T ss_pred             EEecCCC
Confidence            9998764

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=6.3e-21  Score=113.54  Aligned_cols=83  Identities=17%  Similarity=0.227  Sum_probs=76.3

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCe-eEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNV-VGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v-~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      .....++|||+|||+++++++|+++|.+||.| ..+.++.++ ++.++|+|||+|.+.++|++|+.. |+..|+|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            34567899999999999999999999999999 889999887 888999999999999999999996 999999999999


Q ss_pred             EeccCC
Q 032044          141 SLAQGR  146 (148)
Q Consensus       141 ~~~~~~  146 (148)
                      .++.++
T Consensus        89 ~~a~~~   94 (114)
T 2cpy_A           89 HVVTLE   94 (114)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=2e-20  Score=109.03  Aligned_cols=82  Identities=33%  Similarity=0.575  Sum_probs=73.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||+++++++|+++|.+||.|   .++.+ .++.++++|||+|.+.++|++|+..||+..++|+.|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            44567899999999999999999999999976   45555 567889999999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus        87 ~a~~~~   92 (101)
T 2fc9_A           87 LQGPRG   92 (101)
T ss_dssp             ECSSCC
T ss_pred             EcCCCC
Confidence            998764

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.85  E-value=5.1e-21  Score=116.87  Aligned_cols=83  Identities=20%  Similarity=0.368  Sum_probs=76.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCC---eeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGN---VVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAM  138 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~---v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l  138 (148)
                      .....++|||+|||+++++++|+++|++||.   |..+.++.++. +.++|+|||+|.+.++|++|+. +|+..++|+.|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            3446789999999999999999999999999   88999999976 8999999999999999999999 99999999999


Q ss_pred             EEEeccCC
Q 032044          139 RVSLAQGR  146 (148)
Q Consensus       139 ~v~~~~~~  146 (148)
                      .|.++.++
T Consensus       118 ~V~~a~~~  125 (136)
T 2hgl_A          118 EVFKSHRT  125 (136)
T ss_dssp             EEEECCHH
T ss_pred             EEEECChH
Confidence            99998643

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

Probab=99.85  E-value=3.2e-20  Score=107.42  Aligned_cols=79  Identities=20%  Similarity=0.424  Sum_probs=71.5

Q ss_pred             CCCCCcceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           61 LYAETDFKLFVGNLSW-SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      ....++++|||+|||. ++++++|+++|++||.|..+.+.        +|+|||+|.+.++|++|+..|||..++|+.|+
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   88 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLI   88 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4455778999999998 99999999999999999998883        67999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 032044          140 VSLAQGRR  147 (148)
Q Consensus       140 v~~~~~~~  147 (148)
                      |++++++.
T Consensus        89 V~~a~~~~   96 (97)
T 2xnq_A           89 LEVSSSNA   96 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEecCCCC
Confidence            99998763

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=1.6e-20  Score=109.78  Aligned_cols=79  Identities=14%  Similarity=0.202  Sum_probs=70.4

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNG--VELEGRAMRV  140 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~--~~i~g~~l~v  140 (148)
                      ..++++|||+|||+++++++|+++|++||.|..+.++.+      +|+|||+|.+.++|..|+..|++  ..++|+.|+|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            446689999999999999999999999999999988643      68999999999999999998865  4599999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      .+++++.
T Consensus        86 ~~a~~~~   92 (104)
T 1wex_A           86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEccCcc
Confidence            9998763

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=1.7e-20  Score=108.98  Aligned_cols=80  Identities=30%  Similarity=0.495  Sum_probs=73.3

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ...+.++|||+|||+.+++++|+++|.+||.|..+.+.++      +++|||+|.+.++|++|+..|||..++|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            3456789999999999999999999999999999988743      6799999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus        85 ~a~~~~   90 (99)
T 2cpj_A           85 FACHSA   90 (99)
T ss_dssp             ESSCCS
T ss_pred             EcCCCC
Confidence            998764

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

Probab=99.84  E-value=5.9e-20  Score=105.32  Aligned_cols=78  Identities=31%  Similarity=0.558  Sum_probs=71.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||+++++++|+++|++||.|..+.+.        +++|||+|.+.++|++|+..|||..++|+.|+|+
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            34567899999999999999999999999999999886        3399999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus        78 ~a~~~~   83 (92)
T 2dgt_A           78 LSTSRL   83 (92)
T ss_dssp             ESSCCC
T ss_pred             EccCCC
Confidence            998764

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=2.8e-21  Score=116.74  Aligned_cols=84  Identities=19%  Similarity=0.327  Sum_probs=76.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      +....++|||+|||+++++++|+++|.+||.|..+.++.+..++.++|+|||+|.+.++|+.|+. +|+..|+|+.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            44567899999999999999999999999999886666666789999999999999999999999 99999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.++
T Consensus       100 ~a~~~  104 (124)
T 1wel_A          100 PITKK  104 (124)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            98653

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=2.9e-20  Score=107.62  Aligned_cols=80  Identities=30%  Similarity=0.513  Sum_probs=72.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ...+++|||+|||+++++++|+++|.+||.|. +.++.+    .++|+|||+|.+.++|+.|+..|||..++|+.|+|++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            44578999999999999999999999999986 566654    4688999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +++++
T Consensus        91 a~~~~   95 (97)
T 2e5j_A           91 ARQQR   95 (97)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98875

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.84  E-value=1.2e-21  Score=114.34  Aligned_cols=84  Identities=29%  Similarity=0.500  Sum_probs=74.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||+++++++|+++|.+||.|.. .++.+..++.++|+|||+|.+.++|++|+. |||..++|+.|+|.
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~   90 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   90 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEE
Confidence            3446789999999999999999999999998877 555555667889999999999999999999 99999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus        91 ~a~~~~   96 (101)
T 1fj7_A           91 KPKGRD   96 (101)
T ss_dssp             CCSCCC
T ss_pred             EcCCCC
Confidence            998764

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1.5e-20  Score=110.68  Aligned_cols=79  Identities=24%  Similarity=0.310  Sum_probs=72.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ....+|+|+|||+++++++|+++|++| .|..+.++.++. +.++|+|||+|.+.++|++|+ .+|+..++|+.|.|..+
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            345799999999999999999999999 889999998865 889999999999999999999 59999999999999887


Q ss_pred             cC
Q 032044          144 QG  145 (148)
Q Consensus       144 ~~  145 (148)
                      .+
T Consensus        91 ~~   92 (109)
T 2dnn_A           91 TE   92 (109)
T ss_dssp             CH
T ss_pred             Cc
Confidence            64

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.84  E-value=2.4e-20  Score=110.07  Aligned_cols=79  Identities=19%  Similarity=0.262  Sum_probs=70.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYG-NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ...++|||+|||+++++++|+++|++|| .|..+.+...    .++|+|||+|.+.++|++|+..|||..++|+.|+|++
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3567999999999999999999999999 8998877532    3689999999999999999999999999999999999


Q ss_pred             ccCC
Q 032044          143 AQGR  146 (148)
Q Consensus       143 ~~~~  146 (148)
                      +..+
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            8755

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.84  E-value=7.6e-21  Score=110.06  Aligned_cols=82  Identities=22%  Similarity=0.442  Sum_probs=74.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLT----QAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAM  138 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l  138 (148)
                      ..++++|||+|||.++++++|+    ++|++||.|..+.+..   ++.++|+|||+|.+.++|+.|+..|||..++|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3467799999999999999999    9999999999988763   35678999999999999999999999999999999


Q ss_pred             EEEeccCCC
Q 032044          139 RVSLAQGRR  147 (148)
Q Consensus       139 ~v~~~~~~~  147 (148)
                      +|+++.++.
T Consensus        82 ~v~~a~~~~   90 (97)
T 1nu4_A           82 RIQYAKTDS   90 (97)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEccCCC
Confidence            999998864

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.84  E-value=1.7e-20  Score=108.42  Aligned_cols=81  Identities=22%  Similarity=0.464  Sum_probs=72.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ...+.++|||+|||+.+++++|+++|++||.|..+     ..++.++|+|||+|.+.++|+.|+..|||..++|+.|+|.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34467899999999999999999999999987665     2457789999999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus        87 ~a~~~~   92 (96)
T 1fjc_A           87 YTGEKG   92 (96)
T ss_dssp             ECSSSC
T ss_pred             EcCCCC
Confidence            997764

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=3.2e-20  Score=109.62  Aligned_cols=78  Identities=24%  Similarity=0.540  Sum_probs=72.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||+|||..+++++|+++|++||.|..+.+..+      +++|||+|.+.++|+.|+..|||..++|+.|+|.++
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            45679999999999999999999999999999988754      679999999999999999999999999999999999


Q ss_pred             cCCC
Q 032044          144 QGRR  147 (148)
Q Consensus       144 ~~~~  147 (148)
                      +++.
T Consensus        97 ~~~~  100 (109)
T 1x4g_A           97 KESP  100 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.84  E-value=2.7e-20  Score=109.75  Aligned_cols=78  Identities=19%  Similarity=0.405  Sum_probs=72.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ....+++|||+|||.++++++|+++|++||.|..+.+.        +|+|||+|.+.++|+.|+..|||..++|+.|.|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999887        6799999999999999999999999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      +++++.
T Consensus        99 ~a~~~~  104 (108)
T 2jvo_A           99 YSKLPA  104 (108)
T ss_dssp             SCSCCC
T ss_pred             EecCCC
Confidence            998764

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.8e-20  Score=109.83  Aligned_cols=82  Identities=21%  Similarity=0.257  Sum_probs=75.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVG-ARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~-~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ....++|||+|||+++++++|+++|.+||.|.. +.++.+ .++.++|+|||+|.+.++|++|+.. ++..++|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            446789999999999999999999999999987 778777 7889999999999999999999997 9999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.++
T Consensus        90 ~~~~~   94 (104)
T 1wg5_A           90 KSSRA   94 (104)
T ss_dssp             EECTT
T ss_pred             ECCHH
Confidence            98664

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=5.6e-21  Score=113.93  Aligned_cols=85  Identities=26%  Similarity=0.450  Sum_probs=72.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..+.++|||+|||+++++++|+++|.+||.|..+.+.....++.++|+|||+|.+.++|+.|+..|||..++|+.|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            44678999999999999999999999999984332222222677899999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +.++.
T Consensus       102 a~~~~  106 (115)
T 2cpx_A          102 GKNKK  106 (115)
T ss_dssp             CCCCS
T ss_pred             ccCCC
Confidence            98764

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

Probab=99.84  E-value=1.4e-19  Score=105.14  Aligned_cols=80  Identities=29%  Similarity=0.452  Sum_probs=71.8

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhhc--CCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeE
Q 032044           60 PLYAETDFKLFVGNLSWSVTTESLTQAFQEY--GNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRA  137 (148)
Q Consensus        60 ~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~--g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~  137 (148)
                      .....+.++|||+|||+.+++++|+++|.+|  |.|..+.+.        +++|||+|.+.++|+.|+..|||..++|+.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (99)
T 2cpd_A            9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSP   80 (99)
T ss_dssp             CSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEE
T ss_pred             ccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            3445567899999999999999999999999  888888663        569999999999999999999999999999


Q ss_pred             EEEEeccCCC
Q 032044          138 MRVSLAQGRR  147 (148)
Q Consensus       138 l~v~~~~~~~  147 (148)
                      |+|.+++++.
T Consensus        81 l~v~~a~~~~   90 (99)
T 2cpd_A           81 IEVTLAKPVD   90 (99)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999998764

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=5.1e-20  Score=104.05  Aligned_cols=77  Identities=25%  Similarity=0.411  Sum_probs=70.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHh-CCceeCCeEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL-NGVELEGRAMRV  140 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l-~~~~i~g~~l~v  140 (148)
                      .....++|||+|||.++++++|+++|++||.|..+.+..+      +|+|||+|.+.++|+.|+..| +|..++|+.|+|
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v   81 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV   81 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCE
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEE
Confidence            3456789999999999999999999999999999988753      689999999999999999999 999999999999


Q ss_pred             Eecc
Q 032044          141 SLAQ  144 (148)
Q Consensus       141 ~~~~  144 (148)
                      ++++
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9974

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.84  E-value=1.6e-20  Score=111.99  Aligned_cols=81  Identities=25%  Similarity=0.450  Sum_probs=74.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      +.++++|||+|||+++++++|+++|++||.|..+.++.+   +.++|+|||+|.+.++|..|+..|||..++|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            446679999999999999999999999999999999865   34589999999999999999999999999999999999


Q ss_pred             ccCC
Q 032044          143 AQGR  146 (148)
Q Consensus       143 ~~~~  146 (148)
                      +.++
T Consensus        82 a~~~   85 (115)
T 3lqv_A           82 YNAN   85 (115)
T ss_dssp             CCHH
T ss_pred             ecCC
Confidence            9764

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.4e-20  Score=109.82  Aligned_cols=82  Identities=15%  Similarity=0.220  Sum_probs=74.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||+++++++|+++|++||. ..+.++.++ ++.++|+|||+|.+.++|++|+. +|+..++|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            3456679999999999999999999999995 499999986 89999999999999999999995 79999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.+.
T Consensus        88 ~~~~~   92 (102)
T 1wez_A           88 LNSTA   92 (102)
T ss_dssp             EECCC
T ss_pred             ECCCC
Confidence            98765

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.83  E-value=2.9e-20  Score=108.40  Aligned_cols=76  Identities=21%  Similarity=0.436  Sum_probs=70.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||.++++++|+++|++||.|..+.+.      .++|+|||+|.+.++|..|+..|||..++|+.|+|.+++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            46799999999999999999999999999999887      247899999999999999999999999999999999998


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      ++
T Consensus       100 ~~  101 (101)
T 2la4_A          100 ER  101 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

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

Probab=99.83  E-value=7.8e-20  Score=104.39  Aligned_cols=77  Identities=31%  Similarity=0.601  Sum_probs=70.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ....++|||+|||+++++++|+++|++||.|..+.+.        +++|||+|.+.++|+.|+..|||..++|+.|+|++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            4467799999999999999999999999999999886        33899999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +.+++
T Consensus        78 a~~~~   82 (90)
T 2dnp_A           78 STKGQ   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            97764

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

Probab=99.83  E-value=1e-19  Score=106.44  Aligned_cols=77  Identities=30%  Similarity=0.531  Sum_probs=70.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..+.++|||+|||+++++++|+++|.+||.|..+.++        +++|||+|.+.++|++|+..||+..++|+.|.|.+
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            3456799999999999999999999999999998875        44899999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +.++.
T Consensus        80 a~~~~   84 (103)
T 2dgu_A           80 AKPPD   84 (103)
T ss_dssp             CCCCC
T ss_pred             cCCCc
Confidence            97764

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.83  E-value=5e-21  Score=105.78  Aligned_cols=75  Identities=21%  Similarity=0.423  Sum_probs=71.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        68 ~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      +|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+. +++..++|+.|.|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            58999999999999999999999999999999988889999999999999999999999 5999999999999875

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.83  E-value=6.4e-21  Score=106.89  Aligned_cols=73  Identities=23%  Similarity=0.453  Sum_probs=67.1

Q ss_pred             cceEEEcCCCCCC------CHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCe-EE
Q 032044           66 DFKLFVGNLSWSV------TTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR-AM  138 (148)
Q Consensus        66 ~~~l~i~nlp~~~------~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~-~l  138 (148)
                      +++|||+|||..+      ++++|+++|++||.|..+.++  +.++.++|+|||+|.+.++|+.|+..|||..++|+ .|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3689999999999      679999999999999999887  46788999999999999999999999999999999 88


Q ss_pred             EE
Q 032044          139 RV  140 (148)
Q Consensus       139 ~v  140 (148)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.83  E-value=1.3e-19  Score=114.17  Aligned_cols=81  Identities=31%  Similarity=0.549  Sum_probs=77.5

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      +++|||+|||+++++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|+.|+..|+|..++|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            57899999999999999999999999999999999988899999999999999999999999999999999999999876


Q ss_pred             C
Q 032044          146 R  146 (148)
Q Consensus       146 ~  146 (148)
                      +
T Consensus        82 ~   82 (167)
T 1fxl_A           82 S   82 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.83  E-value=1.2e-19  Score=118.95  Aligned_cols=84  Identities=30%  Similarity=0.436  Sum_probs=77.6

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+++++.++.++|+|||+|.+.++|++|+..+++..+.|+.+++.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccCC
Q 032044          143 AQGR  146 (148)
Q Consensus       143 ~~~~  146 (148)
                      +...
T Consensus        92 ~~~~   95 (213)
T 4f02_A           92 SQRD   95 (213)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            8654

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.83  E-value=1.9e-20  Score=123.89  Aligned_cols=81  Identities=26%  Similarity=0.509  Sum_probs=76.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYG--NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..++|||+|||+++++++|+++|.+||  .|..+.|+.++.++.++|||||+|.+.++|++|+..||+..|+|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 032044          143 AQG  145 (148)
Q Consensus       143 ~~~  145 (148)
                      +.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

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

Probab=99.83  E-value=2e-20  Score=109.03  Aligned_cols=75  Identities=29%  Similarity=0.530  Sum_probs=70.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ++|||+|||+++++++|+++|++||.|..+.+..+     ++|+|||+|.+.++|+.|+..|||..++|+.|+|+++.++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            47999999999999999999999999999998865     6889999999999999999999999999999999999765

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.83  E-value=5.9e-21  Score=112.44  Aligned_cols=83  Identities=20%  Similarity=0.337  Sum_probs=76.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCC---eeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGN---VVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAM  138 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~---v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l  138 (148)
                      .....++|||+|||+++++++|+++|.+||.   |..+.++.++. +.++|+|||+|.+.++|++|+. +|+..++|+.|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            3456789999999999999999999999988   89999998876 8899999999999999999999 99999999999


Q ss_pred             EEEeccCC
Q 032044          139 RVSLAQGR  146 (148)
Q Consensus       139 ~v~~~~~~  146 (148)
                      +|.++.++
T Consensus        85 ~V~~a~~~   92 (107)
T 2lmi_A           85 EVYEINNE   92 (107)
T ss_dssp             CCEECCHH
T ss_pred             EEEECCHH
Confidence            99998653

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.83  E-value=2.3e-20  Score=109.01  Aligned_cols=81  Identities=22%  Similarity=0.530  Sum_probs=75.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ...+++|||+|||+++++++|+++|++||.|..+.++.++ ++.++|+|||+|.+.++|+.|+.  ++..++|+.|.|.+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGP   82 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEE
Confidence            3456899999999999999999999999999999999997 88999999999999999999999  99999999999988


Q ss_pred             ccCC
Q 032044          143 AQGR  146 (148)
Q Consensus       143 ~~~~  146 (148)
                      +.++
T Consensus        83 a~~~   86 (102)
T 2xs2_A           83 AIRK   86 (102)
T ss_dssp             EEEC
T ss_pred             CCcC
Confidence            7654

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.82  E-value=9.8e-20  Score=114.99  Aligned_cols=83  Identities=27%  Similarity=0.486  Sum_probs=78.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ++++|+|+|||+++++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|+.|+..++|..++|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            46799999999999999999999999999999999998889999999999999999999999999999999999999987


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      ++.
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            653

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=6.1e-20  Score=105.44  Aligned_cols=77  Identities=36%  Similarity=0.564  Sum_probs=69.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCC-ceeCCeEEEEE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGN-VVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNG-VELEGRAMRVS  141 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~-v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~-~~i~g~~l~v~  141 (148)
                      ...++|||+|||+++++++|+++|++||. +..+.+.       ++++|||+|.+.++|+.|+..||| ..++|+.|+|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45679999999999999999999999999 6655552       477999999999999999999999 99999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ++.++.
T Consensus        79 ~a~~~~   84 (93)
T 2cqh_A           79 YSVSKK   84 (93)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            998764

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.82  E-value=1.2e-19  Score=107.36  Aligned_cols=76  Identities=30%  Similarity=0.582  Sum_probs=70.1

Q ss_pred             CCCcceEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           63 AETDFKLFVGNLSWS-VTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ....++|||+|||++ +++++|+++|.+||.|..+.+        ++++|||+|.+.++|+.|+..|||..++|+.|+|+
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   95 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            345579999999999 999999999999999999988        46799999999999999999999999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.++
T Consensus        96 ~a~~~  100 (110)
T 1wf1_A           96 MAGEP  100 (110)
T ss_dssp             ESCCC
T ss_pred             ECCCC
Confidence            99754

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=2.6e-20  Score=109.76  Aligned_cols=79  Identities=15%  Similarity=0.294  Sum_probs=70.7

Q ss_pred             CCCcceEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhC--CceeCCeEEE
Q 032044           63 AETDFKLFVGNLSWS-VTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN--GVELEGRAMR  139 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~--~~~i~g~~l~  139 (148)
                      ..++++|||+|||++ +++++|+++|++||.|..+.+++      .+|+|||+|.+.++|+.|+..|+  +..++|+.|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            456789999999998 99999999999999999998863      37899999999999999999886  4669999999


Q ss_pred             EEeccCCC
Q 032044          140 VSLAQGRR  147 (148)
Q Consensus       140 v~~~~~~~  147 (148)
                      |.+++++.
T Consensus        96 V~~a~~~~  103 (112)
T 1x4f_A           96 VDLSEKYK  103 (112)
T ss_dssp             EEEECSCS
T ss_pred             EEECcccc
Confidence            99998764

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=1.2e-19  Score=104.81  Aligned_cols=80  Identities=29%  Similarity=0.357  Sum_probs=71.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEE-EEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGA-RVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~-~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ...+++|||+|||+++++++|+++|.+||.|..+ .++.++.++    .|||+|.+.++|+.|+..|||..++|+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456899999999999999999999999999999 477665433    39999999999999999999999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.++
T Consensus        88 ~a~~~   92 (96)
T 2e44_A           88 YIPDE   92 (96)
T ss_dssp             ECCCC
T ss_pred             EcCcc
Confidence            99876

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.82  E-value=2e-19  Score=112.18  Aligned_cols=80  Identities=20%  Similarity=0.338  Sum_probs=71.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG--RAMRVS  141 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g--~~l~v~  141 (148)
                      ....+|||+||++.+++++|+++|++||.|.++.+...    .++++|||+|.+.++|+.|+..|||..|.|  +.|+|+
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            34467899999999999999999999999999988643    257899999999999999999999999965  999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      +++++.
T Consensus       120 ~Ak~~~  125 (164)
T 1sjr_A          120 FSKLTS  125 (164)
T ss_dssp             ECSSSS
T ss_pred             EecCCc
Confidence            998763

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.82  E-value=9.2e-20  Score=108.36  Aligned_cols=80  Identities=16%  Similarity=0.219  Sum_probs=72.2

Q ss_pred             cceEEEcCC----CCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecC----HHH----HHHHHH--HhCCc
Q 032044           66 DFKLFVGNL----SWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST----KAE----METALE--SLNGV  131 (148)
Q Consensus        66 ~~~l~i~nl----p~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~----~~~----a~~a~~--~l~~~  131 (148)
                      +..|+|+||    |+.+++.+|+++|+.||.|..+.++.++.++.++|+|||+|.+    ++.    |.+|+.  .++|.
T Consensus         2 p~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~   81 (136)
T 2j8a_A            2 SCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGC   81 (136)
T ss_dssp             CCEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCE
T ss_pred             CcEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCC
Confidence            358999999    9999999999999999999999999999999999999999996    333    888988  78999


Q ss_pred             eeCCeEEEEEeccC
Q 032044          132 ELEGRAMRVSLAQG  145 (148)
Q Consensus       132 ~i~g~~l~v~~~~~  145 (148)
                      .|+|+.|+|.+.+.
T Consensus        82 ~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           82 FIMGFKFEVILNKH   95 (136)
T ss_dssp             EETTEEEEEEECCT
T ss_pred             eecCcEEEEEECcc
Confidence            99999999998653

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.82  E-value=5.2e-21  Score=117.17  Aligned_cols=122  Identities=15%  Similarity=0.172  Sum_probs=73.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEE
Q 032044           18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGAR   97 (148)
Q Consensus        18 g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~   97 (148)
                      |+|+.+|..++.+-.++.....+ ..+....-....   ..........++|||+|||+++++++|+++|++|| +..+.
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~---~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~   76 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGD---SEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVH   76 (139)
T ss_dssp             -----------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEE
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCCC---cccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEE
Confidence            56778887777776666543322 233222111111   11122334567999999999999999999999999 67999


Q ss_pred             EEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           98 VLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        98 ~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ++.++. +.++|+|||+|.+.++|++|+ .+|+..++|+.|.|.++.++
T Consensus        77 i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~  123 (139)
T 2hgn_A           77 IEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTT  123 (139)
T ss_dssp             CCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCS
T ss_pred             EEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCC
Confidence            998865 889999999999999999999 69999999999999998765

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.71  E-value=7.1e-22  Score=118.03  Aligned_cols=84  Identities=26%  Similarity=0.454  Sum_probs=78.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeE--------EEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVG--------ARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG  135 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~--------~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g  135 (148)
                      .+.++|||+|||.++++++|+++|++||.|..        +.++.++.++.++|+|||+|.+.++|++|+..|||..++|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            35678999999999999999999999999988        8888888888899999999999999999999999999999


Q ss_pred             eEEEEEeccCCC
Q 032044          136 RAMRVSLAQGRR  147 (148)
Q Consensus       136 ~~l~v~~~~~~~  147 (148)
                      +.|+|+++.++.
T Consensus        85 ~~l~V~~a~~~~   96 (116)
T 2lcw_A           85 NPIKVSFATRRA   96 (116)
Confidence            999999997763

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.82  E-value=3.8e-20  Score=114.34  Aligned_cols=82  Identities=28%  Similarity=0.492  Sum_probs=72.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEE--------EEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGA--------RVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELE  134 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~--------~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~  134 (148)
                      ..++++|||+|||+++++++|+++|++||.|..+        .+.   .++.++|+|||+|.+.++|..|+..|||..++
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~  118 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNEKAAAKALKEANGYVLF  118 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSHHHHHHHHHHHTTBEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec---cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeC
Confidence            4466799999999999999999999999988763        333   35778999999999999999999999999999


Q ss_pred             CeEEEEEeccCCC
Q 032044          135 GRAMRVSLAQGRR  147 (148)
Q Consensus       135 g~~l~v~~~~~~~  147 (148)
                      |+.|.|.++++++
T Consensus       119 g~~l~V~~a~~~~  131 (143)
T 3egn_A          119 GKPMVVQFARSAR  131 (143)
T ss_dssp             TEECEEEECCCSC
T ss_pred             CcEEEEEECCCCC
Confidence            9999999997653

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.81  E-value=1.4e-19  Score=115.33  Aligned_cols=82  Identities=37%  Similarity=0.595  Sum_probs=77.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||+|||+.+++++|+++|.+||.|..+.+..++ ++.++|+|||+|.+.++|+.|+..|||..++|+.|.|+++
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456899999999999999999999999999999999887 7889999999999999999999999999999999999998


Q ss_pred             cCC
Q 032044          144 QGR  146 (148)
Q Consensus       144 ~~~  146 (148)
                      ...
T Consensus       165 ~~~  167 (177)
T 2f3j_A          165 ASQ  167 (177)
T ss_dssp             SSG
T ss_pred             cCC
Confidence            654

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=7.5e-20  Score=108.34  Aligned_cols=77  Identities=12%  Similarity=0.117  Sum_probs=70.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||+|||+++++++|+++|++||.|..+.++.      .+++|||+|.+.++|+.|+..|||..++|+.|.|.|+
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3567999999999999999999999999999988763      4679999999999999999999999999999999998


Q ss_pred             cCC
Q 032044          144 QGR  146 (148)
Q Consensus       144 ~~~  146 (148)
                      ..+
T Consensus        82 ~~~   84 (111)
T 1whx_A           82 PIG   84 (111)
T ss_dssp             ETT
T ss_pred             CCC
Confidence            653

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.81  E-value=5.9e-19  Score=106.30  Aligned_cols=77  Identities=21%  Similarity=0.392  Sum_probs=69.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeE-EEEEecCHHHHHHHHHHhCCceeCC--eEEEEE
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGY-GFVCYSTKAEMETALESLNGVELEG--RAMRVS  141 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~-~fv~f~~~~~a~~a~~~l~~~~i~g--~~l~v~  141 (148)
                      .--.|+|+||++.+++++|+++|++||.|..+.+...     .+++ |||+|.+.++|+.|+..|||..|.|  +.|+|+
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            4456889999999999999999999999999988754     2466 9999999999999999999999988  999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      +++++
T Consensus       102 ~ak~~  106 (130)
T 3zzy_A          102 FSKLT  106 (130)
T ss_dssp             ECSCS
T ss_pred             ecCCC
Confidence            99875

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

Probab=99.81  E-value=1.1e-19  Score=105.00  Aligned_cols=76  Identities=21%  Similarity=0.459  Sum_probs=69.5

Q ss_pred             CCCcceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           63 AETDFKLFVGNLSW-SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        63 ~~~~~~l~i~nlp~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ..++++|||+|||+ .+++++|+++|++||.|..+.+.        +|+|||+|.+.++|+.|+..|||..+.|+.|+|+
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34678999999998 99999999999999999999884        6799999999999999999999999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.++
T Consensus        79 ~a~~~   83 (96)
T 2kvi_A           79 VSSSN   83 (96)
T ss_dssp             EEECC
T ss_pred             EcCcC
Confidence            98765

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=6.4e-20  Score=110.15  Aligned_cols=80  Identities=19%  Similarity=0.254  Sum_probs=72.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCe----eEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNV----VGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v----~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      ....+|||+|||+++++++|+++|++||.|    ..+.++.+ .++.++|+|||+|.+.++|++|+.. |+..++|+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            356799999999999999999999999975    68889888 5789999999999999999999995 99999999999


Q ss_pred             EEeccC
Q 032044          140 VSLAQG  145 (148)
Q Consensus       140 v~~~~~  145 (148)
                      |..+.+
T Consensus        99 V~~a~~  104 (123)
T 2dha_A           99 LFRSTA  104 (123)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            988754

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.81  E-value=3.1e-19  Score=101.47  Aligned_cols=75  Identities=16%  Similarity=0.276  Sum_probs=69.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||+++++++|+++|++| .|..+.+.      .++|+|||+|.+.++|+.|+..|||..++|+.|+|+++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            46789999999999999999999999 89988874      468999999999999999999999999999999999986


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      .+
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=4.3e-19  Score=102.08  Aligned_cols=78  Identities=21%  Similarity=0.342  Sum_probs=69.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||+|||+++++++|+++|.+||.|..+  +.++.++.   +|||+|.+.++|+.|+. |||..++|+.|.|+++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            345699999999999999999999999999987  55545444   99999999999999999 9999999999999998


Q ss_pred             cCCC
Q 032044          144 QGRR  147 (148)
Q Consensus       144 ~~~~  147 (148)
                      .++.
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            7653

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.80  E-value=8.7e-19  Score=113.21  Aligned_cols=84  Identities=36%  Similarity=0.610  Sum_probs=77.7

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+.. ++..++|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            345778999999999999999999999999999999999988899999999999999999999985 9999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.++
T Consensus        88 ~~~~~   92 (196)
T 1l3k_A           88 RAVSR   92 (196)
T ss_dssp             ECCC-
T ss_pred             cccCc
Confidence            98654

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.80  E-value=5.6e-19  Score=126.56  Aligned_cols=84  Identities=29%  Similarity=0.629  Sum_probs=79.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..+.++|||+|||+.+++++|.++|.+||.|..+.|+.+..++.++|||||+|.+.++|+.||..|||..|+|+.|.|.+
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ccCC
Q 032044          143 AQGR  146 (148)
Q Consensus       143 ~~~~  146 (148)
                      +.++
T Consensus       179 a~~~  182 (437)
T 3pgw_S          179 ERGR  182 (437)
T ss_pred             eCCC
Confidence            9764

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.80  E-value=1.2e-18  Score=112.58  Aligned_cols=117  Identities=10%  Similarity=0.144  Sum_probs=90.1

Q ss_pred             CHHHHHHHHHHh--CCCeecCcEEEEeecCCCCCCCCC-----CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE
Q 032044           26 TVEDCNAVIENL--DGREYLGRILRVNFSDKPKPKLPL-----YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARV   98 (148)
Q Consensus        26 ~~~~a~~a~~~l--~~~~~~~~~i~v~~~~~~~~~~~~-----~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~   98 (148)
                      +.+.+..|+...  ....+.+....+..... .+....     .....++|||+|||+++++++|+++|++||.|..+.+
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~-~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i  141 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPS-KPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM  141 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTT-SCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEeccc-CCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEE
Confidence            567788888765  44455555555554421 111111     1224579999999999999999999999999999999


Q ss_pred             EEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           99 LYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        99 ~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      +++. ++.++|+|||+|.+.++|+.|+..+ +..++|+.|.|.++..
T Consensus       142 ~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          142 RRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             EECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             EECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            9885 4888999999999999999999855 4599999999998754

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.1e-18  Score=99.05  Aligned_cols=77  Identities=25%  Similarity=0.434  Sum_probs=69.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..+.++|||+|+  ++++++|+++|++||.|..+.+.      .++|+|||+|.+.++|++|+..|||..++|+.|+|.+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            446789999996  89999999999999999999884      3578999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +.++.
T Consensus        84 a~~~~   88 (97)
T 1x5p_A           84 ARKQP   88 (97)
T ss_dssp             CSSCC
T ss_pred             CCCCC
Confidence            98764

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.79  E-value=1.1e-19  Score=109.39  Aligned_cols=80  Identities=24%  Similarity=0.319  Sum_probs=72.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCee--EEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVV--GARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~--~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ....++|||+|||+++++++|+++|++| .|.  .+.++.++. +.++|+|||+|.+.++|++|+. +++..|+|+.|.|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V  115 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEV  115 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEE
Confidence            3456789999999999999999999999 566  888988876 8999999999999999999999 5789999999999


Q ss_pred             EeccC
Q 032044          141 SLAQG  145 (148)
Q Consensus       141 ~~~~~  145 (148)
                      .++.+
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            98764

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.79  E-value=3.2e-18  Score=102.61  Aligned_cols=75  Identities=19%  Similarity=0.299  Sum_probs=67.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeE-EEEEecCHHHHHHHHHHhCCceeCC--eEEEEEec
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGY-GFVCYSTKAEMETALESLNGVELEG--RAMRVSLA  143 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~-~fv~f~~~~~a~~a~~~l~~~~i~g--~~l~v~~~  143 (148)
                      ..|+|+|||+.+++++|+++|++||.|..+.+...      .|+ |||+|.+.++|..|+..|||..|.|  +.|+|.++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            34679999999999999999999999999988642      265 9999999999999999999999987  69999999


Q ss_pred             cCCC
Q 032044          144 QGRR  147 (148)
Q Consensus       144 ~~~~  147 (148)
                      +++.
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            8763

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=9.6e-19  Score=98.61  Aligned_cols=73  Identities=21%  Similarity=0.287  Sum_probs=65.2

Q ss_pred             cce-EEEcCCCCCCCHHH----HHHHHhhcC-CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           66 DFK-LFVGNLSWSVTTES----LTQAFQEYG-NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        66 ~~~-l~i~nlp~~~~~~~----l~~~f~~~g-~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      +.+ |||.|||..+++++    |+++|.+|| .|..+       ++   |+|||.|.+.++|++|++.|+|..+.|++|+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            445 99999999999988    558999995 99887       22   8999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 032044          140 VSLAQGRRS  148 (148)
Q Consensus       140 v~~~~~~~~  148 (148)
                      |+++..+++
T Consensus        78 v~~A~~~sd   86 (96)
T 2diu_A           78 VSFTPKNRE   86 (96)
T ss_dssp             EESSCCSCC
T ss_pred             EEecCCCcc
Confidence            999988764

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.79  E-value=2.4e-18  Score=100.66  Aligned_cols=82  Identities=13%  Similarity=0.111  Sum_probs=72.1

Q ss_pred             CCcceEEEcCCCC-----CCCHHHHHHHHhhcCCeeEEEEEEcCCC-CCceeEEEEEecCHHHHHHHHHHhCCceeCCeE
Q 032044           64 ETDFKLFVGNLSW-----SVTTESLTQAFQEYGNVVGARVLYDGES-GRSRGYGFVCYSTKAEMETALESLNGVELEGRA  137 (148)
Q Consensus        64 ~~~~~l~i~nlp~-----~~~~~~l~~~f~~~g~v~~~~~~~~~~~-~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~  137 (148)
                      .++++|+|.|+..     +-++++|++.|++||.|..+.++.++.+ +.++|+|||+|.+.++|++|+..|||..++|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4567899999963     2378999999999999999999987654 578999999999999999999999999999999


Q ss_pred             EEEEeccC
Q 032044          138 MRVSLAQG  145 (148)
Q Consensus       138 l~v~~~~~  145 (148)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999864

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.79  E-value=3.7e-19  Score=105.97  Aligned_cols=76  Identities=26%  Similarity=0.388  Sum_probs=66.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeE-----E
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRA-----M  138 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~-----l  138 (148)
                      ...++|||.|||+++++++|+++|.+||.|..+.++.+       ++|||+|.+.++|+.|+..|||..++|+.     +
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            45679999999999999999999999999999988643       79999999999999999999999999988     7


Q ss_pred             EEEeccCC
Q 032044          139 RVSLAQGR  146 (148)
Q Consensus       139 ~v~~~~~~  146 (148)
                      +|..+.++
T Consensus        87 ~v~~~~~~   94 (115)
T 3beg_B           87 RVKVDGPR   94 (115)
T ss_dssp             EEEECC--
T ss_pred             EeccCCCC
Confidence            88776654

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=6.5e-19  Score=103.86  Aligned_cols=77  Identities=23%  Similarity=0.331  Sum_probs=68.3

Q ss_pred             CCCcceEEE--cCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee-----CC
Q 032044           63 AETDFKLFV--GNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL-----EG  135 (148)
Q Consensus        63 ~~~~~~l~i--~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i-----~g  135 (148)
                      ..+..+|||  +||++++++++|+++|++||.|..+.++.      .+|||||+|.+.++|++|+..|||..+     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            345678999  77999999999999999999999887752      278999999999999999999999998     68


Q ss_pred             eEEEEEeccC
Q 032044          136 RAMRVSLAQG  145 (148)
Q Consensus       136 ~~l~v~~~~~  145 (148)
                      ++|.|.++..
T Consensus        96 ~~l~v~~a~~  105 (114)
T 2cq2_A           96 ITLYLNFVEK  105 (114)
T ss_dssp             EECEEEEESC
T ss_pred             cEEEEEeccc
Confidence            9999999864

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.78  E-value=2e-18  Score=108.63  Aligned_cols=79  Identities=29%  Similarity=0.506  Sum_probs=73.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ++|||+|||.++++++|+++|++||.|..+.+..++. +.++|+|||+|.+.++|+.|+..++|..+.|+.|.+.++.++
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            4799999999999999999999999999999998854 678999999999999999999999999999999999998665

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.78  E-value=2.1e-18  Score=98.18  Aligned_cols=77  Identities=27%  Similarity=0.448  Sum_probs=62.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCce--eCCeEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVE--LEGRAMR  139 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~--i~g~~l~  139 (148)
                      ...++.+|||+|||+++++++|+++|++||.|..+.++.+     ++|||||+|.+.++|++    +++..  ++|+.|.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~   77 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVH   77 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEE
Confidence            3456779999999999999999999999999999988753     68999999999999983    55544  5699999


Q ss_pred             EEeccCCC
Q 032044          140 VSLAQGRR  147 (148)
Q Consensus       140 v~~~~~~~  147 (148)
                      |.++.++.
T Consensus        78 v~~a~~k~   85 (89)
T 3d2w_A           78 ISNAEPKH   85 (89)
T ss_dssp             EEECC---
T ss_pred             EEEcCCCC
Confidence            99998764

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.77  E-value=2.6e-18  Score=111.94  Aligned_cols=76  Identities=21%  Similarity=0.281  Sum_probs=70.4

Q ss_pred             CcceEEEcCCC-CCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           65 TDFKLFVGNLS-WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        65 ~~~~l~i~nlp-~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ++++|||+||| ..+++++|+++|++||.|.++.++.+     .+|+|||+|.+.++|+.|+..|||..+.|+.|+|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            46799999999 89999999999999999999998754     3689999999999999999999999999999999998


Q ss_pred             cC
Q 032044          144 QG  145 (148)
Q Consensus       144 ~~  145 (148)
                      +.
T Consensus        78 ~~   79 (205)
T 3tyt_A           78 KQ   79 (205)
T ss_dssp             SC
T ss_pred             cC
Confidence            64

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.77  E-value=2.3e-18  Score=112.78  Aligned_cols=82  Identities=24%  Similarity=0.506  Sum_probs=74.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||.++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..|++..++|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            45789999999999999999999999999999999888788899999999999999999999999999999999998875


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      ..
T Consensus       107 ~~  108 (216)
T 2qfj_A          107 NI  108 (216)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.76  E-value=4.6e-18  Score=96.35  Aligned_cols=72  Identities=21%  Similarity=0.563  Sum_probs=65.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhc----C-------CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCce
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEY----G-------NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVE  132 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~----g-------~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~  132 (148)
                      .+.++|||+|||+++++++|+++|++|    |       .|..+.+..+      +|+|||+|.+.++|+.|+ .|||..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            467899999999999999999999999    8       8888877633      789999999999999999 899999


Q ss_pred             eCCeEEEEEe
Q 032044          133 LEGRAMRVSL  142 (148)
Q Consensus       133 i~g~~l~v~~  142 (148)
                      ++|+.|+|+.
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999874

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=3.1e-18  Score=101.83  Aligned_cols=64  Identities=22%  Similarity=0.469  Sum_probs=58.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCC---CCceeEEEEEecCHHHHHHHHHHh
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGES---GRSRGYGFVCYSTKAEMETALESL  128 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~~~~~fv~f~~~~~a~~a~~~l  128 (148)
                      ..+++|||+|||+++++++|+++|++||.|. +.++.+..+   +.++|||||+|.+.++|++|+..+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~   72 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC   72 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh
Confidence            4567999999999999999999999999998 777766665   688999999999999999999988

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.76  E-value=9.3e-18  Score=106.47  Aligned_cols=82  Identities=24%  Similarity=0.444  Sum_probs=74.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCC--CceeEEEEEecCHHHHHHHHHHhCCceeC---CeEEE
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESG--RSRGYGFVCYSTKAEMETALESLNGVELE---GRAMR  139 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~--~~~~~~fv~f~~~~~a~~a~~~l~~~~i~---g~~l~  139 (148)
                      .+++|||+|||+++++++|+++|++||.|..+.++.++.++  .++|+|||+|.+.++|+.|+..++|..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            45799999999999999999999999999999999997776  78999999999999999999999998775   57788


Q ss_pred             EEeccCC
Q 032044          140 VSLAQGR  146 (148)
Q Consensus       140 v~~~~~~  146 (148)
                      +.++.++
T Consensus        82 ~~~~~~~   88 (175)
T 3nmr_A           82 MKPADSE   88 (175)
T ss_dssp             EEECGGG
T ss_pred             Ecccccc
Confidence            8877654

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.3e-18  Score=97.87  Aligned_cols=76  Identities=20%  Similarity=0.380  Sum_probs=65.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      .+++|||+|||+++++++|+++|++||.|..+.++.+     ++|+|||+|.+.++|++|...  +..++|+.|.|.++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecC
Confidence            5679999999999999999999999999999988744     688999999999999864331  355699999999998


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      ++.
T Consensus        77 ~~~   79 (88)
T 1wf0_A           77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.74  E-value=4.8e-18  Score=107.11  Aligned_cols=80  Identities=29%  Similarity=0.666  Sum_probs=73.7

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ++++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+..  +..++|+.|.+.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            467999999999999999999999999999999999988899999999999999999999994  678999999998876


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      ++
T Consensus        80 ~~   81 (167)
T 2cjk_A           80 PR   81 (167)
T ss_dssp             CH
T ss_pred             ch
Confidence            53

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=6.4e-17  Score=95.84  Aligned_cols=83  Identities=16%  Similarity=0.303  Sum_probs=70.4

Q ss_pred             CCCCCcceEEEcCCCCCCC-----------HHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 032044           61 LYAETDFKLFVGNLSWSVT-----------TESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN  129 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~~~-----------~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  129 (148)
                      ..+.++++|+|.||.....           +++|+++|++||.|..+.+ .++   .++|+|||+|.+.++|+.|+..||
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~ln   85 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLD   85 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcC
Confidence            3455778999999954432           5799999999999999965 443   278999999999999999999999


Q ss_pred             CceeCCeEEEEEeccCCC
Q 032044          130 GVELEGRAMRVSLAQGRR  147 (148)
Q Consensus       130 ~~~i~g~~l~v~~~~~~~  147 (148)
                      |..++|+.|.|.++.++.
T Consensus        86 g~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           86 GRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             TCEETTEECEEEECCSCC
T ss_pred             CCEECCcEEEEEEeCCCC
Confidence            999999999999988753

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.74  E-value=2.9e-17  Score=111.77  Aligned_cols=81  Identities=22%  Similarity=0.454  Sum_probs=73.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLT----QAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAM  138 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l  138 (148)
                      ..+.++|||+|||+++++++|+    ++|.+||.|..+.+.+   ++.++|+|||+|.+.++|+.|+..|||..+.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            4467899999999999999977    8999999999998875   56789999999999999999999999999999999


Q ss_pred             EEEeccCC
Q 032044          139 RVSLAQGR  146 (148)
Q Consensus       139 ~v~~~~~~  146 (148)
                      +|.++..+
T Consensus        83 ~v~~a~~~   90 (282)
T 3pgw_A           83 RIQYAKTD   90 (282)
T ss_pred             EEEEeccC
Confidence            99998764

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.72  E-value=2.6e-17  Score=108.86  Aligned_cols=80  Identities=24%  Similarity=0.408  Sum_probs=70.7

Q ss_pred             CCCCcceEEEcCCCCCC---------CHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCce
Q 032044           62 YAETDFKLFVGNLSWSV---------TTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVE  132 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~---------~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~  132 (148)
                      .....++|||+|||..+         ++++|+++|++||.|..+.++.      ++|+|||+|.+.++|+.|+..|+|..
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            34567899999999998         7999999999999999999874      37899999999999999999999999


Q ss_pred             e------------CCeEEEEEeccCCC
Q 032044          133 L------------EGRAMRVSLAQGRR  147 (148)
Q Consensus       133 i------------~g~~l~v~~~~~~~  147 (148)
                      +            .|+.|.|+|+.++.
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             EeccccccccccCCCCEEEEEEccCCC
Confidence            9            89999999998654

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.72  E-value=3.6e-17  Score=108.32  Aligned_cols=79  Identities=28%  Similarity=0.477  Sum_probs=72.7

Q ss_pred             CCCcceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           63 AETDFKLFVGNLSW-SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        63 ~~~~~~l~i~nlp~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ..++++|||+|||+ ++++++|+++|++||.|..+.+..++     +|+|||+|.+.++|++|+..|+|..+.|+.|.|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34678999999999 99999999999999999999998663     7899999999999999999999999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.++
T Consensus       106 ~a~~~  110 (229)
T 2adc_A          106 LSKHQ  110 (229)
T ss_dssp             CCSCC
T ss_pred             EecCc
Confidence            98754

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.71  E-value=6.7e-17  Score=94.52  Aligned_cols=81  Identities=16%  Similarity=0.213  Sum_probs=69.6

Q ss_pred             CcceEEEcCC--CCCCC--------HHHHHHHHhhcCCeeEEEEEEcCCC--CCceeEEEEEecCHHHHHHHHHHhCCce
Q 032044           65 TDFKLFVGNL--SWSVT--------TESLTQAFQEYGNVVGARVLYDGES--GRSRGYGFVCYSTKAEMETALESLNGVE  132 (148)
Q Consensus        65 ~~~~l~i~nl--p~~~~--------~~~l~~~f~~~g~v~~~~~~~~~~~--~~~~~~~fv~f~~~~~a~~a~~~l~~~~  132 (148)
                      +++.|.|.|+  |..+.        +++|++.|++||.|.++.+++++.+  +.++|+|||+|.+.++|++|+..|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            5678999998  44443        3689999999999999999877654  3578999999999999999999999999


Q ss_pred             eCCeEEEEEeccC
Q 032044          133 LEGRAMRVSLAQG  145 (148)
Q Consensus       133 i~g~~l~v~~~~~  145 (148)
                      ++|+.|++.++..
T Consensus        84 f~GR~i~v~~~~~   96 (105)
T 3v4m_A           84 FANRVVVTKYCDP   96 (105)
T ss_dssp             ETTEECEEEEECH
T ss_pred             eCCCEEEEEEeCH
Confidence            9999999999754

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.70  E-value=8.6e-18  Score=106.81  Aligned_cols=83  Identities=29%  Similarity=0.512  Sum_probs=71.1

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ....+++|||+|||.++++++|+++|.+||.+..+ ++.+..++.++|+|||+|.+.++|++|++ |||..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            45578899999999999999999999999876552 23333556788999999999999999995 99999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.++
T Consensus        87 ~~~~~   91 (175)
T 1fje_B           87 KPKGR   91 (175)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            98764

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.69  E-value=2.4e-16  Score=93.86  Aligned_cols=80  Identities=18%  Similarity=0.238  Sum_probs=69.2

Q ss_pred             CcceEEEcCCCC--CC---CHHHHHHHHhhcCCeeEEEEEEcCC----CCCceeEEEEEecCHHHHHHHHHHhCCceeCC
Q 032044           65 TDFKLFVGNLSW--SV---TTESLTQAFQEYGNVVGARVLYDGE----SGRSRGYGFVCYSTKAEMETALESLNGVELEG  135 (148)
Q Consensus        65 ~~~~l~i~nlp~--~~---~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g  135 (148)
                      ++++|+|.|+-.  .+   .+++|++.|++||.|..+.++.++.    ++.++|++||+|.+.++|.+|+..|||..++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            567899999842  22   3689999999999999999998754    34567999999999999999999999999999


Q ss_pred             eEEEEEecc
Q 032044          136 RAMRVSLAQ  144 (148)
Q Consensus       136 ~~l~v~~~~  144 (148)
                      +.|++.++.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999875

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.69  E-value=3.7e-16  Score=105.34  Aligned_cols=79  Identities=29%  Similarity=0.512  Sum_probs=71.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||+++++++|+++|++||.|..+.+.+      .+|+|||+|.+.++|..|+..++|..+.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~   91 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIR   91 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEee
Confidence            345678999999999999999999999999999998853      36899999999999999999999999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.+.
T Consensus        92 ~a~~~   96 (261)
T 3sde_A           92 FATHG   96 (261)
T ss_dssp             ECCCS
T ss_pred             ecccC
Confidence            98764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.69  E-value=5e-17  Score=105.23  Aligned_cols=76  Identities=29%  Similarity=0.499  Sum_probs=70.4

Q ss_pred             cceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           66 DFKLFVGNLSW-SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        66 ~~~l~i~nlp~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      +++|||+|||+ .+++++|+++|++||.|..+.+..++     +|+|||+|.+.++|+.|+..|||..++|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            56899999999 99999999999999999999887653     7799999999999999999999999999999999987


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      ++
T Consensus        78 ~~   79 (198)
T 1qm9_A           78 HQ   79 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.68  E-value=4e-17  Score=95.36  Aligned_cols=72  Identities=19%  Similarity=0.318  Sum_probs=62.4

Q ss_pred             EcCCCCCCCHHHHHHHH------------hhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 032044           71 VGNLSWSVTTESLTQAF------------QEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAM  138 (148)
Q Consensus        71 i~nlp~~~~~~~l~~~f------------~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l  138 (148)
                      ..|||..+++++|++.|            ++||.|..+.++++.. +.++|+|||+|.+.++|++|+..|||..++|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            45667777777776665            9999999999988743 6789999999999999999999999999999999


Q ss_pred             EEEec
Q 032044          139 RVSLA  143 (148)
Q Consensus       139 ~v~~~  143 (148)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.67  E-value=1.6e-16  Score=94.56  Aligned_cols=79  Identities=22%  Similarity=0.260  Sum_probs=49.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCC---CCCCCcceEEEcCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP---LYAETDFKLFVGNLSWS   77 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~---~~~~~~~~l~i~nlp~~   77 (148)
                      .|.+|+|++++  +.++|||||+|.+.++|++|+..|++..+.|++|.|.++........   .......+|||+|||++
T Consensus        31 ~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~~~~~~~~~~~~~~lyv~Nl~~~  108 (115)
T 4f25_A           31 NILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPG  108 (115)
T ss_dssp             CEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC-----------------------
T ss_pred             CEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCccccccccccccCCCCceEeCCCCCC
Confidence            47899999995  45899999999999999999999999999999999999876544322   22334567999999999


Q ss_pred             CCHH
Q 032044           78 VTTE   81 (148)
Q Consensus        78 ~~~~   81 (148)
                      +|++
T Consensus       109 ~T~~  112 (115)
T 4f25_A          109 STRA  112 (115)
T ss_dssp             ----
T ss_pred             cccc
Confidence            9876

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.65  E-value=9.7e-16  Score=96.93  Aligned_cols=75  Identities=19%  Similarity=0.539  Sum_probs=65.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhc----C-------CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEY----G-------NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL  133 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~----g-------~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i  133 (148)
                      +.++|||+|||+++++++|+++|++|    |       .|..+.+.      .++|+|||+|.+.++|+.|+ .+||..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            56799999999999999999999999    6       55555553      24789999999999999999 7999999


Q ss_pred             CCeEEEEEeccCC
Q 032044          134 EGRAMRVSLAQGR  146 (148)
Q Consensus       134 ~g~~l~v~~~~~~  146 (148)
                      +|+.|.|.++.+.
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999997654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.63  E-value=1.6e-15  Score=97.91  Aligned_cols=75  Identities=19%  Similarity=0.545  Sum_probs=64.7

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhc----C-------CeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEY----G-------NVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL  133 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~----g-------~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i  133 (148)
                      .+++|||+|||+++++++|+++|++|    |       .|..+.+      +.++|+|||+|.+.++|++|+ .|||..+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            46799999999999999999999999    4       4444444      235789999999999999999 7999999


Q ss_pred             CCeEEEEEeccCC
Q 032044          134 EGRAMRVSLAQGR  146 (148)
Q Consensus       134 ~g~~l~v~~~~~~  146 (148)
                      +|+.|.|.++.+.
T Consensus        76 ~g~~i~v~~~~~~   88 (198)
T 2yh0_A           76 QGQSLKIRRPHDY   88 (198)
T ss_dssp             TTEEEEEECCCCC
T ss_pred             cCceEEEeCCCCC
Confidence            9999999998654

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=1.4e-14  Score=83.74  Aligned_cols=65  Identities=22%  Similarity=0.361  Sum_probs=57.6

Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           76 WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        76 ~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      ..+++++|+++|++||.|..+.++     +.++|||||+|.+.++|+.|+..+++  +.|++|+|+|++++.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            568999999999999999999887     35789999999999999999997554  679999999998764

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.61  E-value=6.7e-15  Score=87.03  Aligned_cols=78  Identities=15%  Similarity=0.175  Sum_probs=65.6

Q ss_pred             CCcceEEEcCCCCCCC----------HHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 032044           64 ETDFKLFVGNLSWSVT----------TESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL  133 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~----------~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i  133 (148)
                      .++++|.|.|+-....          +++|++.|++||.|..+.+.++.    ++|++||+|.+.++|++|+..|||.++
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            4566888988844322          35889999999999999886542    489999999999999999999999999


Q ss_pred             CCeEEEEEeccC
Q 032044          134 EGRAMRVSLAQG  145 (148)
Q Consensus       134 ~g~~l~v~~~~~  145 (148)
                      +|+.|.+.++..
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999999753

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.57  E-value=8.4e-15  Score=84.76  Aligned_cols=54  Identities=22%  Similarity=0.487  Sum_probs=51.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|++|++.|++..+.|++|.|.|+.+
T Consensus        45 ~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           45 EVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            478999999999999999999999999999999999999999999999999853

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.56  E-value=2.8e-14  Score=98.96  Aligned_cols=78  Identities=24%  Similarity=0.344  Sum_probs=65.7

Q ss_pred             CCCCCcceEEEcC--CCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC---C
Q 032044           61 LYAETDFKLFVGN--LSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELE---G  135 (148)
Q Consensus        61 ~~~~~~~~l~i~n--lp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~---g  135 (148)
                      ....++.+|||+|  |+..+++++|+++|++||.|..+.+..      .+|||||+|.+.++|++|+..|||..+.   |
T Consensus        13 ~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g   86 (345)
T 3tht_A           13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLG   86 (345)
T ss_dssp             CCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             ecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccC
Confidence            3455777999999  588999999999999999998876642      4789999999999999999999999883   4


Q ss_pred             e--EEEEEecc
Q 032044          136 R--AMRVSLAQ  144 (148)
Q Consensus       136 ~--~l~v~~~~  144 (148)
                      +  .+.+.++.
T Consensus        87 ~~~~ly~~~~~   97 (345)
T 3tht_A           87 QKITLYLNFVE   97 (345)
T ss_dssp             CEEECEEEECS
T ss_pred             CceEEEEEEee
Confidence            4  67777764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.54  E-value=1.2e-14  Score=82.80  Aligned_cols=58  Identities=26%  Similarity=0.484  Sum_probs=51.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHh-CCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENL-DGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l-~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|++|++++++.+|.++|||||+|.+.++|++|++.+ ++..+.|++|.|.++.++...
T Consensus        28 ~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~~~   86 (91)
T 2lxi_A           28 QAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPKI   86 (91)
T ss_dssp             CCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCCCC
T ss_pred             EeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCCCC
Confidence            3789999999999999999999999999999999876 456799999999999765443

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.52  E-value=1.1e-14  Score=82.87  Aligned_cols=58  Identities=24%  Similarity=0.370  Sum_probs=49.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.++++++++.+|+++|||||+|.+.++|++|++.+++..+.|++|.|.++.++...
T Consensus        29 ~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~~~   86 (90)
T 3p5t_L           29 DILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEHH   86 (90)
T ss_dssp             CCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC------
T ss_pred             ceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCCccc
Confidence            4789999999999999999999999999999999999999999999999998765543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.51  E-value=6.7e-14  Score=82.44  Aligned_cols=55  Identities=18%  Similarity=0.324  Sum_probs=51.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .|++|+|++|+.||+++|||||+|.+.++|++|++.||+..+.|++|.|.++...
T Consensus        32 ~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~~   86 (110)
T 3s8s_A           32 EVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKG   86 (110)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSTT
T ss_pred             CeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            4789999999999999999999999999999999999999999999999998643

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.50  E-value=3.9e-14  Score=81.21  Aligned_cols=53  Identities=26%  Similarity=0.574  Sum_probs=49.1

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCC----eecCcEEEEeecCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGR----EYLGRILRVNFSDK   54 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~----~~~~~~i~v~~~~~   54 (148)
                      |.+|++++|+.||+++|||||+|.+.++|++|++.+++.    .+.|++|.|.|+..
T Consensus        38 v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           38 VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             GGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             EEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            678999999999999999999999999999999999986    48999999999864

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.46  E-value=2.9e-13  Score=75.62  Aligned_cols=55  Identities=31%  Similarity=0.640  Sum_probs=51.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .|.++++++++.+|+++|||||+|.+.++|+.|+..+++..+.|++|.|.++.++
T Consensus        27 ~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A           27 SYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             TEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            3788999999999999999999999999999999999999999999999998764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=7e-13  Score=74.09  Aligned_cols=73  Identities=25%  Similarity=0.331  Sum_probs=61.3

Q ss_pred             CcceEEEcCCC----CCCCH----HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCe
Q 032044           65 TDFKLFVGNLS----WSVTT----ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR  136 (148)
Q Consensus        65 ~~~~l~i~nlp----~~~~~----~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~  136 (148)
                      +..+|.|.-.|    .++..    .+|.+.|.+||.|..+++..+.        +||+|.+.++|.+|+. |||..++|+
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr   76 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCe
Confidence            44577776665    23434    6788999999999999998652        8999999999999999 999999999


Q ss_pred             EEEEEeccCC
Q 032044          137 AMRVSLAQGR  146 (148)
Q Consensus       137 ~l~v~~~~~~  146 (148)
                      .|+|+++++.
T Consensus        77 ~LkV~lkt~d   86 (91)
T 2dnr_A           77 TITIALKSPS   86 (91)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEEEeCCCC
Confidence            9999998875

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=5.3e-13  Score=77.64  Aligned_cols=58  Identities=29%  Similarity=0.516  Sum_probs=53.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|++++++.++.++|||||+|.+.++|++|+..|++..+.|++|.|.++.+....
T Consensus        41 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (103)
T 2cq0_A           41 SISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS   98 (103)
T ss_dssp             CEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCS
T ss_pred             CeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCCCC
Confidence            4789999999999999999999999999999999999999999999999999776544

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=4.1e-13  Score=77.97  Aligned_cols=59  Identities=36%  Similarity=0.595  Sum_probs=54.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~   59 (148)
                      .|++|++++++.+++++|||||+|.+.++|+.|+..|++..+.|++|.|.++.+.....
T Consensus        38 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   96 (102)
T 2cqb_A           38 DITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKE   96 (102)
T ss_dssp             CCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCCC
T ss_pred             CEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCCCC
Confidence            47899999999999999999999999999999999999999999999999998766544

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.44  E-value=3.3e-13  Score=76.10  Aligned_cols=55  Identities=29%  Similarity=0.514  Sum_probs=50.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .|.++++++++.+|.++|||||+|.+.++|+.|+..+++..+.|++|.|.++.++
T Consensus        32 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           32 RISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             CEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            4789999999989999999999999999999999999999999999999998653

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.44  E-value=6.5e-13  Score=76.68  Aligned_cols=58  Identities=34%  Similarity=0.425  Sum_probs=53.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|++|++++++.+++++|||||+|.+.++|+.|+..+++..+.|++|.|.++..+...
T Consensus        34 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   91 (99)
T 1whw_A           34 PLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             CEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTT
T ss_pred             CEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCccc
Confidence            4788999999889999999999999999999999999999999999999999876654

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.44  E-value=4.2e-13  Score=77.08  Aligned_cols=57  Identities=28%  Similarity=0.610  Sum_probs=52.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|+.|+..+++..+.|+.|.|.++.++..
T Consensus        28 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A           28 PVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDI   84 (96)
T ss_dssp             CEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSSG
T ss_pred             CEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCCC
Confidence            478999999999999999999999999999999999999999999999999976653

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.44  E-value=1.9e-13  Score=79.22  Aligned_cols=54  Identities=20%  Similarity=0.388  Sum_probs=50.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecC-cEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG-RILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~-~~i~v~~~~~   54 (148)
                      .|.+|++++++.||+++|||||+|.+.++|++|+..|++..+.| ++|.|.++.+
T Consensus        38 ~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~   92 (100)
T 3ns6_A           38 KVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKD   92 (100)
T ss_dssp             CEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHH
T ss_pred             CEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECch
Confidence            47899999999999999999999999999999999999999999 9999998753

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.44  E-value=6.9e-13  Score=78.65  Aligned_cols=59  Identities=20%  Similarity=0.308  Sum_probs=54.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~   59 (148)
                      .|++|++++++.+++++|||||+|.+.++|++|+..|++..+.|++|.|.++.++....
T Consensus        51 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~  109 (115)
T 2cpz_A           51 NVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK  109 (115)
T ss_dssp             CCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCCCC
T ss_pred             CeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCcCC
Confidence            47899999999899999999999999999999999999999999999999997665543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=7.9e-13  Score=75.87  Aligned_cols=58  Identities=26%  Similarity=0.562  Sum_probs=52.9

Q ss_pred             Cccee-EeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKL-TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i-~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.++ ++++++.+|.++|||||+|.+.++|++|+..|++..+.|++|.|.++.++...
T Consensus        31 ~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   89 (96)
T 1x5t_A           31 VILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK   89 (96)
T ss_dssp             CBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCC
T ss_pred             CeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccCCC
Confidence            36788 99999889999999999999999999999999999999999999999766544

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.43  E-value=7.8e-13  Score=75.76  Aligned_cols=58  Identities=31%  Similarity=0.556  Sum_probs=53.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|++++++.+++++|||||+|.+.++|++|+..+++..+.|++|.|.++.++...
T Consensus        31 ~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   88 (95)
T 2dnz_A           31 KIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDG   88 (95)
T ss_dssp             CEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCCC
T ss_pred             CEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccCC
Confidence            4789999999989999999999999999999999999999999999999999776544

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.43  E-value=1.2e-12  Score=77.66  Aligned_cols=58  Identities=29%  Similarity=0.526  Sum_probs=53.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|++|++++++.+++++|||||+|.+.++|++|+..|++..+.|+.|.|.++......
T Consensus        41 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   98 (115)
T 2dgo_A           41 RISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPA   98 (115)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCC
T ss_pred             CeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCCCC
Confidence            4789999999989999999999999999999999999999999999999998766543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.42  E-value=1e-12  Score=75.86  Aligned_cols=58  Identities=21%  Similarity=0.516  Sum_probs=52.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~   59 (148)
                      .|.+|++++++.+++++|||||+|.+.++|++|+. +++..+.|++|.|.++.++....
T Consensus        36 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~~~~   93 (99)
T 2dgs_A           36 VVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRDSKS   93 (99)
T ss_dssp             CEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCCCCCC
T ss_pred             CeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCCcccC
Confidence            47899999999999999999999999999999998 99999999999999998765543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.42  E-value=1e-12  Score=76.46  Aligned_cols=56  Identities=23%  Similarity=0.491  Sum_probs=51.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |.+|++++++.+|+++|||||+|.+.++|++|+ .+++..+.|++|.|.++......
T Consensus        41 i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dng_A           41 IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQD   96 (103)
T ss_dssp             EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCCCCC
T ss_pred             ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCCCCC
Confidence            678999999999999999999999999999999 79999999999999999766544

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=1.2e-12  Score=77.57  Aligned_cols=76  Identities=12%  Similarity=0.131  Sum_probs=66.5

Q ss_pred             CCCcceEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecC-HHHHHHHHHHhC--CceeCCeEE
Q 032044           63 AETDFKLFVGNLSWS-VTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST-KAEMETALESLN--GVELEGRAM  138 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~-~~~a~~a~~~l~--~~~i~g~~l  138 (148)
                      ....+.|+|+||++. ++.++|+++|++||.|.++.+..+..      .|||+|.+ ++.|..|+..++  +..|+|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            346778999999999 99999999999999999999876643      59999999 899999999995  688999888


Q ss_pred             EEEecc
Q 032044          139 RVSLAQ  144 (148)
Q Consensus       139 ~v~~~~  144 (148)
                      .+++..
T Consensus        89 ~~evL~   94 (121)
T 1owx_A           89 TWEVLE   94 (121)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            887653

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.41  E-value=5.9e-13  Score=74.71  Aligned_cols=53  Identities=38%  Similarity=0.678  Sum_probs=49.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|.++.+++++.+|+++|||||+|.+.++|+.|+..+++..+.|++|.|.++.
T Consensus        33 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A           33 DITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             CEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            47889999999999999999999999999999999999999999999999863

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=8.4e-13  Score=76.63  Aligned_cols=58  Identities=36%  Similarity=0.642  Sum_probs=53.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|++|++++++.+++++|||||+|.+.++|..|+..|++..+.|++|.|.++......
T Consensus        38 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   95 (102)
T 1x5s_A           38 QISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN   95 (102)
T ss_dssp             CCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCCC
T ss_pred             CeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            4789999999999999999999999999999999999999999999999998766544

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.40  E-value=1.3e-12  Score=75.55  Aligned_cols=56  Identities=20%  Similarity=0.446  Sum_probs=51.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|.+|+++.++ +|+++|||||+|.+.++|.+|+..|++..+.|++|.|.++.++..
T Consensus        43 ~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   98 (100)
T 2do4_A           43 TVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPS   98 (100)
T ss_dssp             CEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCSC
T ss_pred             CeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            47899999998 999999999999999999999999999999999999999876543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=6.9e-13  Score=77.14  Aligned_cols=59  Identities=29%  Similarity=0.423  Sum_probs=53.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~   59 (148)
                      .|.+|.+++++.+++++|||||+|.+.++|++|+..|++..+.|++|.|.++.......
T Consensus        39 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   97 (103)
T 2dnm_A           39 RVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDL   97 (103)
T ss_dssp             CEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSCCSCC
T ss_pred             CEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcCCCCC
Confidence            47889999999999999999999999999999999999999999999999998665443

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.39  E-value=7e-13  Score=77.82  Aligned_cols=55  Identities=33%  Similarity=0.611  Sum_probs=51.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|..|+..+++..+.|++|.|.++.++
T Consensus        52 ~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k  106 (108)
T 2jrs_A           52 RIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER  106 (108)
T ss_dssp             CEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSS
T ss_pred             CeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccC
Confidence            4789999999999999999999999999999999999999999999999998755

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=1.2e-12  Score=74.92  Aligned_cols=54  Identities=35%  Similarity=0.623  Sum_probs=50.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      .|.+|.+++++.+++++|||||+|.+.++|++|+..|++..+.|++|.|.++..
T Consensus        41 ~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           41 PIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             CEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCSC
T ss_pred             CeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecCC
Confidence            478999999999999999999999999999999999999999999999998753

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.39  E-value=1.7e-12  Score=77.07  Aligned_cols=56  Identities=30%  Similarity=0.615  Sum_probs=51.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|++|.+++++ +|+++|||||+|.+.++|++|+..|++..+.|++|.|.++..+..
T Consensus        33 ~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   88 (116)
T 2fy1_A           33 PISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF   88 (116)
T ss_dssp             CCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSSC
T ss_pred             CEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            47899999998 999999999999999999999999999999999999999876553

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.39  E-value=1.1e-12  Score=81.87  Aligned_cols=54  Identities=22%  Similarity=0.377  Sum_probs=51.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      .|.+|++++|+.+|+++|||||+|.+.++|++|+..|++..+.|++|.|.++.+
T Consensus        83 ~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~  136 (156)
T 3n9u_C           83 DVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATR  136 (156)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCH
T ss_pred             cEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCC
Confidence            478999999999999999999999999999999999999999999999998853

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=7.6e-13  Score=77.32  Aligned_cols=55  Identities=24%  Similarity=0.509  Sum_probs=51.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .|.+|.+++++.+|.++|||||+|.+.++|+.|+..+++..+.|++|.|.++..+
T Consensus        49 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~  103 (106)
T 1p27_B           49 EIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR  103 (106)
T ss_dssp             CEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEES
T ss_pred             CeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCC
Confidence            4789999999999999999999999999999999999999999999999998654

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=1.4e-12  Score=76.09  Aligned_cols=58  Identities=26%  Similarity=0.398  Sum_probs=53.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|++++++.++.++|||||+|.+.++|++|+..|++..+.|++|.|.++......
T Consensus        41 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (105)
T 1x5u_A           41 PVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKN   98 (105)
T ss_dssp             CEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSCC
T ss_pred             CeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCcC
Confidence            4788999999989999999999999999999999999999999999999999776544

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.38  E-value=2.4e-12  Score=75.76  Aligned_cols=58  Identities=24%  Similarity=0.346  Sum_probs=53.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhC------CCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLD------GREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~------~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|++++++.+|.++|||||+|.+.++|..|+..++      +..+.|++|.|.++.+....
T Consensus        41 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           41 DLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA  104 (111)
T ss_dssp             CEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCCC
T ss_pred             CeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCccC
Confidence            47899999999999999999999999999999999999      99999999999999766544

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.38  E-value=1.3e-12  Score=74.66  Aligned_cols=53  Identities=19%  Similarity=0.505  Sum_probs=49.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|.+|++++++.+++++|||||+|.+.++|++|+..+++..+.|++|.|.++.
T Consensus        42 ~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           42 KVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             CEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            47889999999999999999999999999999999999999999999999863

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.38  E-value=1e-12  Score=79.52  Aligned_cols=56  Identities=38%  Similarity=0.678  Sum_probs=52.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|++|+..|++..+.|++|.|.++..++
T Consensus        72 ~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~~  127 (129)
T 2kxn_B           72 PIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR  127 (129)
T ss_dssp             CEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSSS
T ss_pred             CeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            47899999999999999999999999999999999999999999999999987654

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

Probab=99.38  E-value=6.7e-13  Score=76.92  Aligned_cols=70  Identities=26%  Similarity=0.355  Sum_probs=56.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCC-----CCCCcceEEEcCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPL-----YAETDFKLFVGNLS   75 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~-----~~~~~~~l~i~nlp   75 (148)
                      .|.+|+++++     ++|||||+|.+.++|+.|+..|++..+.|++|.|.++.........     ......+|||+||+
T Consensus        26 ~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           26 PLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             CeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCcccCCCCCccccCCCceecCCCC
Confidence            3678888887     7899999999999999999999999999999999998765533221     11236689999986

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=1.9e-12  Score=73.58  Aligned_cols=54  Identities=17%  Similarity=0.287  Sum_probs=49.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.+|+++++ .+|+++|||||+|.+.++|++|+. +++..+.|+.|.|.++....
T Consensus        35 ~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~~~   88 (91)
T 2dgw_A           35 KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSGP   88 (91)
T ss_dssp             CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESSCC
T ss_pred             CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCcCC
Confidence            4789999999 799999999999999999999999 99999999999999987553

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.38  E-value=1.6e-12  Score=73.55  Aligned_cols=55  Identities=25%  Similarity=0.511  Sum_probs=50.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.++++++++.+|+++|||||+|.+.++|++|+ .+++..+.|++|.|.++....
T Consensus        32 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~~   86 (89)
T 3ucg_A           32 SVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTNR   86 (89)
T ss_dssp             CEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTTS
T ss_pred             CEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCCC
Confidence            4788999999989999999999999999999999 899999999999999987643

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.37  E-value=3.1e-13  Score=80.14  Aligned_cols=76  Identities=20%  Similarity=0.285  Sum_probs=65.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      .|.+|.++++   +.++|||||+|.+.++|..|+..|++..+.|+.|.|.++.+....             .+++...++
T Consensus        34 ~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~-------------~~~~~~~~~   97 (115)
T 3lqv_A           34 PIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAF-------------QKMDTKKKE   97 (115)
T ss_dssp             CEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHHHT-------------TTSCHHHHH
T ss_pred             CeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCChhh-------------hhhhHhHhH
Confidence            3678888865   456999999999999999999999999999999999998754332             567888899


Q ss_pred             HHHHHHHhhcCC
Q 032044           81 ESLTQAFQEYGN   92 (148)
Q Consensus        81 ~~l~~~f~~~g~   92 (148)
                      +++.++|++||.
T Consensus        98 ~~l~~~~~~~g~  109 (115)
T 3lqv_A           98 EQLKLLKEKYGI  109 (115)
T ss_dssp             HHHHHHHHHHCC
T ss_pred             HHHHHHHHHhCC
Confidence            999999999984

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.37  E-value=1.6e-12  Score=74.86  Aligned_cols=59  Identities=22%  Similarity=0.338  Sum_probs=52.5

Q ss_pred             CcceeEeeecCC---CCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYDRE---TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~~~---~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~   59 (148)
                      .|++|++++++.   +++++|||||+|.+.++|++|+..|++..+.|++|.|.++.......
T Consensus        31 ~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   92 (98)
T 2cpf_A           31 AIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPA   92 (98)
T ss_dssp             CEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSSCCC
T ss_pred             CeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCCCCC
Confidence            478899999887   66999999999999999999999999999999999999997665443

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.37  E-value=2.5e-12  Score=75.12  Aligned_cols=58  Identities=29%  Similarity=0.360  Sum_probs=53.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCee---cCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREY---LGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~---~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|.+|+..|++..+   .+++|.|.++......
T Consensus        39 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~~~   99 (106)
T 2dgp_A           39 KIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRG   99 (106)
T ss_dssp             CCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCSCC
T ss_pred             CeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCccccc
Confidence            478999999999999999999999999999999999999987   8999999999776544

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.37  E-value=1.6e-12  Score=75.02  Aligned_cols=48  Identities=33%  Similarity=0.614  Sum_probs=46.4

Q ss_pred             eEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            5 LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         5 i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      +++++++.+|+++|||||+|.+.++|+.|++.|++..+.|++|.|+++
T Consensus        51 v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A   98 (99)
T 2la6_A           51 INLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA   98 (99)
T ss_dssp             EEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             EEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEec
Confidence            999999999999999999999999999999999999999999999986

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.37  E-value=1.4e-12  Score=76.65  Aligned_cols=56  Identities=29%  Similarity=0.465  Sum_probs=51.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.+|++++++.+|.++|||||+|.+.++|..|+..|++..+.|++|.|.++....
T Consensus        52 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  107 (110)
T 1oo0_B           52 EIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG  107 (110)
T ss_dssp             CEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEESS
T ss_pred             CEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccCC
Confidence            37889999999999999999999999999999999999999999999999986543

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.37  E-value=1.9e-12  Score=74.60  Aligned_cols=55  Identities=20%  Similarity=0.327  Sum_probs=50.5

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      |.++.++.++.+|+++|||||+|.+.++|++|+..+++..+.|++|.|+++..+.
T Consensus        42 v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (98)
T 2cqp_A           42 IPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS   96 (98)
T ss_dssp             CTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESSCSS
T ss_pred             ccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcCCCC
Confidence            5678899998999999999999999999999999999999999999999987543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.36  E-value=3e-12  Score=74.87  Aligned_cols=59  Identities=25%  Similarity=0.400  Sum_probs=53.4

Q ss_pred             CcceeEeeec-CCCCCcccEEEEEeCCHHHHHHHHHHh-CCCeecCcEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYD-RETGRSRGFAFVTMSTVEDCNAVIENL-DGREYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~-~~~~~~~g~afv~f~~~~~a~~a~~~l-~~~~~~~~~i~v~~~~~~~~~~   59 (148)
                      .|++|+++++ +.++.++|||||+|.+.++|++|+..+ ++..+.|++|.|.++.......
T Consensus        41 ~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~~~  101 (107)
T 2cph_A           41 ELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ  101 (107)
T ss_dssp             CEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCCCC
T ss_pred             CeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCCCCC
Confidence            4788999999 789999999999999999999999999 9999999999999998765543

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=1.4e-12  Score=75.97  Aligned_cols=56  Identities=36%  Similarity=0.688  Sum_probs=52.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.++++++++.+|.++|||||+|.+.++|+.|+..+++..+.|++|.|.++....
T Consensus        34 ~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   89 (104)
T 1p1t_A           34 PVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK   89 (104)
T ss_dssp             CCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTT
T ss_pred             CeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCcc
Confidence            47899999999999999999999999999999999999999999999999987654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.36  E-value=3.3e-12  Score=78.18  Aligned_cols=58  Identities=26%  Similarity=0.504  Sum_probs=53.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|++|++++++.+|+++|||||+|.+.++|.+|+..+++..+.|+.|.|.++......
T Consensus        68 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  125 (139)
T 1u6f_A           68 PIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR  125 (139)
T ss_dssp             CEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCC
T ss_pred             CeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            4789999999999999999999999999999999999999999999999999766544

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.36  E-value=1.8e-12  Score=74.81  Aligned_cols=55  Identities=16%  Similarity=0.468  Sum_probs=51.2

Q ss_pred             cc-eeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcE----EEEeecCCCC
Q 032044            2 LS-KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRI----LRVNFSDKPK   56 (148)
Q Consensus         2 i~-~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~----i~v~~~~~~~   56 (148)
                      |. ++++++++.+|+++|||||+|.+.++|++|+..|++..+.|+.    |.|.|+....
T Consensus        36 i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~~   95 (99)
T 2div_A           36 TVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSG   95 (99)
T ss_dssp             CCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCCS
T ss_pred             cceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCCC
Confidence            66 8999999999999999999999999999999999999999999    9999987654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.36  E-value=1.9e-12  Score=75.38  Aligned_cols=57  Identities=18%  Similarity=0.282  Sum_probs=52.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCe-ecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGRE-YLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~-~~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|++++++ +|.++|||||+|.+.++|..|+..+++.. +.|++|.|.++......
T Consensus        36 ~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~~~   93 (104)
T 2dhg_A           36 SCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASR   93 (104)
T ss_dssp             TEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCCSC
T ss_pred             CeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCCcC
Confidence            47899999998 99999999999999999999999999999 99999999998765543

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.36  E-value=2.4e-12  Score=80.45  Aligned_cols=58  Identities=33%  Similarity=0.517  Sum_probs=53.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|++|++++++.+|+++|||||+|.+.++|..|+..|++..+.|++|.|.++.+..+.
T Consensus        96 ~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  153 (158)
T 2kn4_A           96 RVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  153 (158)
T ss_dssp             CEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCC
T ss_pred             CeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            4789999999989999999999999999999999999999999999999999866544

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.35  E-value=4e-12  Score=73.73  Aligned_cols=56  Identities=29%  Similarity=0.508  Sum_probs=51.5

Q ss_pred             ceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            3 SKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         3 ~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .++++++++.+++++|||||+|.+.++|++|+..|++..+.|++|.|.++.++...
T Consensus        40 ~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   95 (102)
T 2fc8_A           40 VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG   95 (102)
T ss_dssp             SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCSS
T ss_pred             eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCCC
Confidence            47899999989999999999999999999999999999999999999999766543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.35  E-value=4.4e-12  Score=74.89  Aligned_cols=55  Identities=29%  Similarity=0.548  Sum_probs=51.0

Q ss_pred             eeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         4 ~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|++++++.+|+++|||||+|.+.++|++|+..|++..+.|++|.|.++......
T Consensus        52 ~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           52 MIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             SEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCCS
T ss_pred             CEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCCCC
Confidence            6999999899999999999999999999999999999999999999998776543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.35  E-value=3.7e-12  Score=74.25  Aligned_cols=54  Identities=19%  Similarity=0.302  Sum_probs=49.2

Q ss_pred             CcceeEeeecCCC-CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRET-GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~-~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      +|++|.|++++.+ ++++|+|||+|.+.++|.+|+..|||..+.|++|.+.++..
T Consensus        39 ~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           39 KVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNL   93 (105)
T ss_dssp             CEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCH
Confidence            4789999998754 68999999999999999999999999999999999998853

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.35  E-value=1.9e-12  Score=73.07  Aligned_cols=56  Identities=16%  Similarity=0.358  Sum_probs=50.9

Q ss_pred             CcceeEeeecCCCCC-cccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGR-SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~-~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.++.+++++.++. ++|||||+|.+.++|++|+..+++..+.|++|.|.++.++.
T Consensus        30 ~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (88)
T 4a8x_A           30 KIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPW   86 (88)
T ss_dssp             CEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECCCC
T ss_pred             CEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCCCC
Confidence            377899999987766 99999999999999999999999999999999999987654

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.35  E-value=3.7e-12  Score=74.26  Aligned_cols=58  Identities=33%  Similarity=0.473  Sum_probs=52.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecC---cEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG---RILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~---~~i~v~~~~~~~~~~   59 (148)
                      .|++|++++++ +|.++|||||+|.+.++|++|+..|++..+.+   ++|.|.++.......
T Consensus        41 ~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~~~~  101 (105)
T 2dnh_A           41 VIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESG  101 (105)
T ss_dssp             CEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSCCCS
T ss_pred             CeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCcccC
Confidence            47899999997 89999999999999999999999999999988   999999998766543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.35  E-value=5.4e-12  Score=75.77  Aligned_cols=58  Identities=28%  Similarity=0.319  Sum_probs=52.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~   59 (148)
                      .|++|++++++ +|+++|||||+|.+.++|..|+..+++..+.|++|.|.++.......
T Consensus        61 ~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  118 (124)
T 2kt5_A           61 TLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLE  118 (124)
T ss_dssp             CCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCTTCCC
T ss_pred             CeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCCCC
Confidence            47899999998 99999999999999999999999999999999999999987655443

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.34  E-value=4.9e-12  Score=73.50  Aligned_cols=57  Identities=25%  Similarity=0.518  Sum_probs=51.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~   59 (148)
                      .|.+|+++++  +|.++|||||+|.+.++|+.|+..|++..+.|++|.|.++.++....
T Consensus        41 ~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   97 (103)
T 2d9p_A           41 TITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQ   97 (103)
T ss_dssp             CEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCCCC
T ss_pred             CEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecccccCC
Confidence            4788999998  89999999999999999999999999999999999999998765543

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.34  E-value=8.1e-13  Score=74.96  Aligned_cols=56  Identities=32%  Similarity=0.650  Sum_probs=48.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|+++++++++.+|+++|||||+|.+.+ |.+|+..+++..+.|++|.|.++.....
T Consensus        27 ~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~~   82 (90)
T 2ki2_A           27 KVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKKS   82 (90)
T ss_dssp             CCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC-----
T ss_pred             CEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            4789999999999999999999999999 9999999999999999999999876543

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.34  E-value=4.1e-12  Score=73.96  Aligned_cols=56  Identities=16%  Similarity=0.385  Sum_probs=51.3

Q ss_pred             cceeEeeecCCC-CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRET-GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~~-~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |.+|++++++.+ |+++|||||+|.+.++|++|+ .+++..+.|++|.|.++..+...
T Consensus        41 i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~   97 (104)
T 1wi8_A           41 ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCCC
T ss_pred             ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccCCCCC
Confidence            578999999887 999999999999999999999 89999999999999999776544

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.33  E-value=2.4e-12  Score=74.94  Aligned_cols=51  Identities=18%  Similarity=0.301  Sum_probs=47.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      +|.+|+|++++ +++++|||||+|.+.++|.+|+..|||..+.|++|.|.++
T Consensus        53 ~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           53 EVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             CEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             ceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            47899999986 5899999999999999999999999999999999999986

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.33  E-value=1.3e-12  Score=71.65  Aligned_cols=51  Identities=24%  Similarity=0.441  Sum_probs=47.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      .|.++++++++.+|+++|||||+|.+.++|++|++ +++..+.|+++.|.++
T Consensus        25 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           25 KVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            47889999999899999999999999999999998 9999999999999864

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.33  E-value=8.2e-12  Score=74.93  Aligned_cols=57  Identities=21%  Similarity=0.517  Sum_probs=51.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|++|++++++.+|.++|||||+|.+.++|..|+ .+++..+.|+.|.|.++......
T Consensus        62 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~  118 (124)
T 2jwn_A           62 SINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMPG  118 (124)
T ss_dssp             CEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCCCSS
T ss_pred             CEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCCCCC
Confidence            4789999999999999999999999999999999 79999999999999998765443

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.33  E-value=4.6e-12  Score=74.11  Aligned_cols=52  Identities=31%  Similarity=0.438  Sum_probs=49.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|++|++++++ +|+++|||||+|.+.++|++|+..|++..+.|++|.|.++.
T Consensus        55 ~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           55 TLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            47899999998 99999999999999999999999999999999999999874

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.32  E-value=3.3e-12  Score=73.12  Aligned_cols=52  Identities=19%  Similarity=0.277  Sum_probs=48.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      |.++.++.++.+|+++|||||+|.+.++|++|+..+++..+.|++|.|.++.
T Consensus        42 i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           42 IPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             CTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             ccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            6678899999999999999999999999999999999999999999999875

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.32  E-value=1.3e-11  Score=72.89  Aligned_cols=56  Identities=23%  Similarity=0.473  Sum_probs=50.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|++|++++++ +|+++|||||+|.+.++|+.|+..|++..+.|++|.|.++.....
T Consensus        41 ~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   96 (114)
T 2do0_A           41 VVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALP   96 (114)
T ss_dssp             CEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCCCC
T ss_pred             CeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccCCC
Confidence            47889999997 699999999999999999999999999999999999999865433

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.31  E-value=5.9e-12  Score=70.70  Aligned_cols=73  Identities=22%  Similarity=0.330  Sum_probs=61.4

Q ss_pred             CCcceEEEcCCCCC-----CCH----HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC
Q 032044           64 ETDFKLFVGNLSWS-----VTT----ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELE  134 (148)
Q Consensus        64 ~~~~~l~i~nlp~~-----~~~----~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~  134 (148)
                      .+..+|.|.-++..     +..    .+|.+.|.+||.+..+++..++        +||+|.+.++|.+|+. |||..++
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~   83 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeC
Confidence            45568888887632     333    5688999999999999998662        9999999999999999 9999999


Q ss_pred             CeEEEEEeccC
Q 032044          135 GRAMRVSLAQG  145 (148)
Q Consensus       135 g~~l~v~~~~~  145 (148)
                      |+.|+|++..+
T Consensus        84 Gr~L~V~~k~~   94 (95)
T 1ufw_A           84 GRAVKISGPSS   94 (95)
T ss_dssp             TEEEEEECCCC
T ss_pred             CeEEEEeccCC
Confidence            99999998654

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.31  E-value=8e-12  Score=71.71  Aligned_cols=53  Identities=11%  Similarity=0.140  Sum_probs=48.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|++|++++++.+   +|||||+|.+.++|++|+..+++..+.|++|.|.++.+..
T Consensus        39 ~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   91 (96)
T 2dgx_A           39 KVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGAS   91 (96)
T ss_dssp             CEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCSS
T ss_pred             cEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            4788999999755   8999999999999999999999999999999999986554

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.31  E-value=8.4e-12  Score=74.05  Aligned_cols=55  Identities=29%  Similarity=0.414  Sum_probs=50.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|++|++++++.+++++|||||+|.+.++|++|+..+++ .+.|++|.|.++....
T Consensus        43 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~~   97 (116)
T 2cqd_A           43 DIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGA   97 (116)
T ss_dssp             CEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTTC
T ss_pred             CeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEcccCC
Confidence            478999999999999999999999999999999999998 8999999999986543

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.31  E-value=8.7e-12  Score=77.73  Aligned_cols=57  Identities=21%  Similarity=0.368  Sum_probs=53.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|++|+|++++.++.++|||||+|.+.++|++|+..|++..+.+++|.|.++.....
T Consensus        65 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  121 (156)
T 1h2v_Z           65 DIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE  121 (156)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCCT
T ss_pred             CeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            478999999999999999999999999999999999999999999999999976544

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.31  E-value=4.7e-12  Score=73.81  Aligned_cols=57  Identities=19%  Similarity=0.282  Sum_probs=52.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|++++++.+++++|||||+|.+.++|++|+.. ++..+.|++|.|.++.++...
T Consensus        42 ~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a~~~~~~   98 (105)
T 2dh8_A           42 EVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQ   98 (105)
T ss_dssp             CEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCSCCSSCC
T ss_pred             CeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEccCCCCC
Confidence            478999999999999999999999999999999997 999999999999998766543

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.31  E-value=2.5e-12  Score=74.36  Aligned_cols=53  Identities=17%  Similarity=0.396  Sum_probs=48.8

Q ss_pred             cceeEeeecC-CCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            2 LSKLTVLYDR-ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         2 i~~i~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      |.+|++++++ .+|+++|||||+|.+.++|.+|+ .+++..+.|+.|.|.++...
T Consensus        45 i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~   98 (100)
T 2j76_E           45 ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQA   98 (100)
T ss_dssp             EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEECCCS
T ss_pred             CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEeccCC
Confidence            5789999998 68999999999999999999999 79999999999999998654

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.30  E-value=6.3e-12  Score=71.91  Aligned_cols=52  Identities=31%  Similarity=0.486  Sum_probs=48.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|++|++++++ +|+++|||||+|.+.++|++|+..|++..+.|++|.|.++.
T Consensus        42 ~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           42 PLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             CEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            47899999997 49999999999999999999999999999999999999875

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.30  E-value=4.4e-12  Score=76.34  Aligned_cols=57  Identities=25%  Similarity=0.529  Sum_probs=52.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|.+|.+++++.++.++|||||+|.+.++|+.|+..|++..+.|+.|.|.++.....
T Consensus        48 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  104 (126)
T 3ex7_B           48 EIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP  104 (126)
T ss_dssp             CEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSS
T ss_pred             CeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCC
Confidence            478899999999999999999999999999999999999999999999999865443

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.29  E-value=3.5e-12  Score=77.70  Aligned_cols=58  Identities=33%  Similarity=0.517  Sum_probs=53.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|++++++.+++++|||||+|.+.++|++|+..|++..+.|++|.|.++......
T Consensus        73 ~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           73 RVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  130 (135)
T ss_dssp             CCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCC
T ss_pred             CEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            4789999999989999999999999999999999999999999999999999765543

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.29  E-value=1.1e-11  Score=72.98  Aligned_cols=56  Identities=18%  Similarity=0.204  Sum_probs=49.8

Q ss_pred             CcceeEeeecCCCC---CcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETG---RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~---~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.+|++++++.++   +++|||||+|.+.++|++|+..|++..+.|++|.|.++..+.
T Consensus        44 ~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           44 KIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             CEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCS
T ss_pred             CEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEeccccc
Confidence            47889999987754   566999999999999999999999999999999999987654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.29  E-value=3.2e-12  Score=76.06  Aligned_cols=51  Identities=22%  Similarity=0.412  Sum_probs=48.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      |.+|++++++.+|+++|||||+|.+.++|++|+..|++..+.|++|.|+++
T Consensus        67 i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A           67 VISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             EEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC
T ss_pred             EEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            778999999989999999999999999999999999999999999999986

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.29  E-value=1.1e-11  Score=72.73  Aligned_cols=56  Identities=23%  Similarity=0.302  Sum_probs=50.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|++|++++++.+|+++|||||+|.+.++|.+|+..+ +..+.|+.|.|.++.....
T Consensus        51 ~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a~~~~~  106 (109)
T 2rs2_A           51 EVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVAFPRRA  106 (109)
T ss_dssp             CEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEECCCCCC
T ss_pred             CeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEccCCCC
Confidence            4789999999999999999999999999999999965 5889999999999876543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.28  E-value=1.5e-11  Score=72.94  Aligned_cols=57  Identities=26%  Similarity=0.417  Sum_probs=51.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|+.|+.. ++..+.|++|.|.++.++...
T Consensus        53 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~~~~  109 (116)
T 1x4b_A           53 KLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREES  109 (116)
T ss_dssp             CCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSSCCCC
T ss_pred             CEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCCCccC
Confidence            478999999999999999999999999999999996 999999999999998766543

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.28  E-value=1.6e-11  Score=80.74  Aligned_cols=67  Identities=19%  Similarity=0.248  Sum_probs=59.8

Q ss_pred             CCHHHHHHHHhhcCCeeEEEEEEcCC----CCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           78 VTTESLTQAFQEYGNVVGARVLYDGE----SGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        78 ~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..+++|.+.|.+||.|..+.++.+..    ++.++|++||+|.+.++|++|+..|||..++|+.|.+.++.
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            35578999999999999999986543    34789999999999999999999999999999999999875

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.28  E-value=3.1e-11  Score=70.08  Aligned_cols=56  Identities=20%  Similarity=0.468  Sum_probs=49.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|++|++++++.+  ++|||||+|.+.++|++|+..|++..+.|++|.|.++..+...
T Consensus        41 ~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2cqi_A           41 PCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ   96 (103)
T ss_dssp             CEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTCC
T ss_pred             CEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCccc
Confidence            4788999998543  7899999999999999999999999999999999999876544

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.28  E-value=9.1e-12  Score=72.61  Aligned_cols=53  Identities=21%  Similarity=0.483  Sum_probs=48.2

Q ss_pred             CcceeEeeecCCC--CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRET--GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~--~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      +|++|+|++++.+  ++++|+|||+|.+.++|.+|+..|||..+.|++|.+.++.
T Consensus        41 ~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~   95 (105)
T 3v4m_A           41 LVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   95 (105)
T ss_dssp             CEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeC
Confidence            4789999998755  4789999999999999999999999999999999999874

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.28  E-value=6.5e-12  Score=76.82  Aligned_cols=52  Identities=38%  Similarity=0.688  Sum_probs=48.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      .|+++++++++.+|+++|||||+|.+.++|++|+..+++..+.|++|.|.++
T Consensus        89 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           89 DITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             CEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            4788999999999999999999999999999999999999999999999874

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.28  E-value=1.4e-11  Score=72.31  Aligned_cols=56  Identities=18%  Similarity=0.294  Sum_probs=50.5

Q ss_pred             cceeEee-ecCCCCCcccEEEEEeCCHHHHHHHHHHhC--CCeecCcEEEEeecCCCCC
Q 032044            2 LSKLTVL-YDRETGRSRGFAFVTMSTVEDCNAVIENLD--GREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         2 i~~i~~~-~~~~~~~~~g~afv~f~~~~~a~~a~~~l~--~~~~~~~~i~v~~~~~~~~   57 (148)
                      |.++.++ .++.+|.++|||||+|.+.++|..|+..++  +..+.|++|.|.++.+...
T Consensus        36 v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~~   94 (109)
T 2dis_A           36 VLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID   94 (109)
T ss_dssp             EEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCS
T ss_pred             ceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCCC
Confidence            7788888 788889999999999999999999999996  5899999999999976554

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.27  E-value=1.3e-11  Score=72.34  Aligned_cols=51  Identities=18%  Similarity=0.278  Sum_probs=46.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      +|.+|+|++++ +|+++|||||+|.+.++|++|+ .+++..+.|+.|.|..+.
T Consensus        41 ~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           41 RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            47899999997 4999999999999999999999 599999999999998764

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.27  E-value=4.1e-12  Score=77.02  Aligned_cols=55  Identities=31%  Similarity=0.568  Sum_probs=50.2

Q ss_pred             cce--eEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCC----eecCcEEEEeecCCCCC
Q 032044            2 LSK--LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGR----EYLGRILRVNFSDKPKP   57 (148)
Q Consensus         2 i~~--i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~----~~~~~~i~v~~~~~~~~   57 (148)
                      |++  |+|++|+.+|+++|||||+|.+. +|.+|+..+++.    .+.|++|.|.++.+...
T Consensus        50 v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           50 LSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSKR  110 (131)
T ss_dssp             CCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSCC
T ss_pred             cceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCCC
Confidence            544  99999999999999999999999 999999999999    99999999999876544

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.27  E-value=4.6e-12  Score=69.68  Aligned_cols=51  Identities=25%  Similarity=0.356  Sum_probs=47.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      .|.++.+++++.+|+++|||||+|.+.++|+.|+..++ ..+.|+++.|+++
T Consensus        26 ~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A           26 EVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            37889999999899999999999999999999999888 9999999999875

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.27  E-value=6.4e-12  Score=74.33  Aligned_cols=53  Identities=26%  Similarity=0.490  Sum_probs=49.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|++|+ .+++..+.|+.|.|.++..
T Consensus        51 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           51 KVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             CEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            4789999999999999999999999999999999 8999999999999998754

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.27  E-value=1.3e-11  Score=69.47  Aligned_cols=51  Identities=25%  Similarity=0.458  Sum_probs=46.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      .|.++++++++.+|+++|||||+|.+.++|++|+. +++..+.|++|.|.++
T Consensus        37 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           37 EVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             CEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            47899999999999999999999999999999997 5888899999999864

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.26  E-value=1.6e-11  Score=68.53  Aligned_cols=46  Identities=15%  Similarity=0.162  Sum_probs=41.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      .|.++++..      ++|||||+|.+.++|++|+..||+..+.|++|.|.++
T Consensus        33 ~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A           33 PLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            356777754      6899999999999999999999999999999999977

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.26  E-value=4.5e-11  Score=69.35  Aligned_cols=56  Identities=25%  Similarity=0.441  Sum_probs=49.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|++|++++++.  .++|||||+|.+.++|++|+..|++..+.|++|.|.++..+...
T Consensus        41 ~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   96 (103)
T 2cq3_A           41 KILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMT   96 (103)
T ss_dssp             CEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCCC
T ss_pred             CeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCCCC
Confidence            478899999863  38999999999999999999999999999999999999776544

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.26  E-value=5.7e-12  Score=83.30  Aligned_cols=54  Identities=24%  Similarity=0.388  Sum_probs=51.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      +|++|+|++++.+|+++|||||+|.+.++|++||..|++..|.|+.|.|.++..
T Consensus        96 ~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~  149 (229)
T 3q2s_C           96 DILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNK  149 (229)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCH
T ss_pred             ceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCC
Confidence            488999999999999999999999999999999999999999999999998753

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.25  E-value=1.4e-11  Score=70.08  Aligned_cols=55  Identities=16%  Similarity=0.292  Sum_probs=49.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|++++++++  +|+++|||||+|.+.++|+.|+..|++..+.|++|.|.++.....
T Consensus        34 ~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   88 (92)
T 2dgv_A           34 HVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASG   88 (92)
T ss_dssp             CEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCCSS
T ss_pred             CEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCCC
Confidence            3678888874  789999999999999999999999999999999999999876544

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.25  E-value=1.7e-12  Score=72.79  Aligned_cols=53  Identities=11%  Similarity=0.305  Sum_probs=48.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|.++++++++.+|+++|||||+|.+.++|+.|+..|++..+.|+.+.+.++.
T Consensus        31 ~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A           31 KIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            47889999999999999999999999999999999999999999988777653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.25  E-value=4.4e-11  Score=69.18  Aligned_cols=55  Identities=24%  Similarity=0.524  Sum_probs=48.9

Q ss_pred             ceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            3 SKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         3 ~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      -+|+++++ .+++++|||||+|.+.++|++|+..+++..+.|++|.|.++.++...
T Consensus        40 g~v~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   94 (101)
T 2fc9_A           40 TFIKVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSP   94 (101)
T ss_dssp             SEEECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCCCC
T ss_pred             CEEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCCC
Confidence            35677777 68999999999999999999999999999999999999999776543

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.24  E-value=4.8e-11  Score=69.25  Aligned_cols=56  Identities=23%  Similarity=0.337  Sum_probs=50.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|+.|+.  ++..+.|+.|.|.++......
T Consensus        41 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a~~~~~~   96 (103)
T 2cqg_A           41 EVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPNSKQSQ   96 (103)
T ss_dssp             CEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECCCTTCCC
T ss_pred             CeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEecCCCCcC
Confidence            47899999999999999999999999999999998  577899999999998765543

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.24  E-value=1.7e-11  Score=77.08  Aligned_cols=57  Identities=30%  Similarity=0.501  Sum_probs=52.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|.+|.+++++.+|.++|||||+|.+.++|..|+..|++..+.|++|.|.|+.....
T Consensus        98 ~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A           98 EIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             CEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             CEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            478999999999999999999999999999999999999999999999999865543

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.24  E-value=2.1e-11  Score=72.04  Aligned_cols=54  Identities=31%  Similarity=0.519  Sum_probs=48.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCee--------cCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREY--------LGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~--------~~~~i~v~~~~~~   55 (148)
                      .|.+|++++++ +|.++|||||+|.+.++|+.|+..|++..+        .++++.|.|+.++
T Consensus        51 ~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           51 QVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             CEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECCCS
T ss_pred             CEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccCCC
Confidence            47899999998 999999999999999999999999999998        5788999988743

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.24  E-value=1.2e-11  Score=72.11  Aligned_cols=53  Identities=19%  Similarity=0.338  Sum_probs=47.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCc-EEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGR-ILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~-~i~v~~~~~~   55 (148)
                      .|.+|.++  +.+|+++|||||+|.+.++|..|+..|+|..+.|+ +|.|.++...
T Consensus        47 ~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~~  100 (105)
T 2nlw_A           47 KITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECSCCC
T ss_pred             CEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEcchH
Confidence            36788888  36899999999999999999999999999999998 9999998654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.24  E-value=1.1e-11  Score=72.00  Aligned_cols=51  Identities=20%  Similarity=0.329  Sum_probs=47.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|.+|++++++. |+++|||||+|.+.++|..|+. +++..+.|++|.|.+..
T Consensus        37 ~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           37 QVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             CEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            478999999986 9999999999999999999999 89999999999998753

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.23  E-value=1.9e-11  Score=73.54  Aligned_cols=52  Identities=25%  Similarity=0.489  Sum_probs=45.4

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      |.+|.+.   .+++++|||||+|.+.++|..|+..|+|..+.|++|.|.|+..+.
T Consensus        60 I~~v~i~---~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~~  111 (127)
T 2a3j_A           60 ILDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ  111 (127)
T ss_dssp             EEEEEEC---CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCCC
T ss_pred             eEEEEec---cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCcc
Confidence            5566553   367899999999999999999999999999999999999987654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.22  E-value=1.8e-11  Score=72.89  Aligned_cols=50  Identities=28%  Similarity=0.439  Sum_probs=47.0

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      |.+|++++++. |+++|||||+|.+.++|++|+. +++..+.|+.|.|.++.
T Consensus        47 v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~   96 (118)
T 2db1_A           47 VAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSH   96 (118)
T ss_dssp             GGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEEEC
T ss_pred             ceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECC
Confidence            68999999975 9999999999999999999999 99999999999999874

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.22  E-value=1.7e-11  Score=72.81  Aligned_cols=53  Identities=19%  Similarity=0.354  Sum_probs=48.1

Q ss_pred             CcceeEeeecCC----CCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRE----TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~----~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      +|++|.|++++.    +++++|++||+|.+.++|.+|+..|||..+.|++|.+.++.
T Consensus        51 ~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~  107 (118)
T 3ue2_A           51 AVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  107 (118)
T ss_dssp             CEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcC
Confidence            478999999865    45788999999999999999999999999999999999874

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.22  E-value=1.4e-11  Score=75.01  Aligned_cols=50  Identities=28%  Similarity=0.424  Sum_probs=47.1

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      |.+|++++++. |+++|||||+|.+.++|++|+. +++..+.|++|.|.++.
T Consensus        74 v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~  123 (136)
T 2hgl_A           74 AAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSH  123 (136)
T ss_dssp             STTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECC
T ss_pred             eeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECC
Confidence            68999999986 9999999999999999999999 99999999999999874

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.22  E-value=2.5e-11  Score=70.43  Aligned_cols=53  Identities=21%  Similarity=0.233  Sum_probs=47.8

Q ss_pred             ceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            3 SKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         3 ~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .+|+|++++ +|+++|||||+|.+.++|++|+. +++..+.++.|.|.++.....
T Consensus        42 ~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~~~~~   94 (102)
T 1wez_A           42 MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGT   94 (102)
T ss_dssp             SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCC
T ss_pred             eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCCCCC
Confidence            489999997 99999999999999999999995 799999999999998765543

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.21  E-value=1.6e-11  Score=72.61  Aligned_cols=51  Identities=22%  Similarity=0.259  Sum_probs=46.9

Q ss_pred             ceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            3 SKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         3 ~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .+|+|++++ +|+++|||||+|.+.++|++|+.. ++..+.|++|.|.++...
T Consensus        44 ~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~~~   94 (114)
T 2cpy_A           44 NAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTLE   94 (114)
T ss_dssp             TTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEECHH
T ss_pred             CeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECCHH
Confidence            679999998 999999999999999999999986 999999999999987643

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=3.7e-11  Score=71.09  Aligned_cols=56  Identities=27%  Similarity=0.442  Sum_probs=47.0

Q ss_pred             eeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCC
Q 032044            4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         4 ~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~   59 (148)
                      ++.+..+..+|+++|||||+|.+.++|+.|+..|++..+.|++|.|.++.......
T Consensus        54 ~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~  109 (115)
T 2cpx_A           54 GPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRS  109 (115)
T ss_dssp             SSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSCCC
T ss_pred             ceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCCCCC
Confidence            33344444488999999999999999999999999999999999999998765543

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.19  E-value=1e-11  Score=67.89  Aligned_cols=51  Identities=18%  Similarity=0.296  Sum_probs=46.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      .|.++.+++++.+|.++|||||+|.+.++|+.|+. +++..+.|+++.|.++
T Consensus        25 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           25 EVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            37889999999999999999999999999999998 5889999999988764

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.17  E-value=1.1e-11  Score=71.71  Aligned_cols=51  Identities=24%  Similarity=0.436  Sum_probs=45.8

Q ss_pred             EeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            6 TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         6 ~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .+++++.+|+++|||||+|.+.++|++|++ +++..+.|++|.|.++.....
T Consensus        47 ~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~~~~   97 (101)
T 1fj7_A           47 LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDG   97 (101)
T ss_dssp             CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSCCCC
T ss_pred             EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCCCCC
Confidence            567777789999999999999999999998 999999999999999876543

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.17  E-value=1.8e-11  Score=71.65  Aligned_cols=51  Identities=22%  Similarity=0.306  Sum_probs=47.2

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      |.+|++++++. |+++|||||+|.+.++|++|+. +++..+.|+.|.|.++..
T Consensus        41 v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~   91 (107)
T 2lmi_A           41 ENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEINN   91 (107)
T ss_dssp             TTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEECCH
T ss_pred             cceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEECCH
Confidence            78899999986 9999999999999999999999 999999999999988753

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.17  E-value=1.3e-11  Score=68.55  Aligned_cols=47  Identities=19%  Similarity=0.383  Sum_probs=41.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCc-EEEE
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGR-ILRV   49 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~-~i~v   49 (148)
                      .|.++.++  +.+|+++|||||+|.+.++|..|+..|++..+.|+ +|.|
T Consensus        33 ~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A           33 KITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            36778877  45899999999999999999999999999999998 7765

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.16  E-value=6.8e-11  Score=69.36  Aligned_cols=53  Identities=26%  Similarity=0.482  Sum_probs=47.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .|++|++++++  +.++|||||+|.+.++|++|+..+++..+.|++|.|.++..+
T Consensus        55 ~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  107 (109)
T 2err_A           55 KILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR  107 (109)
T ss_dssp             CCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             CEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            47889999985  359999999999999999999999999999999999998654

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.16  E-value=8.2e-11  Score=68.43  Aligned_cols=53  Identities=23%  Similarity=0.310  Sum_probs=46.9

Q ss_pred             cce-eEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            2 LSK-LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         2 i~~-i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      |.+ |.++++ .+|+++|||||+|.+.++|++|+.. ++..+.++.|.|.++....
T Consensus        42 v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~~~~   95 (104)
T 1wg5_A           42 VPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             EEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEECTTT
T ss_pred             cceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECCHHH
Confidence            344 888888 6999999999999999999999996 9999999999999886544

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.15  E-value=2.4e-10  Score=66.93  Aligned_cols=54  Identities=24%  Similarity=0.388  Sum_probs=46.5

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |++|++..   ++.++|||||+|.+.++|++|+..|++..+.|++|.|.++......
T Consensus        49 v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~  102 (109)
T 1x4a_A           49 IRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT  102 (109)
T ss_dssp             EEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCCCC
T ss_pred             eEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCCCC
Confidence            66777754   4568999999999999999999999999999999999998765543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.15  E-value=8.2e-11  Score=70.08  Aligned_cols=54  Identities=11%  Similarity=0.212  Sum_probs=46.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCC----HHH----HHHHHH--HhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMST----VED----CNAVIE--NLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~----~~~----a~~a~~--~l~~~~~~~~~i~v~~~~~   54 (148)
                      .|.+++++.|+.||+++|||||+|.+    +++    |.+|+.  .+++..+.|++|.|.+...
T Consensus        32 eV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           32 EISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNKH   95 (136)
T ss_dssp             CCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEECCT
T ss_pred             CeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEECcc
Confidence            37899999999999999999999996    433    888988  7899999999999997653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.75  E-value=4.3e-12  Score=75.30  Aligned_cols=53  Identities=30%  Similarity=0.561  Sum_probs=49.3

Q ss_pred             eEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            5 LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         5 i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      |++++++.+++++|||||+|.+.++|++|+..|++..+.|++|.|.++.++..
T Consensus        45 v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           45 INLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRAD   97 (116)
Confidence            88999988999999999999999999999999999999999999999876544

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.13  E-value=2.9e-11  Score=72.53  Aligned_cols=52  Identities=17%  Similarity=0.197  Sum_probs=46.5

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      |.++.++.+..+|+++|||||+|.+.++|.+|+. +++..+.|+.|.|.++..
T Consensus        52 v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~  103 (124)
T 1wel_A           52 VEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITK  103 (124)
T ss_dssp             CTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECH
T ss_pred             ccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCH
Confidence            5566677777899999999999999999999999 999999999999998753

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.13  E-value=9.7e-11  Score=74.46  Aligned_cols=55  Identities=29%  Similarity=0.370  Sum_probs=50.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|++|.+++++ +|.++|||||+|.+.++|..|+..+++..+.|++|.|.++....
T Consensus       114 ~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~~~  168 (177)
T 2f3j_A          114 TLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI  168 (177)
T ss_dssp             CCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEESSGG
T ss_pred             CeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            47899999998 99999999999999999999999999999999999999986543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.12  E-value=1.4e-10  Score=67.30  Aligned_cols=53  Identities=23%  Similarity=0.366  Sum_probs=45.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCC--CeecCcEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDG--REYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~--~~~~~~~i~v~~~~~~~~~~   59 (148)
                      +|++|+++++      +|||||+|.+.++|..|+..+++  ..+.|++|.|.++..+....
T Consensus        42 ~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~~~   96 (105)
T 1sjq_A           42 KVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT   96 (105)
T ss_dssp             CEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSCCC
T ss_pred             CEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCCCCc
Confidence            4788898875      69999999999999999998764  78999999999997665443

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=99.11  E-value=1.6e-09  Score=62.06  Aligned_cols=72  Identities=19%  Similarity=0.217  Sum_probs=64.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhc-----CCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEY-----GNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAM  138 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~-----g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l  138 (148)
                      ...++|-+-|||..++...|+.+.+++     |.+..+.+..+      .+-|+|+|.+...|-+|.-.|+|.+|.|++|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD------H~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT------TTEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC------CCceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            346789999999999999999999999     99998887755      3359999999999999999999999999999


Q ss_pred             EEE
Q 032044          139 RVS  141 (148)
Q Consensus       139 ~v~  141 (148)
                      ++.
T Consensus        93 r~g   95 (117)
T 2l9w_A           93 RSG   95 (117)
T ss_dssp             EEE
T ss_pred             Eec
Confidence            875

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.11  E-value=4.2e-10  Score=65.93  Aligned_cols=52  Identities=19%  Similarity=0.446  Sum_probs=45.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|+++++      +|||||+|.+.++|..|+..|++..+.|++|.|.++......
T Consensus        51 ~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  102 (109)
T 1x4g_A           51 QIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM  102 (109)
T ss_dssp             CEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCSS
T ss_pred             CeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCCC
Confidence            3677888776      689999999999999999999999999999999999766543

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.11  E-value=5.5e-11  Score=68.20  Aligned_cols=52  Identities=17%  Similarity=0.395  Sum_probs=45.4

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      |.+|.+++   +|.++|||||+|.+.++|..|+..|++..+.|++|.|.++.+..
T Consensus        39 i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   90 (97)
T 1nu4_A           39 ILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS   90 (97)
T ss_dssp             EEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCC
T ss_pred             EEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCCC
Confidence            55666663   57789999999999999999999999999999999999987654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.09  E-value=5.4e-10  Score=64.08  Aligned_cols=51  Identities=25%  Similarity=0.371  Sum_probs=43.9

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |.+|.+.      +++|||||+|.+.++|.+|+..|++..+.|++|.|.++.++...
T Consensus        40 i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~   90 (97)
T 1x5p_A           40 IIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPML   90 (97)
T ss_dssp             EEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCCC
T ss_pred             EEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCCC
Confidence            5566663      57899999999999999999999999999999999998765543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.09  E-value=1.4e-10  Score=66.36  Aligned_cols=51  Identities=20%  Similarity=0.489  Sum_probs=44.5

Q ss_pred             eeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         4 ~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      +|.++  ..++.++|||||+|.+.++|..|+..+++..+.|++|.|.++.++.
T Consensus        42 ~v~~~--~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (96)
T 1fjc_A           42 EIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             EECCE--EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             cEEEe--CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            34455  3578999999999999999999999999999999999999987654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.09  E-value=2.4e-10  Score=65.66  Aligned_cols=50  Identities=20%  Similarity=0.218  Sum_probs=42.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCe--ecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGRE--YLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~--~~~~~i~v~~~~~~~   56 (148)
                      +|+++++++      ++|||||+|.+.++|..|+..+++..  +.|++|.|.|+..+.
T Consensus        47 ~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           47 PISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             CEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             CEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            467788774      46899999999999999999998875  789999999997654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.08  E-value=6.1e-11  Score=68.68  Aligned_cols=53  Identities=23%  Similarity=0.490  Sum_probs=48.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.++++++++ +|+++|||||+|.+.++|+.|+.  ++..+.|+++.|.++....
T Consensus        35 ~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~~~   87 (102)
T 2xs2_A           35 SVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRKQ   87 (102)
T ss_dssp             CEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEECC
T ss_pred             CeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCcCc
Confidence            47899999998 99999999999999999999998  8999999999998876443

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.08  E-value=2.7e-10  Score=81.81  Aligned_cols=56  Identities=21%  Similarity=0.525  Sum_probs=52.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|++|.|+.++.+|.++|||||+|.+.++|..||..|++..|.|++|.|.++....
T Consensus       128 ~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          128 PIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRT  183 (437)
T ss_pred             CeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            47899999999999999999999999999999999999999999999999987543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.08  E-value=6.7e-10  Score=66.77  Aligned_cols=53  Identities=19%  Similarity=0.297  Sum_probs=45.2

Q ss_pred             CcceeEeeecCCCCCcccE-EEEEeCCHHHHHHHHHHhCCCeecC--cEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGF-AFVTMSTVEDCNAVIENLDGREYLG--RILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~-afv~f~~~~~a~~a~~~l~~~~~~~--~~i~v~~~~~~~~~   58 (148)
                      +|.+|.++.+.     +|+ |||+|.+.++|..|++.|+|..+.+  ++|+|+|+......
T Consensus        54 ~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l~  109 (130)
T 3zzy_A           54 TVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLN  109 (130)
T ss_dssp             CEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSCC
T ss_pred             CEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCcee
Confidence            47788877642     577 9999999999999999999999988  99999999876543

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.08  E-value=4.8e-10  Score=69.89  Aligned_cols=53  Identities=17%  Similarity=0.219  Sum_probs=45.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecC--cEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG--RILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~--~~i~v~~~~~~~~   57 (148)
                      .|++|.+..+.    ++|||||+|.+.++|+.|+..|+|..|.+  ++|.|+|+.....
T Consensus        72 ~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~l  126 (164)
T 1sjr_A           72 TVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  126 (164)
T ss_dssp             CEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSSC
T ss_pred             CEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCcc
Confidence            47788886542    57899999999999999999999999965  9999999987643

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.07  E-value=3.1e-10  Score=66.66  Aligned_cols=50  Identities=20%  Similarity=0.246  Sum_probs=42.4

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      |..+++..    +.++|||||+|.+.++|++|++.|++..+.|++|.|.++..+
T Consensus        56 v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           56 TTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             CSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             eEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            55666643    248899999999999999999999999999999999998654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.07  E-value=7.8e-11  Score=70.49  Aligned_cols=50  Identities=18%  Similarity=0.146  Sum_probs=45.0

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      |.+|.|++++ +|+++|||||+|.+.++|++|+.. ++..+.++.|.|..+.
T Consensus        54 v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~a~  103 (123)
T 2dha_A           54 KEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFRST  103 (123)
T ss_dssp             GGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEEEC
T ss_pred             cceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEECC
Confidence            5789999994 999999999999999999999985 8999999998887653

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.07  E-value=8.8e-10  Score=63.67  Aligned_cols=53  Identities=13%  Similarity=0.237  Sum_probs=44.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHh--CCCeecCcEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENL--DGREYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l--~~~~~~~~~i~v~~~~~~~~~~   59 (148)
                      .|.+|.++++      +|||||+|.+.++|..|+..+  ++..+.|++|.|.|+..+....
T Consensus        41 ~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~~   95 (101)
T 2cq1_A           41 KVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKT   95 (101)
T ss_dssp             CEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSSCCC
T ss_pred             CEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcccCcC
Confidence            3677777764      699999999999999999976  5678999999999998665543

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.06  E-value=5.6e-10  Score=66.23  Aligned_cols=53  Identities=23%  Similarity=0.357  Sum_probs=45.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhC--CCeecCcEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLD--GREYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~--~~~~~~~~i~v~~~~~~~~~~   59 (148)
                      +|++|+++++      +|||||+|.+.++|.+|+..++  +..+.|++|.|.++..+....
T Consensus        57 ~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~~~  111 (119)
T 2ad9_A           57 KVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT  111 (119)
T ss_dssp             CCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSCCC
T ss_pred             CEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCCCCc
Confidence            4788888876      6999999999999999999887  468999999999997766544

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.06  E-value=1.3e-09  Score=64.20  Aligned_cols=52  Identities=31%  Similarity=0.486  Sum_probs=44.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.+|.| .++   .++|||||+|.+.++|.+|+..|++..+.|++|.|.++.+..
T Consensus        52 ~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           52 QIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             CCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCC
T ss_pred             CEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCC
Confidence            4678844 554   389999999999999999999999999999999999987644

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

Probab=99.06  E-value=8.5e-10  Score=62.33  Aligned_cols=49  Identities=16%  Similarity=0.297  Sum_probs=43.3

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |++++++        +|||||+|.+.++|++|+..+++..+.|++|.|.++..+...
T Consensus        35 i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   83 (90)
T 2dnq_A           35 VLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKA   83 (90)
T ss_dssp             EEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCCC
T ss_pred             EEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCCC
Confidence            5677776        589999999999999999999999999999999999776554

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.05  E-value=8.5e-11  Score=70.55  Aligned_cols=48  Identities=25%  Similarity=0.256  Sum_probs=43.8

Q ss_pred             eeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         4 ~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      +|+|++++. |+++|||||+|.+.++|++|+. +++..+.|++|.|.++.
T Consensus        72 ~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~a~  119 (126)
T 2hgm_A           72 GITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKSS  119 (126)
T ss_dssp             EEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEEEC
T ss_pred             EEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            899999986 9999999999999999999998 57799999999998764

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.05  E-value=3.6e-10  Score=66.65  Aligned_cols=49  Identities=16%  Similarity=0.360  Sum_probs=43.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      +|++|.|.++.    ++|+|||+|.+.++|.+|+..|||..+.|++|.+.++.
T Consensus        43 ~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           43 GVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVP   91 (114)
T ss_dssp             CCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEc
Confidence            47788886653    58999999999999999999999999999999999874

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.05  E-value=4.2e-10  Score=65.37  Aligned_cols=53  Identities=9%  Similarity=0.111  Sum_probs=43.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCC--CeecCcEEEEeecCCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDG--REYLGRILRVNFSDKPKPKL   59 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~--~~~~~~~i~v~~~~~~~~~~   59 (148)
                      +|.+|.++++      +|||||+|.+.++|..|+..+++  ..+.|++|.|.|+..+....
T Consensus        41 ~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~~~   95 (104)
T 1wex_A           41 TICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITR   95 (104)
T ss_dssp             CEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCCC
T ss_pred             CEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCccccC
Confidence            3677777753      69999999999999999998765  45899999999997765443

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.04  E-value=5.6e-10  Score=62.86  Aligned_cols=48  Identities=25%  Similarity=0.280  Sum_probs=42.4

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      |.++++.      +++|||||+|.+.++|++|+..+++..+.|+++.|.++...
T Consensus        31 v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A           31 LKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             eEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            5666663      57899999999999999999999999999999999998543

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.04  E-value=4e-10  Score=65.19  Aligned_cols=51  Identities=29%  Similarity=0.415  Sum_probs=43.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCC--eecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGR--EYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~--~~~~~~i~v~~~~~~~~   57 (148)
                      +|.+|.++++      +|||||+|.+.++|..|+..|++.  .+.|++|.|.++...+.
T Consensus        42 ~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~   94 (102)
T 1x4d_A           42 VISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKR   94 (102)
T ss_dssp             CEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCTT
T ss_pred             CEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCCCC
Confidence            4778888865      389999999999999999988754  59999999999975543

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.04  E-value=6.3e-11  Score=72.36  Aligned_cols=54  Identities=19%  Similarity=0.233  Sum_probs=47.9

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      |.+|+|++++. |+++|||||+|.+.++|++|+ .+++..+.++.|.|.++.....
T Consensus        72 i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           72 PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence            45899999975 999999999999999999999 6899999999999998765543

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.04  E-value=5.7e-10  Score=63.94  Aligned_cols=49  Identities=18%  Similarity=0.371  Sum_probs=42.9

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeec--CcEEEEeecCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL--GRILRVNFSDKPK   56 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~--~~~i~v~~~~~~~   56 (148)
                      |++|.++.+      +|||||+|.+.++|++|+..|++..+.  |++|.|.++.++.
T Consensus        44 v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           44 IRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             EEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             eeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence            567777654      689999999999999999999999999  9999999987654

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.03  E-value=1.5e-09  Score=63.39  Aligned_cols=51  Identities=22%  Similarity=0.327  Sum_probs=44.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecC-----cEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG-----RILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~-----~~i~v~~~~~~~~~   58 (148)
                      .|++|+++++       |||||+|.+.++|++|+..|++..+.|     ++|.|.++.+....
T Consensus        41 ~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~~~~   96 (108)
T 1x4c_A           41 DVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPS   96 (108)
T ss_dssp             CEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCCSCC
T ss_pred             CEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCCCCC
Confidence            3677888776       899999999999999999999999999     99999998775543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.03  E-value=4.6e-10  Score=64.78  Aligned_cols=47  Identities=21%  Similarity=0.387  Sum_probs=42.1

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      |.+++++      +++|||||+|.+.++|..|+..|++..+.|++|.|.|+.+
T Consensus        54 i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           54 ILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             CSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             EEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            6677776      4679999999999999999999999999999999998864

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.02  E-value=2.2e-10  Score=70.28  Aligned_cols=47  Identities=23%  Similarity=0.538  Sum_probs=42.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044           12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus        12 ~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .+|+++|||||+|.+.++|..|+..|++..+.|++|.|.++......
T Consensus        87 ~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~~  133 (143)
T 3egn_A           87 KEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPK  133 (143)
T ss_dssp             EETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECEEEECCCSCC-
T ss_pred             cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCc
Confidence            47899999999999999999999999999999999999999765443

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.02  E-value=9e-10  Score=63.12  Aligned_cols=48  Identities=19%  Similarity=0.304  Sum_probs=42.3

Q ss_pred             eEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            5 LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         5 i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      ++++.+    +++|||||+|.+.++|+.|+..|++..+.|++|.|.++.++.
T Consensus        48 ~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           48 LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            455554    688999999999999999999999999999999999987654

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.01  E-value=9.6e-10  Score=63.22  Aligned_cols=51  Identities=24%  Similarity=0.371  Sum_probs=44.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|.+|+++++      +|||||+|.+.++|++|+..|++..+.|++|.|.++.++..
T Consensus        41 ~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpj_A           41 KAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS   91 (99)
T ss_dssp             CCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCSC
T ss_pred             CeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCCC
Confidence            3667777744      69999999999999999999999999999999999976554

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

Probab=99.00  E-value=7.5e-10  Score=68.45  Aligned_cols=50  Identities=32%  Similarity=0.492  Sum_probs=45.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .|.+|+++++     ++|||||+|.+.++|..|+..|++..+.|++|.|.++.++
T Consensus        99 ~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           99 PLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             CEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             CEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            3678888876     5799999999999999999999999999999999998765

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.00  E-value=1.3e-09  Score=63.81  Aligned_cols=48  Identities=29%  Similarity=0.591  Sum_probs=42.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|++|+++        +|||||+|.+.++|+.|+..|++..+.|++|.|.++....
T Consensus        57 ~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  104 (108)
T 2jvo_A           57 PMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA  104 (108)
T ss_dssp             CCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC
T ss_pred             CEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCC
Confidence            36677777        6999999999999999999999999999999999987654

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.00  E-value=1.2e-09  Score=64.01  Aligned_cols=49  Identities=31%  Similarity=0.587  Sum_probs=42.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |++|.+        ++|||||+|.+.++|+.|+..|++..+.|++|.|.++..++..
T Consensus        55 v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~  103 (110)
T 1wf1_A           55 VAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPD  103 (110)
T ss_dssp             CSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCCSC
T ss_pred             eEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCCCC
Confidence            556666        5799999999999999999999999999999999999765543

>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=98.98  E-value=3.4e-09  Score=61.32  Aligned_cols=49  Identities=20%  Similarity=0.549  Sum_probs=42.4

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |.+|+++        +|||||+|.+.++|++|+..|++..+.|++|.|.++.++...
T Consensus        38 i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   86 (103)
T 2dgu_A           38 LERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK   86 (103)
T ss_dssp             EEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             EEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCccc
Confidence            5666665        459999999999999999999999999999999999766543

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

Probab=98.98  E-value=3.4e-09  Score=60.88  Aligned_cols=41  Identities=27%  Similarity=0.460  Sum_probs=38.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044           17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus        17 ~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      +|||||+|.+.++|+.|+..|++..+.|++|.|.++.+...
T Consensus        51 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpd_A           51 RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   91 (99)
T ss_dssp             SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            67999999999999999999999999999999999976554

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.97  E-value=1.9e-09  Score=60.79  Aligned_cols=41  Identities=12%  Similarity=0.262  Sum_probs=38.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044           18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus        18 g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |+|||+|.+.++|++|++.|+|..+.|++|.|.++......
T Consensus        47 G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~sd~   87 (96)
T 2diu_A           47 CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNREL   87 (96)
T ss_dssp             TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSCCC
T ss_pred             CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCcce
Confidence            99999999999999999999999999999999999876544

>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=98.97  E-value=2.3e-09  Score=61.44  Aligned_cols=39  Identities=18%  Similarity=0.326  Sum_probs=36.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044           17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus        17 ~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      +|||||+|.+.++|.+|+..+++..+.|++|.|+++...
T Consensus        57 ~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           57 NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            799999999999999999999999999999999998654

>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=98.97  E-value=1.4e-09  Score=60.74  Aligned_cols=46  Identities=22%  Similarity=0.322  Sum_probs=40.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHh-CCCeecCcEEEEeecC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENL-DGREYLGRILRVNFSD   53 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l-~~~~~~~~~i~v~~~~   53 (148)
                      |.+++++++      +|||||+|.+.++|..|+..| ++..+.|++|.|+|+.
T Consensus        39 i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           39 IRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             EEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             EeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            667777763      699999999999999999988 9999999999999863

>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=98.96  E-value=1.3e-09  Score=64.02  Aligned_cols=51  Identities=25%  Similarity=0.397  Sum_probs=42.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhC--CCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLD--GREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~--~~~~~~~~i~v~~~~~~~~   57 (148)
                      +|.+|.+++      ++|||||+|.+.++|..|+..++  +..+.|++|.|.++.....
T Consensus        52 ~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~~  104 (112)
T 1x4f_A           52 KIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKK  104 (112)
T ss_dssp             CCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSS
T ss_pred             CEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccccc
Confidence            477888864      46999999999999999999875  4569999999999876544

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

Probab=98.96  E-value=4.4e-09  Score=59.58  Aligned_cols=49  Identities=27%  Similarity=0.457  Sum_probs=42.6

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |.+|++++        +||||+|.+.++|++|+..|++..+.|++|.|.++..+...
T Consensus        37 v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   85 (92)
T 2dgt_A           37 VIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRT   85 (92)
T ss_dssp             CCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCCSC
T ss_pred             eEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCCCC
Confidence            66777763        49999999999999999999999999999999999766543

>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=98.96  E-value=1.6e-09  Score=63.74  Aligned_cols=49  Identities=22%  Similarity=0.371  Sum_probs=40.9

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCee-----cCcEEEEeecCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREY-----LGRILRVNFSDKPK   56 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~-----~~~~i~v~~~~~~~   56 (148)
                      |++|.++.      ++|||||+|.+.++|++|+..|||..+     .++++++.++....
T Consensus        54 v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~~p  107 (114)
T 2cq2_A           54 VDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQ  107 (114)
T ss_dssp             EEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESCCC
T ss_pred             eEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEecccCc
Confidence            56666653      369999999999999999999999988     68899999886443

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

Probab=98.94  E-value=4.6e-09  Score=59.27  Aligned_cols=49  Identities=33%  Similarity=0.521  Sum_probs=42.4

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |.+|++++        +||||+|.+.++|+.|+..|++..+.|++|.|.++.+....
T Consensus        36 v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   84 (90)
T 2dnp_A           36 VIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKK   84 (90)
T ss_dssp             EEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCCC
T ss_pred             EEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCCC
Confidence            56777763        49999999999999999999999999999999999766443

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.93  E-value=4.8e-09  Score=60.38  Aligned_cols=51  Identities=16%  Similarity=0.266  Sum_probs=41.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|.++     ++++|||||+|.+.++|..|+..+  ..+.+++|.|.|+..+...
T Consensus        43 ~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~--~~~~g~~l~V~~a~~~~~~   93 (100)
T 2d9o_A           43 EVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNE--VGLVDNPLKISWLEGQPQD   93 (100)
T ss_dssp             CEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTC--CBCSSSBCEEECSSCCCCC
T ss_pred             CEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhc--CCCCCCeEEEEEccCCCCC
Confidence            36778877     368999999999999999999964  4467999999998766543

>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=98.93  E-value=2.2e-09  Score=63.09  Aligned_cols=48  Identities=10%  Similarity=0.054  Sum_probs=41.7

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      |.+|.++.      ++|||||+|.+.++|+.|+..|++..+.|++|.|.|+...
T Consensus        37 i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A           37 LGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             EEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            55666653      5689999999999999999999999999999999998643

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.93  E-value=5.8e-09  Score=62.32  Aligned_cols=51  Identities=14%  Similarity=0.339  Sum_probs=42.9

Q ss_pred             CcceeEeeecCCCCCcccE-EEEEeCCHHHHHHHHHHhCCCeecC--cEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGF-AFVTMSTVEDCNAVIENLDGREYLG--RILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~-afv~f~~~~~a~~a~~~l~~~~~~~--~~i~v~~~~~~~~   57 (148)
                      .|.+|.++..      .|| |||+|.+.++|..|+..|+|..|.|  ++|.|.++.....
T Consensus        51 ~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l  104 (124)
T 2e5i_A           51 KVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRL  104 (124)
T ss_dssp             CEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSCC
T ss_pred             CEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCcc
Confidence            3678888652      285 9999999999999999999999987  6999999976653

>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=98.90  E-value=4.6e-09  Score=59.60  Aligned_cols=43  Identities=33%  Similarity=0.501  Sum_probs=39.1

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCC-CeecCcEEEEeecCCCCCC
Q 032044           16 SRGFAFVTMSTVEDCNAVIENLDG-REYLGRILRVNFSDKPKPK   58 (148)
Q Consensus        16 ~~g~afv~f~~~~~a~~a~~~l~~-~~~~~~~i~v~~~~~~~~~   58 (148)
                      ++|||||+|.+.++|++|+..+++ ..+.|++|.|.++.+....
T Consensus        43 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~~   86 (93)
T 2cqh_A           43 KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   86 (93)
T ss_dssp             ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcccc
Confidence            579999999999999999999999 9999999999999766543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.90  E-value=4.7e-09  Score=59.72  Aligned_cols=51  Identities=25%  Similarity=0.389  Sum_probs=42.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |.+|  +.++.+|+   ||||+|.+.++|++|+. +++..+.|++|.|.++......
T Consensus        35 v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~~   85 (94)
T 2e5g_A           35 VASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEFQ   85 (94)
T ss_dssp             EEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCCC
T ss_pred             eEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCCC
Confidence            4454  67776765   99999999999999999 9999999999999988655443

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

Probab=98.89  E-value=2.8e-09  Score=60.95  Aligned_cols=48  Identities=15%  Similarity=0.296  Sum_probs=41.6

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      |.+|.+.        +|||||+|.+.++|+.|+..|++..+.|++|.|.++.....
T Consensus        38 v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   85 (96)
T 2kvi_A           38 IMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNAR   85 (96)
T ss_dssp             CCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCCC
T ss_pred             EEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCCC
Confidence            5666663        68999999999999999999999999999999999865543

>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=98.89  E-value=3.2e-09  Score=59.48  Aligned_cols=35  Identities=23%  Similarity=0.576  Sum_probs=32.7

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEee
Q 032044           16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF   51 (148)
Q Consensus        16 ~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~   51 (148)
                      ++|||||+|.+.++|.+|+ .+++..+.|++|.|+.
T Consensus        52 ~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           52 DKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             SSSEEEEEESSHHHHHHHG-GGTTCEETTEECEEEC
T ss_pred             CCcEEEEEcCCHHHHHHHH-hcCCCEECCeEEEEeC
Confidence            3799999999999999999 8999999999999874

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.86  E-value=8.5e-09  Score=60.78  Aligned_cols=47  Identities=19%  Similarity=0.210  Sum_probs=37.3

Q ss_pred             cceeEeeecCCC---CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEee
Q 032044            2 LSKLTVLYDRET---GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF   51 (148)
Q Consensus         2 i~~i~~~~~~~~---~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~   51 (148)
                      |. +.++.++.+   |+++|||||+|.+.++|++|+..++  .++|+.+.+..
T Consensus        35 i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~~   84 (114)
T 2dnl_A           35 LV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCVS   84 (114)
T ss_dssp             CC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEEC
T ss_pred             EE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEecc
Confidence            44 677777766   7999999999999999999999873  35666666653

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.85  E-value=6.1e-09  Score=59.43  Aligned_cols=51  Identities=22%  Similarity=0.294  Sum_probs=44.1

Q ss_pred             Cccee-EeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKL-TVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i-~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .|.++ .+++++.+|    .|||+|.+.++|..|+..+++..+.|++|.|.++.+.
T Consensus        41 ~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   92 (96)
T 2e44_A           41 VVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE   92 (96)
T ss_dssp             CEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCC
T ss_pred             CeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCcc
Confidence            36778 477776554    3999999999999999999999999999999999766

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=98.85  E-value=7.6e-09  Score=66.60  Aligned_cols=52  Identities=19%  Similarity=0.323  Sum_probs=45.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      .|.+|+++++. +|+++|||||+|.+.++|..|+..+ +..+.|++|.|.+...
T Consensus       135 ~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          135 QVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             CEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             CEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            47889999986 6999999999999999999999854 5689999999998754

>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=98.81  E-value=9.2e-09  Score=60.76  Aligned_cols=48  Identities=21%  Similarity=0.288  Sum_probs=39.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcE-----EEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRI-----LRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~-----i~v~~~~~~   55 (148)
                      .|.+|.++.+       |||||+|.+.++|++|+..|++..+.|++     +.+....+.
T Consensus        42 ~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~~   94 (115)
T 3beg_B           42 DVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR   94 (115)
T ss_dssp             CEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC--
T ss_pred             CeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCCC
Confidence            3667777765       89999999999999999999999999988     677665543

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.80  E-value=9.6e-09  Score=67.42  Aligned_cols=53  Identities=19%  Similarity=0.354  Sum_probs=47.2

Q ss_pred             CcceeEeeecCC----CCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRE----TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~----~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      +|.++.|.++..    +++++|++||+|.+.++|.+|+..|+|..+.|++|.+.++.
T Consensus       155 ~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          155 AVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             CEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             CeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            478889986654    44899999999999999999999999999999999999875

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=98.68  E-value=3.3e-08  Score=65.42  Aligned_cols=49  Identities=14%  Similarity=0.257  Sum_probs=42.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCee------------cCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREY------------LGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~------------~~~~i~v~~~~~~   55 (148)
                      .|++|+|+.      ++|||||+|.+.++|+.|+..|++..+            .|+.|.|.|+...
T Consensus       169 ~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          169 DIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             CEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC--
T ss_pred             CEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCC
Confidence            478888885      469999999999999999999999999            8999999999754

>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=98.61  E-value=1.1e-07  Score=53.57  Aligned_cols=47  Identities=19%  Similarity=0.275  Sum_probs=35.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCe--ecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGRE--YLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~--~~~~~i~v~~~~~~~   56 (148)
                      .|.+|+++++     ++|||||+|.+.++|++    +++..  +.|+++.+.++.++.
T Consensus        37 ~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k~   85 (89)
T 3d2w_A           37 EVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPKH   85 (89)
T ss_dssp             CEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC---
T ss_pred             CEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCCC
Confidence            4678888874     78999999999999984    34544  459999999987554

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.59  E-value=1.1e-07  Score=53.16  Aligned_cols=45  Identities=20%  Similarity=0.367  Sum_probs=40.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      +|.+++++.++        +||+|.+.++|.+|++ |+|..+.|+.|+|....+
T Consensus        41 ~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~   85 (91)
T 2dnr_A           41 EVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNRTITIALKSP   85 (91)
T ss_dssp             CEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCC
T ss_pred             CeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCC
Confidence            36678888875        8999999999999998 999999999999998753

>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=98.53  E-value=9.8e-08  Score=53.47  Aligned_cols=51  Identities=14%  Similarity=0.154  Sum_probs=39.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.+|+++++     ++|||||+|.+.++|++|..  ....+.+++|.+.++.++...
T Consensus        31 ~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A           31 DVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             CCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCCC
T ss_pred             CeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecCCCCCC
Confidence            3677888765     78999999999999986543  234568999999998766544

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.45  E-value=3e-07  Score=51.64  Aligned_cols=44  Identities=16%  Similarity=0.320  Sum_probs=39.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      +|..++++.++        +||+|.+.++|.+|++ |+|..+.|+.++|.+..
T Consensus        50 ~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           50 TIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             CCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             CEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccC
Confidence            36678888886        9999999999999998 99999999999998654

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=98.42  E-value=2.9e-06  Score=47.60  Aligned_cols=77  Identities=13%  Similarity=0.127  Sum_probs=60.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCC--ceeEEEEEecCHHHHHHHHHHhCCceeCC-----eEEE
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGR--SRGYGFVCYSTKAEMETALESLNGVELEG-----RAMR  139 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~--~~~~~fv~f~~~~~a~~a~~~l~~~~i~g-----~~l~  139 (148)
                      .+|.|++||++++++++.+.+.....+....+..+..+..  ...-|||.|.+.+++......++|+.+-+     .+..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            4789999999999999999999988777666665543322  23568999999999999999999987632     2345


Q ss_pred             EEec
Q 032044          140 VSLA  143 (148)
Q Consensus       140 v~~~  143 (148)
                      |++|
T Consensus        82 VE~A   85 (91)
T 1uw4_A           82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            6655

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=98.31  E-value=1.1e-06  Score=61.12  Aligned_cols=46  Identities=24%  Similarity=0.482  Sum_probs=36.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeec---Cc--EEEEeecC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL---GR--ILRVNFSD   53 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~---~~--~i~v~~~~   53 (148)
                      |++|.+..      ++|||||+|.+.++|++|++.|||..+.   |+  ++++.|..
T Consensus        47 V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           47 VDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE   97 (345)
T ss_dssp             EEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECS
T ss_pred             eEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEee
Confidence            55555532      5799999999999999999999999873   34  68888874

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.16  E-value=1.5e-05  Score=45.48  Aligned_cols=75  Identities=16%  Similarity=0.131  Sum_probs=59.9

Q ss_pred             CcceEEEcCCCCCCCH-----HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           65 TDFKLFVGNLSWSVTT-----ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~-----~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      -+++|++.||+..+-.     ..++++|..|+......+.+.-     + =..|.|.++++|.+|-..||+..++|+.++
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF-----R-Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-----K-RVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT-----T-EEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc-----e-EEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            4568999999886522     5778999999987765554331     1 257999999999999999999999999999


Q ss_pred             EEeccC
Q 032044          140 VSLAQG  145 (148)
Q Consensus       140 v~~~~~  145 (148)
                      +-++.+
T Consensus        78 ~YFgq~   83 (104)
T 1wey_A           78 LYFAQT   83 (104)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            988653

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=98.10  E-value=3.8e-05  Score=43.18  Aligned_cols=56  Identities=25%  Similarity=0.356  Sum_probs=45.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHh
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL  128 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l  128 (148)
                      .....+++ +.|+.+...||.++|++||.+ .|.++-+-       .|||.|.+++.|..|+..+
T Consensus        14 ~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           14 KRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            34456777 999999999999999999954 45555332       5999999999999999976

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=98.10  E-value=4.1e-05  Score=44.89  Aligned_cols=74  Identities=16%  Similarity=0.194  Sum_probs=59.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC-eEEEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG-RAMRVS  141 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g-~~l~v~  141 (148)
                      ....+-|.|-+.|+.. ...+.+.|++||.|......    .  ....-.|.|.++.+|++||+ .||..++| ..|-|.
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~--~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~   92 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----N--TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVK   92 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----S--SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----C--CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEE
Confidence            3456789999999985 67889999999999887652    1  23478899999999999999 79999985 667777


Q ss_pred             ecc
Q 032044          142 LAQ  144 (148)
Q Consensus       142 ~~~  144 (148)
                      ++.
T Consensus        93 p~~   95 (119)
T 1wwh_A           93 PCI   95 (119)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            653

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.98  E-value=2.6e-05  Score=44.02  Aligned_cols=79  Identities=10%  Similarity=0.065  Sum_probs=55.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCC--ceeEEEEEecCHHHHHHHHHHhCCceeCC-----eE
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGR--SRGYGFVCYSTKAEMETALESLNGVELEG-----RA  137 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~--~~~~~fv~f~~~~~a~~a~~~l~~~~i~g-----~~  137 (148)
                      .+-+|.|+.||+++|++++.+.+.+.-.+....+..+..+..  ...-|||.|.+.++.......++|..+-+     .+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            345799999999999999888888765543333332222221  12458999999999999999999987632     34


Q ss_pred             EEEEec
Q 032044          138 MRVSLA  143 (148)
Q Consensus       138 l~v~~~  143 (148)
                      ..|++|
T Consensus        88 a~VE~A   93 (97)
T 2l08_A           88 AVVEFA   93 (97)
T ss_dssp             EEEEEC
T ss_pred             eEEEec
Confidence            556665

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.95  E-value=0.00019  Score=40.81  Aligned_cols=72  Identities=25%  Similarity=0.248  Sum_probs=56.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhh---c--CCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQE---Y--GNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~---~--g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      ...+|.|.|||+.++++.|.-+|+.   .  |.|..+....        +-|+|+|.+.+.|++.++ -..+.++|..|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~-k~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLA-QADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHT-CSCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhc-CCcceecCeEEE
Confidence            3468999999999999999999986   2  3576665531        358999999999999988 336778888888


Q ss_pred             EEeccC
Q 032044          140 VSLAQG  145 (148)
Q Consensus       140 v~~~~~  145 (148)
                      |...-+
T Consensus        78 V~P~~~   83 (104)
T 2dhx_A           78 LRPAPP   83 (104)
T ss_dssp             EEECCC
T ss_pred             EEcCCC
Confidence            877544

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.82  E-value=3.1e-05  Score=43.68  Aligned_cols=54  Identities=24%  Similarity=0.335  Sum_probs=44.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN  129 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  129 (148)
                      ..+++ +.|+.+...||.++|++||. ..|.++-+-       .|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            45666 99999999999999999984 345555332       59999999999999999774

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.37  E-value=0.00042  Score=41.20  Aligned_cols=78  Identities=19%  Similarity=0.286  Sum_probs=54.7

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEEEEc--------CCCC-----CceeEEEEEecCHHHHHHHHHHhCCc
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVG-ARVLYD--------GESG-----RSRGYGFVCYSTKAEMETALESLNGV  131 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~-~~~~~~--------~~~~-----~~~~~~fv~f~~~~~a~~a~~~l~~~  131 (148)
                      ..-|.|-+.|++. ...+-+.|++||.|.. ......        +...     .....-.|+|.++.+|++||+ .||.
T Consensus         7 e~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            3457788887775 4678889999998765 211100        0000     023466899999999999999 9999


Q ss_pred             eeCCeEEEEEeccC
Q 032044          132 ELEGRAMRVSLAQG  145 (148)
Q Consensus       132 ~i~g~~l~v~~~~~  145 (148)
                      .++|.-|-|.++++
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99999888887653

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.27  E-value=0.00076  Score=38.83  Aligned_cols=43  Identities=16%  Similarity=0.352  Sum_probs=35.0

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEe
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN   50 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~   50 (148)
                      |.+|.+..|- .     =|+|+|.+...|-+|.-.|+|..|.|++|++.
T Consensus        53 i~KI~L~pDH-~-----GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           53 IRKILLVSDF-N-----GAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             CSEEEEETTT-T-----EEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             eeEEEEecCC-C-----ceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            3455555553 2     29999999999999998899999999999987

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.09  E-value=0.00088  Score=39.54  Aligned_cols=46  Identities=0%  Similarity=0.016  Sum_probs=36.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCC-HHHHHHHHHHhC--CCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMST-VEDCNAVIENLD--GREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~-~~~a~~a~~~l~--~~~~~~~~i~v~~~   52 (148)
                      .|..|.++++..      .|||.|.+ ..+|..|+..++  +..|.+..+.++..
T Consensus        45 ~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL   93 (121)
T 1owx_A           45 EIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   93 (121)
T ss_dssp             CEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             CEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEEC
Confidence            367788888764      39999999 899999999884  66788877777644

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.73  E-value=0.0038  Score=35.50  Aligned_cols=52  Identities=15%  Similarity=0.151  Sum_probs=42.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCC
Q 032044           18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVT   79 (148)
Q Consensus        18 g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~   79 (148)
                      +-|+|+|.+.+.|++.+. .....+.+.++.|.+..+.         .+.++.+.+||++++
T Consensus        48 ~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV~P~~~~---------~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           48 CGGVLTFREPADAERVLA-QADHELHGAQLSLRPAPPR---------APARLLLQGLPPGTS   99 (104)
T ss_dssp             TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEEEECCCC---------CCCCCCCCSCCCCCC
T ss_pred             CcEEEEEcChHHHHHHhc-CCcceecCeEEEEEcCCCC---------CcceEeeecCCCCCC
Confidence            459999999999999997 3478889999999875433         445799999998865

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.70  E-value=0.0014  Score=47.45  Aligned_cols=55  Identities=7%  Similarity=0.147  Sum_probs=40.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHH
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE  126 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~  126 (148)
                      .+.|+|. .|...++.+|.+.|.+||.|.++.+..+     ...|+.|+|.+.++++.++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~-----~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES-----FGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS-----SSEEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc-----CCeEEEEEeCCHHHHHHHHh
Confidence            4679997 6889999999999999999999877643     13699999999999887754

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=94.63  E-value=0.2  Score=36.89  Aligned_cols=55  Identities=24%  Similarity=0.321  Sum_probs=43.4

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhC
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN  129 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  129 (148)
                      +..++++ +|..+...+|.+.|+.||.+ .+.++-       ...|||.|.+.+.|..+++.+.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~wid-------dt~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWID-------DTSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECS-------SSEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEc-------CCeEEEEECCHHHHHHHHHHHH
Confidence            4456665 99999999999999999954 444432       2259999999999999999885

>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=93.63  E-value=0.31  Score=27.75  Aligned_cols=37  Identities=16%  Similarity=0.262  Sum_probs=33.6

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044           18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus        18 g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      .-..|.|.+.++|.+|-..|++..++|+.+++-++.+
T Consensus        47 RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A           47 KRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             TEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             eEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            3578999999999999999999999999999998763

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=91.82  E-value=0.18  Score=29.98  Aligned_cols=37  Identities=14%  Similarity=0.147  Sum_probs=32.1

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044           16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus        16 ~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      ....-.|.|.+..+|++||. .||..+.|.-|-|.+..
T Consensus        61 g~NWikItYds~~~A~rAL~-~NG~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           61 GNSWTKITYDNPASAVDALL-ENGAVFNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEEEEEBSSHHHHHHHHT-TTTCEETTEECEEEECC
T ss_pred             CCcEEEEEcCCHHHHHHHHH-hCCeEeCcEEEEEEECC
Confidence            34577999999999999998 79999999988888764

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=81.71  E-value=4.7  Score=23.51  Aligned_cols=37  Identities=11%  Similarity=0.161  Sum_probs=30.3

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCCeecC-cEEEEeecC
Q 032044           16 SRGFAFVTMSTVEDCNAVIENLDGREYLG-RILRVNFSD   53 (148)
Q Consensus        16 ~~g~afv~f~~~~~a~~a~~~l~~~~~~~-~~i~v~~~~   53 (148)
                      ....-.|.|.+..+|++||. .||..+.+ ..|-|.+..
T Consensus        58 ~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           58 TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECC
Confidence            45688999999999999998 69999874 667777653

---

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	148
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	6e-22
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-08
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-21
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	9e-21
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-13
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-20
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	8e-08
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-20
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-09
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-20
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	7e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	8e-20
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	8e-08
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	9e-20
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	6e-05
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-19
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-06
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-19
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-09
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-19
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	9e-06
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-19
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-18
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-06
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-18
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-08
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-18
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-06
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-18
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-18
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-06
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-18
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-18
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-05
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	5e-18
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	9e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-18
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-18
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	7e-18
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-05
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	8e-18
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-18
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-17
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	8e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-17
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-17
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	6e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-17
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-17
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-17
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	0.002
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-17
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	5e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-17
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	6e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-17
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-17
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	8e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-17
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-06
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	9e-17
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-05
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-16
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-16
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-16
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-06
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-16
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	9e-16
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-15
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-15
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-05
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-15
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-15
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-15
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-15
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-04
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	5e-15
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	6e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	8e-15
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-14
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	8e-04
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-14
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-14
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	4e-04
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-14
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-04
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	7e-14
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-13
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-13
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	6e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-13
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	0.001
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	6e-13
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-12
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	0.001
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	3e-12
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-12
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-04
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	6e-12
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 7e-12
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-11
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-11
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	4e-11
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.004
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	5e-11
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	9e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-10
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	6e-10
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	8e-10
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-09
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-09
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	0.003
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-09
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	5e-09
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-08
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-08
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-08
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.002
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	9e-08
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-07
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	2e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	5e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	9e-07
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	1e-05

>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 = 81.5 bits (201), Expect = 6e-22
 Identities = 25/77 (32%), Positives = 43/77 (55%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L+VG+L   VT   L + F   G ++  RV  D  + RS GY +V +   A+ E AL++
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 128 LNGVELEGRAMRVSLAQ 144
           +N   ++G+ +R+  +Q
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 46.5 bits (110), Expect = 2e-08
 Identities = 12/48 (25%), Positives = 23/48 (47%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
          V  D  T RS G+A+V      D    ++ ++     G+ +R+ +S +
Sbjct: 32 VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR 79

>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 = 79.6 bits (196), Expect = 4e-21
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGE-SGRSRGYGFVCYSTKAEME 122
           +T  K+ V N+ +      + + F  +G +   R+      +G  RG+GFV + TK + +
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 123 TALESL-NGVELEGRAMRVSLAQGRRS 148
            A  +L +   L GR + +  A    +
Sbjct: 66  KAFNALCHSTHLYGRRLVLEWADSEVT 92

>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 = 46.9 bits (111), Expect = 2e-08
 Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 1/43 (2%)

Query: 13 TGRSRGFAFVTMSTVEDCNAVIENL-DGREYLGRILRVNFSDK 54
          TG  RGF FV   T +D       L       GR L + ++D 
Sbjct: 47 TGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 89

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 81.2 bits (199), Expect = 9e-21
 Identities = 34/139 (24%), Positives = 58/139 (41%), Gaps = 1/139 (0%)

Query: 9   YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFK 68
            D  T RSRGF FVT +TVE+ +A +     +     +       +   + P    T  K
Sbjct: 40  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK 99

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +FVG +        L   F++YG +    ++ D  SG+ RG+ FV +     ++  +   
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-Q 158

Query: 129 NGVELEGRAMRVSLAQGRR 147
               + G    V  A  ++
Sbjct: 159 KYHTVNGHNCEVRKALSKQ 177

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (146), Expect = 6e-13
 Identities = 26/67 (38%), Positives = 40/67 (59%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           E   KLF+G LS+  T ESL   F+++G +    V+ D  + RSRG+GFV Y+T  E++ 
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 124 ALESLNG 130
           A+ +   
Sbjct: 64  AMNARPH 70

>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 = 78.5 bits (193), Expect = 1e-20
 Identities = 24/81 (29%), Positives = 42/81 (51%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L+VGNLS+  T E + + F + G++    +  D     + G+ FV Y ++A+ E A+  
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           +NG  L+ R +R     G + 
Sbjct: 69  INGTRLDDRIIRTDWDAGFKE 89

>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 = 45.3 bits (107), Expect = 8e-08
 Identities = 11/49 (22%), Positives = 20/49 (40%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
           D+    + GF FV   +  D    +  ++G     RI+R ++    K 
Sbjct: 41 LDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE 89

>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 = 78.5 bits (193), Expect = 2e-20
 Identities = 23/91 (25%), Positives = 43/91 (47%), Gaps = 5/91 (5%)

Query: 58  KLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYST 117
           +LP   E +  L++ NL + +T E +   F +YG +   R +  G +  +RG  +V Y  
Sbjct: 1   RLP--PEVNRILYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYED 55

Query: 118 KAEMETALESLNGVELEGRAMRVSLAQGRRS 148
             + + A + L+G  +  R + V      R+
Sbjct: 56  IFDAKNACDHLSGFNVCNRYLVVLYYNANRA 86

>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 = 50.4 bits (120), Expect = 1e-09
 Identities = 11/50 (22%), Positives = 19/50 (38%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
              T  +RG A+V    + D     ++L G     R L V + +  +  
Sbjct: 38 RVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAF 87

>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 = 77.3 bits (190), Expect = 2e-20
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+F+G LSW  T E L + F ++G V    V+ D  + RSRG+GFV +  +A ++  L  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA- 60

Query: 128 LNGVELEGRAMRVSLA 143
            +  EL+ + +   +A
Sbjct: 61  QSRHELDSKTIDPKVA 76

>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 = 40.0 bits (93), Expect = 7e-06
 Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 1/43 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
           D  T RSRGF FVT       + V+      E   + +    
Sbjct: 34 RDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKV 75

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.2 bits (187), Expect = 8e-20
 Identities = 28/85 (32%), Positives = 48/85 (56%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A T   L+VG L+  V  + L  AF  +G++   ++  D E+ + RG+ FV +    +  
Sbjct: 2   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61

Query: 123 TALESLNGVELEGRAMRVSLAQGRR 147
            A++++N  EL GR +RV+LA+  R
Sbjct: 62  AAIDNMNESELFGRTIRVNLAKPMR 86

>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 = 45.0 bits (106), Expect = 8e-08
 Identities = 21/50 (42%), Positives = 28/50 (56%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           D ET + RGFAFV     ED  A I+N++  E  GR +RVN +   + K
Sbjct: 39 LDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK 88

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 75.8 bits (186), Expect = 9e-20
 Identities = 22/80 (27%), Positives = 45/80 (56%)

Query: 65  TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETA 124
           ++  L V  L   +T   L   F+  G +   R++ D ++G S GY FV ++++ + + A
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 125 LESLNGVELEGRAMRVSLAQ 144
           ++ LNG+ +  + ++VS A+
Sbjct: 61  IKVLNGITVRNKRLKVSYAR 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 = 37.3 bits (86), Expect = 6e-05
 Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP 55
           D +TG S G+AFV  ++  D    I+ L+G     + L+V+++ +P
Sbjct: 36 RDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA-RP 81

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 75.4 bits (185), Expect = 2e-19
 Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 2/78 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L+V NL  ++T + L   F +YG++V   +L D  +GR RG  FV Y+ + E + A+ +
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 128 LNGVELEG--RAMRVSLA 143
           LN V  EG  + + V LA
Sbjct: 68  LNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 39.9 bits (93), Expect = 6e-06
 Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 2/45 (4%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG--RILRVNF 51
           D+ TGR RG AFV  +  E+    I  L+     G  + L V  
Sbjct: 40 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL 84

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.7 bits (183), Expect = 3e-19
 Identities = 20/79 (25%), Positives = 37/79 (46%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KLF+G L   +  + + +    +G +    ++ D  +G S+GY F  Y      + A+  
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 128 LNGVELEGRAMRVSLAQGR 146
           LNG++L  + + V  A   
Sbjct: 63  LNGMQLGDKKLLVQRASVG 81

>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 = 48.5 bits (115), Expect = 4e-09
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 1/50 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           D  TG S+G+AF     +   +  I  L+G +   + L V  +     K
Sbjct: 35 KDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS-VGAK 83

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.1 bits (184), Expect = 3e-19
 Identities = 23/82 (28%), Positives = 46/82 (56%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D  ++VG L   V+   L + F + G VV   +  D  +G+ +GYGFV + ++ + + A+
Sbjct: 9   DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 68

Query: 126 ESLNGVELEGRAMRVSLAQGRR 147
           + ++ ++L G+ +RV+ A    
Sbjct: 69  KIMDMIKLYGKPIRVNKASAHN 90

>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 = 40.0 bits (93), Expect = 9e-06
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           DR TG+ +G+ FV   + ED +  I+ +D  +  G+ +RVN +     K
Sbjct: 43 KDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA-SAHNK 91

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 74.7 bits (183), Expect = 4e-19
 Identities = 17/77 (22%), Positives = 34/77 (44%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
             + V N+ ++V+ + +   F  Y  + G+  L   E G   G   V + ++ E   A+ 
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 127 SLNGVELEGRAMRVSLA 143
            LN   +  R +++ L 
Sbjct: 70  DLNDRPIGSRKVKLVLG 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.4 bits (112), Expect = 1e-08
 Identities = 10/45 (22%), Positives = 19/45 (42%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
           L   E G   G A V   + ++  A + +L+ R    R +++  
Sbjct: 41 CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL 85

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.5 bits (180), Expect = 1e-18
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L V  L W  T + L + F  +G V+  +V  D ++G S+G+GFV ++        +  
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
            +   ++GR     L   ++S
Sbjct: 70  RH--MIDGRWCDCKLPNSKQS 88

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (98), Expect = 1e-06
 Identities = 12/50 (24%), Positives = 19/50 (38%), Gaps = 2/50 (4%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           D +TG S+GF FV  +  E    V+         GR       +  + +
Sbjct: 42 KDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQ 89

>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 = 73.1 bits (179), Expect = 1e-18
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYD---GESGRSRGYGFVCYSTKAEMETAL 125
           LF+ NL++S T E+L   F + G +    +           S G+GFV Y    + + AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 126 ESLNGVELEGRAMRVSLAQ 144
           + L G  ++G  + V +++
Sbjct: 61  KQLQGHTVDGHKLEVRISE 79

>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 = 46.6 bits (110), Expect = 2e-08
 Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 1/47 (2%)

Query: 12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD-KPKP 57
              S GF FV     E     ++ L G    G  L V  S+   KP
Sbjct: 38 GVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKP 84

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 72.7 bits (178), Expect = 1e-18
 Identities = 30/77 (38%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KL V NL + V+   + + F E+G +  A V YD  SGRS G   V +  KA+   A++ 
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 60

Query: 128 LNGVELEGRAMRVSLAQ 144
            NGV L+GR M + L  
Sbjct: 61  YNGVPLDGRPMNIQLVT 77

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (92), Expect = 7e-06
 Identities = 10/46 (21%), Positives = 18/46 (39%)

Query: 8  LYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD 53
          ++   +GRS G A V      D    ++  +G    GR + +    
Sbjct: 32 VHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 77

>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 = 73.2 bits (179), Expect = 2e-18
 Identities = 24/80 (30%), Positives = 44/80 (55%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            LF+ +L      + L Q F  +GNVV A+V  D ++  S+ +GFV Y      + A++S
Sbjct: 20  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 79

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           +NG ++  + ++V L + + 
Sbjct: 80  MNGFQIGMKRLKVQLKRSKN 99

>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 = 41.2 bits (96), Expect = 3e-06
 Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
           D++T  S+ F FV+        A I++++G +   + L+V    + K
Sbjct: 52 IDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK-RSK 98

>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 = 72.7 bits (178), Expect = 2e-18
 Identities = 22/101 (21%), Positives = 43/101 (42%), Gaps = 10/101 (9%)

Query: 48  RVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRS 107
           ++ F D      P     +  ++ G ++  +T + + Q F  +G ++  RV         
Sbjct: 4   QLRFEDVVNQSSP----KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PE 53

Query: 108 RGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRRS 148
           +GY FV +ST      A+ S+NG  +EG  ++    +    
Sbjct: 54  KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD 94

>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 = 41.5 bits (97), Expect = 2e-06
 Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL 59
            +G++FV  ST E     I +++G    G +++  +  K  P +
Sbjct: 52 PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG-KESPDM 95

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.8 bits (178), Expect = 3e-18
 Identities = 22/94 (23%), Positives = 36/94 (38%), Gaps = 1/94 (1%)

Query: 54  KPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFV 113
           +P   L         +F   L+  +    L   F   G V   R++ D  S RS+G  +V
Sbjct: 6   EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 65

Query: 114 CYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
            +     +  A+  L G  L G  + V  +Q  +
Sbjct: 66  EFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEK 98

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (100), Expect = 1e-06
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 9   YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKL 59
            DR + RS+G A+V    ++     I  L G+  LG  + V  S   K +L
Sbjct: 52  SDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNRL 101

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.6 bits (175), Expect = 5e-18
 Identities = 28/80 (35%), Positives = 45/80 (56%), Gaps = 2/80 (2%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D  L+V  L  ++T + L Q F +YG ++ +R+L D  +G SRG GF+ +  + E E A+
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 126 ESLNGVELEGR--AMRVSLA 143
           + LNG +  G    + V  A
Sbjct: 66  KGLNGQKPSGATEPITVKFA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 4e-05
 Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 2/46 (4%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRI--LRVNFS 52
           D+ TG SRG  F+      +    I+ L+G++  G    + V F+
Sbjct: 40 VDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 85

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.0 bits (176), Expect = 5e-18
 Identities = 31/93 (33%), Positives = 49/93 (52%), Gaps = 1/93 (1%)

Query: 54  KPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFV 113
            P  +     E   KLF+G LS+  T ESL   ++++G +    V+ D  S RSRG+GFV
Sbjct: 8   VPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFV 67

Query: 114 CYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
            +S+ AE++ A+       ++GR +    A  R
Sbjct: 68  TFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAR 99

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 9e-06
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 9   YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
            D  + RSRGF FVT S++ + +A +         GR++    +   + +
Sbjct: 54  RDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRA-VAREE 101

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.3 bits (174), Expect = 6e-18
 Identities = 23/81 (28%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGA-RVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +F+GNL   +  + L   F  +G ++   +++ D ++G S+GY F+ +++    + A+E+
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           +NG  L  R + VS A  + S
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 1e-06
 Identities = 15/52 (28%), Positives = 32/52 (61%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          ++ D +TG S+G+AF+  ++ +  +A IE ++G+    R + V+++ K   K
Sbjct: 31 IMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK 82

>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 = 71.8 bits (176), Expect = 6e-18
 Identities = 24/98 (24%), Positives = 44/98 (44%), Gaps = 14/98 (14%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTES-LTQAFQEYGNVVGARVLYDGESGRSRGY 110
           S K  P+       + ++F+GNL+  V  +S +   F +YG +VG  V          G+
Sbjct: 6   SGKTDPR-----SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GF 52

Query: 111 GFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRRS 148
            FV Y  +     A+   +G  + G+ + ++LA   + 
Sbjct: 53  AFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKV 90

>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 = 47.6 bits (113), Expect = 1e-08
 Identities = 14/48 (29%), Positives = 22/48 (45%)

Query: 11 RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
                +GFAFV      +  A +   DGR   G++L +N + +PK  
Sbjct: 44 VGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVN 91

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 71.0 bits (173), Expect = 7e-18
 Identities = 16/79 (20%), Positives = 36/79 (45%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           +  L++ N   S T  ++    Q+   V  +  L       SR + ++  ++K +    +
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 126 ESLNGVELEGRAMRVSLAQ 144
           E LNG+++EG  +   ++ 
Sbjct: 61  EKLNGLKIEGYTLVTKVSN 79

>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 = 37.5 bits (86), Expect = 6e-05
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD 53
           SR FA++ +++ ED    +E L+G +  G  L    S+
Sbjct: 41 TSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN 79

>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 = 70.9 bits (173), Expect = 8e-18
 Identities = 25/77 (32%), Positives = 42/77 (54%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L V  L  ++T E     F   G +   +++ D  +G+S GYGFV Y    + E A+ +
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 128 LNGVELEGRAMRVSLAQ 144
           LNG+ L+ + ++VS A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>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 = 40.5 bits (94), Expect = 5e-06
 Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP 55
           D+ TG+S G+ FV     +D    I  L+G     + ++V+++ +P
Sbjct: 36 RDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA-RP 81

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.3 bits (174), Expect = 8e-18
 Identities = 13/85 (15%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVL-----YDGESGRSRGYGFVCYSTKAEME 122
           +L+VGN+ + +T E++   F     + G            +  + + + F+ + +  E  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 123 TALESLNGVELEGRAMRVSLAQGRR 147
            A+   +G+  +G+++++      +
Sbjct: 63  QAMA-FDGIIFQGQSLKIRRPHDYQ 86

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 7e-07
 Identities = 10/52 (19%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
             +  + + FAF+   +V++    +   DG  + G+ L++    +P    P
Sbjct: 40 LAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR---RPHDYQP 87

>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 = 70.4 bits (172), Expect = 1e-17
 Identities = 29/80 (36%), Positives = 46/80 (57%), Gaps = 1/80 (1%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           E   KLF+G LS+  T ESL   F+++G +    V+ D  + RSRG+GFV Y+T  E++ 
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 124 ALESLNGVELEGRAMRVSLA 143
           A+      +++GR +    A
Sbjct: 64  AMN-ARPHKVDGRVVEPKRA 82

>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 = 39.6 bits (92), Expect = 8e-06
 Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
           D  T RSRGF FVT +TVE+ +A +      +  GR++   
Sbjct: 40 RDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPK 80

>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 = 70.0 bits (171), Expect = 1e-17
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+F+G LSW  T + L   F ++G VV   +  D  +GRSRG+GFV +     ++  ++ 
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD- 59

Query: 128 LNGVELEGRAMRVSLA 143
               +L G+ +    A
Sbjct: 60  QKEHKLNGKVIDPKRA 75

>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 = 70.4 bits (172), Expect = 1e-17
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 6/80 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L+V NL  S + E + + F         RV       + R Y FV +S + +   A+++
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKA 63

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           LNG  L+G  + V+LA+   
Sbjct: 64  LNGKVLDGSPIEVTLAKPVD 83

>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 = 50.8 bits (121), Expect = 6e-10
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 1  MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
            + +         + R +AFV  S  ED    ++ L+G+   G  + V  + KP  K
Sbjct: 28 EFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA-KPVDK 84

>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 = 70.5 bits (172), Expect = 2e-17
 Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 3/85 (3%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
             D +++VGNL   + T+ +   F +YG +    +           + FV +    + E 
Sbjct: 12  NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAED 68

Query: 124 ALESLNGVELEGRAMRVSLAQGRRS 148
           A+   +G + +G  +RV   +  R 
Sbjct: 69  AVYGRDGYDYDGYRLRVEFPRSGRG 93

>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 = 38.9 bits (90), Expect = 2e-05
 Identities = 13/49 (26%), Positives = 17/49 (34%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
            +       FAFV      D    +   DG +Y G  LRV F    + 
Sbjct: 45 DLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG 93

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.1 bits (171), Expect = 2e-17
 Identities = 28/77 (36%), Positives = 43/77 (55%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
           + +  L V  LS   T   L + F +YG +    ++YD +S RSRG+ FV +    + + 
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 124 ALESLNGVELEGRAMRV 140
           A E  NG+EL+GR +RV
Sbjct: 67  AKERANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 4e-05
 Identities = 19/41 (46%), Positives = 25/41 (60%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
          YD+++ RSRGFAFV    V+D     E  +G E  GR +RV
Sbjct: 43 YDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

>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 = 69.6 bits (170), Expect = 3e-17
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG LS     E + + F  +G V    +  D ++ + RG+ F+ +  +  ++  +E 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME- 59

Query: 128 LNGVELEGRAMRVSLA 143
                +      + +A
Sbjct: 60  KKYHNVGLSKCEIKVA 75

>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 = 33.0 bits (75), Expect = 0.002
 Identities = 9/42 (21%), Positives = 15/42 (35%), Gaps = 1/42 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN 50
           D +T + RGF F+T    E    ++E             + 
Sbjct: 33 MDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIK 73

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.3 bits (169), Expect = 3e-17
 Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 7/82 (8%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           KL++GNLS +VT + L Q F +    +       G+     GY FV Y  +     A+E+
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 128 LNG-VELEGRAMRVSLAQGRRS 148
           L+G VEL G+ M V  +  ++ 
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKL 78

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 5e-06
 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGR-EYLGRILRVNFSDKPKPK 58
            +     G+AFV           IE L G+ E  G+I+ V++S   K +
Sbjct: 30 AGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR 79

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 69.0 bits (168), Expect = 4e-17
 Identities = 23/76 (30%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG LS + T E +   F+++G V  A +++D  + R RG+GFV + ++  +E   E 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59

Query: 128 LNGVELEGRAMRVSLA 143
           ++  E+  + +    A
Sbjct: 60  IHFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.7 bits (79), Expect = 6e-04
 Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF 51
          +D+ T R RGF FVT  + +    V E +   E   +++    
Sbjct: 33 FDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKK 74

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 69.4 bits (169), Expect = 5e-17
 Identities = 20/80 (25%), Positives = 38/80 (47%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFV NLS++ + E L + F  YG +       D  + + +G+ FV +        A   
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           ++G   +GR + V  +  ++
Sbjct: 70  VDGQVFQGRMLHVLPSTIKK 89

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.3 bits (91), Expect = 2e-05
 Identities = 17/50 (34%), Positives = 23/50 (46%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           D  T + +GFAFVT    E        +DG+ + GR+L V  S   K  
Sbjct: 42 IDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA 91

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 69.3 bits (169), Expect = 5e-17
 Identities = 18/81 (22%), Positives = 41/81 (50%), Gaps = 5/81 (6%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L   NLS+++T + L + F++   +         + G+S+G  ++ + ++A+ E  LE 
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
             G E++GR++ +     +  
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGG 93

>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 = 42.7 bits (100), Expect = 8e-07
 Identities = 10/46 (21%), Positives = 22/46 (47%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK 54
             + G+S+G A++   +  D    +E   G E  GR + + ++ +
Sbjct: 45 LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 90

>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 = 69.0 bits (168), Expect = 6e-17
 Identities = 32/86 (37%), Positives = 49/86 (56%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A  + KLFVG LS+    +SL Q F +YG +    V+ D E+ RSRG+GFV +    + +
Sbjct: 2   ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 61

Query: 123 TALESLNGVELEGRAMRVSLAQGRRS 148
            A+ ++NG  ++GR +RV  A     
Sbjct: 62  DAMMAMNGKSVDGRQIRVDQAGKSSD 87

>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 = 41.7 bits (97), Expect = 2e-06
 Identities = 19/50 (38%), Positives = 28/50 (56%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           DRET RSRGF FVT   ++D    +  ++G+   GR +RV+ + K    
Sbjct: 39 KDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 88

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.6 bits (167), Expect = 9e-17
 Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
            T  +L V N+ +      L Q F ++G ++   ++++     S+G+GFV +   A+ + 
Sbjct: 9   STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADR 66

Query: 124 ALESLNGVELEGRAMRVSLAQGR 146
           A E L+G  +EGR + V+ A  R
Sbjct: 67  AREKLHGTVVEGRKIEVNNATAR 89

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 1e-05
 Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 1/50 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
                 S+GF FVT     D +   E L G    GR + VN +   +  
Sbjct: 43 IIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA-TARVM 91

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.8 bits (165), Expect = 2e-16
 Identities = 26/80 (32%), Positives = 45/80 (56%), Gaps = 2/80 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            +F+ NL  S+  ++L   F  +GN++  +V+ D     S+GYGFV + T+   E A+E 
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEK 67

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           +NG+ L  R + V   + R+
Sbjct: 68  MNGMLLNDRKVFVGRFKSRK 87

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.2 bits (83), Expect = 2e-04
 Identities = 12/48 (25%), Positives = 19/48 (39%)

Query: 11 RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           +   S+G+ FV   T E     IE ++G     R + V      K +
Sbjct: 42 CDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKER 89

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.3 bits (166), Expect = 2e-16
 Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 8/87 (9%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVL--------YDGESGRSRGYGFVCYSTKA 119
            ++V  L+ SVT + L   F++ G V   +           D E+G+ +G   V Y    
Sbjct: 10  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 69

Query: 120 EMETALESLNGVELEGRAMRVSLAQGR 146
             + A+E  +G + +G  ++VSLA+ +
Sbjct: 70  TAKAAVEWFDGKDFQGSKLKVSLARKK 96

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 2e-07
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
           D+ETG+ +G A V+        A +E  DG+++ G  L+V+ + + KP
Sbjct: 50 LDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA-RKKP 97

>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 = 67.8 bits (165), Expect = 2e-16
 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 4/84 (4%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGA--RVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           +LF+G +      E + +   +    V          +  ++RG+ FV Y +      A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 126 ESLNG--VELEGRAMRVSLAQGRR 147
             L    ++L G  + V  A+   
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEI 86

>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 = 41.2 bits (96), Expect = 3e-06
 Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 3/52 (5%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL--GRILRVNFSDKPKPK 58
             +  ++RGFAFV   +          L        G  + V+++ +P+  
Sbjct: 37 SAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWA-EPEID 87

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.8 bits (165), Expect = 2e-16
 Identities = 17/84 (20%), Positives = 40/84 (47%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
           A+ +  + V NLS       L + F+ +G++    +  D  +G+S+G+ F+ +  + +  
Sbjct: 5   ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 64

Query: 123 TALESLNGVELEGRAMRVSLAQGR 146
            A+  ++G   +   + V  A+  
Sbjct: 65  RAIAGVSGFGYDHLILNVEWAKPS 88

>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 = 41.2 bits (96), Expect = 3e-06
 Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
           D+ TG+S+GFAF++    ED    I  + G  Y   IL V ++ KP 
Sbjct: 42 KDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA-KPS 88

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.3 bits (161), Expect = 9e-16
 Identities = 33/81 (40%), Positives = 48/81 (59%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            +FVGN+ +  T E L   F E G VV  R++YD E+G+ +GYGF  Y  +    +A+ +
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           LNG E  GRA+RV  A   ++
Sbjct: 70  LNGREFSGRALRVDNAASEKN 90

>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 = 41.7 bits (97), Expect = 2e-06
 Identities = 15/41 (36%), Positives = 22/41 (53%)

Query: 18 GFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
          G+ F      E   + + NL+GRE+ GR LRV+ +   K K
Sbjct: 51 GYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNK 91

>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 = 65.9 bits (160), Expect = 1e-15
 Identities = 22/80 (27%), Positives = 40/80 (50%)

Query: 67  FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
           + LFV ++      + + + F +YG +    +  D  +G S+GY  V Y T  +   A E
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 127 SLNGVELEGRAMRVSLAQGR 146
           +LNG E+ G+ ++V     +
Sbjct: 68  ALNGAEIMGQTIQVDWCFVK 87

>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 = 1e-05
 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
           DR TG S+G+A V   T +   A  E L+G E +G+ ++V++    K
Sbjct: 41 LDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC-FVK 87

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.0 bits (160), Expect = 1e-15
 Identities = 21/80 (26%), Positives = 37/80 (46%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L++ NLS  VT   L   F  +    G  + +   +GR RG  F+ +  K     AL  
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 128 LNGVELEGRAMRVSLAQGRR 147
           +NG +L G+ + +   + ++
Sbjct: 80  VNGYKLYGKILVIEFGKNKK 99

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (91), Expect = 2e-05
 Identities = 15/50 (30%), Positives = 24/50 (48%)

Query: 9   YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           +   TGR RG AF+T    E     +  ++G +  G+IL + F    K +
Sbjct: 52  FRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQR 101

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.9 bits (160), Expect = 1e-15
 Identities = 31/84 (36%), Positives = 48/84 (57%), Gaps = 1/84 (1%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
            T  K+FVG L +  T  SL + F+ +G++  A V+ D ++G+SRGYGFV  + +A  E 
Sbjct: 8   TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 67

Query: 124 ALESLNGVELEGRAMRVSLAQGRR 147
           A +  N   ++GR   V+LA    
Sbjct: 68  ACKDPNP-IIDGRKANVNLAYLGA 90

>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 = 65.0 bits (158), Expect = 2e-15
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +LFVGNL   +T E + + F++YG      +  D      +G+GF+   T+   E A   
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 63

Query: 128 LNGVELEGRAMRVSLAQ 144
           L+ + L G+ +RV  A 
Sbjct: 64  LDNMPLRGKQLRVRFAC 80

>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 = 38.0 bits (88), Expect = 4e-05
 Identities = 10/37 (27%), Positives = 14/37 (37%)

Query: 19 FAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP 55
          F F+ + T          LD     G+ LRV F+   
Sbjct: 46 FGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS 82

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.1 bits (158), Expect = 3e-15
 Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 1/85 (1%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
              +  F+GNL + VT ES+ + F+                 R +G+G+  +     + +
Sbjct: 13  SPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLS 72

Query: 124 ALESLNGVELEGRAMRVSLAQGRRS 148
           AL  LN   L  + +RV +A   + 
Sbjct: 73  ALS-LNEESLGNKRIRVDVADQAQD 96

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 3e-05
 Identities = 8/52 (15%), Positives = 21/52 (40%), Gaps = 1/52 (1%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
                  R +GF +     ++   + +  L+      + +RV+ +D+ + K
Sbjct: 47 PREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQDK 97

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 65.7 bits (159), Expect = 4e-15
 Identities = 27/98 (27%), Positives = 48/98 (48%), Gaps = 2/98 (2%)

Query: 52  SDKPKPKLPLYAETD--FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRG 109
             +  P   +  E D    L V  +  +V    L Q F+ YG +   +++ D E+ +SRG
Sbjct: 26  QQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRG 85

Query: 110 YGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
           YGFV + + +  + A+  LNG  +  + ++V+LA    
Sbjct: 86  YGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH 123

>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 = 2e-04
 Identities = 9/42 (21%), Positives = 16/42 (38%), Gaps = 1/42 (2%)

Query: 19  FAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
           + FV   +       I  L+G   L + L+V  +     + P
Sbjct: 86  YGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA-ASGHQRP 126

>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 = 63.9 bits (155), Expect = 5e-15
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 7/83 (8%)

Query: 68  KLFVGNLSWSVTTESLTQA----FQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
            +++ NL+  +  + L ++    F  +G ++   V       + RG  FV +   +    
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSSATN 61

Query: 124 ALESLNGVELEGRAMRVSLAQGR 146
           AL S+ G     + MR+  A+  
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTD 84

>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 = 43.1 bits (101), Expect = 6e-07
 Identities = 9/43 (20%), Positives = 18/43 (41%), Gaps = 1/43 (2%)

Query: 16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
           RG AFV    V      + ++ G  +  + +R+ ++ K    
Sbjct: 45 MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA-KTDSD 86

>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 = 63.5 bits (154), Expect = 8e-15
 Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 2/81 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L+VGNLS  VT   + Q F + G           E   +  Y FV +    +   AL +
Sbjct: 10  TLYVGNLSRDVTEVLILQLFSQIGPCK--SCKMITEHTSNDPYCFVEFYEHRDAAAALAA 67

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           +NG ++ G+ ++V+ A    S
Sbjct: 68  MNGRKILGKEVKVNWATTPSS 88

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 1e-06
 Identities = 12/52 (23%), Positives = 24/52 (46%)

Query: 7  VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
               E   +  + FV      D  A +  ++GR+ LG+ ++VN++  P  +
Sbjct: 38 CKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ 89

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.3 bits (153), Expect = 1e-14
 Identities = 25/94 (26%), Positives = 48/94 (51%), Gaps = 6/94 (6%)

Query: 59  LPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTK 118
           LP        +F+ NLS+    E+L +  Q++G++   RV+   ++  S+G  F  + T+
Sbjct: 1   LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 60

Query: 119 AEMETALESLN------GVELEGRAMRVSLAQGR 146
              +  L + +      G++L+GR ++V LA  R
Sbjct: 61  EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTR 94

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.8 bits (79), Expect = 8e-04
 Identities = 12/56 (21%), Positives = 21/56 (37%), Gaps = 7/56 (12%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENL------DGREYLGRILRVNFSDKPKPK 58
             +T  S+G AF    T E     +          G +  GR L+V+ +   + +
Sbjct: 42 LHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA-VTRDE 96

>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 = 63.1 bits (153), Expect = 2e-14
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 6/82 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++ V NL + VT + L Q F ++G V+            ++    + Y+     + A  S
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLS 64

Query: 128 LNGVEL--EGRAMRVSLAQGRR 147
           L+G  +      +R+  ++   
Sbjct: 65  LDGQNIYNACCTLRIDFSKLTS 86

>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 = 38.1 bits (88), Expect = 5e-05
 Identities = 8/48 (16%), Positives = 17/48 (35%), Gaps = 2/48 (4%)

Query: 15 RSRGFAFVTMSTVEDCNAVIENLDGRE--YLGRILRVNFSDKPKPKLP 60
           ++  A +  +          +LDG+        LR++FS      + 
Sbjct: 43 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVK 90

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 62.7 bits (151), Expect = 2e-14
 Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
            T F LF+GNL+ + +   L  A  E        V+    +G +R +G+V + +  ++E 
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEK 69

Query: 124 ALESLNGVELEGRAMRVSLAQGR 146
           ALE L G+++ G  +++   +GR
Sbjct: 70  ALE-LTGLKVFGNEIKLEKPKGR 91

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 35.3 bits (80), Expect = 4e-04
 Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 2/48 (4%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK 56
           D  TG +R F +V   + ED    +  L G +  G  +++    K +
Sbjct: 46 VDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKP-KGR 91

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 2e-14
 Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           K+FVG +        L   F++YG +    ++ D  SG+ RG+ FV +     ++  +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 128 LNGVELEGRAMRVSLA 143
                + G    V  A
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>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 = 36.2 bits (83), Expect = 1e-04
 Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
           DR +G+ RGFAFVT    +  + ++         G    V  +
Sbjct: 36 TDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA 78

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.3 bits (148), Expect = 7e-14
 Identities = 20/88 (22%), Positives = 32/88 (36%), Gaps = 7/88 (7%)

Query: 60  PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKA 119
           P    +DF++ V  L  S + + L    +E G+             +  G G V Y  K 
Sbjct: 9   PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGD-------VCYADVQKDGMGMVEYLRKE 61

Query: 120 EMETALESLNGVELEGRAMRVSLAQGRR 147
           +ME AL  L+  +        S  +   
Sbjct: 62  DMEYALRKLDDTKFRSHEGETSYIRVYP 89

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.0 bits (90), Expect = 2e-05
 Identities = 5/40 (12%), Positives = 11/40 (27%)

Query: 19 FAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
             V     ED    +  LD  ++       ++      +
Sbjct: 52 MGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPER 91

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.6 bits (146), Expect = 1e-13
 Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 6/80 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQ---EYGNVVGARVLYD---GESGRSRGYGFVCYSTKAEM 121
            +FV  LS  +    + +  +   ++G +    +        S       +V Y    + 
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 122 ETALESLNGVELEGRAMRVS 141
             A++ +N V ++GR ++ S
Sbjct: 70  LRAIQCVNNVVVDGRTLKAS 89

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 2e-04
 Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 3/43 (6%)

Query: 10 DRETGRS---RGFAFVTMSTVEDCNAVIENLDGREYLGRILRV 49
                S      A+VT    ED    I+ ++     GR L+ 
Sbjct: 46 STSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA 88

>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 = 59.4 bits (143), Expect = 2e-13
 Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 68  KLFVGNLSWSVTTES-LTQAFQEYGNVVGARVLYD-GESGRSRGYGFVCYSTKAEMETAL 125
           ++ + NLS  +  E+ L ++F+ +G++    +     E   +    F+ +  K   E AL
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 126 ESLNGVELEGRAMRVSLAQGR 146
           + +N   L  R + VSLA  +
Sbjct: 66  Q-MNRSLLGNREISVSLADKK 85

>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 = 42.8 bits (100), Expect = 6e-07
 Identities = 7/49 (14%), Positives = 18/49 (36%), Gaps = 2/49 (4%)

Query: 9  YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
            +E   +   AF+     +     ++ ++      R + V+ +   KP
Sbjct: 40 GQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA-DKKP 86

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 5e-13
 Identities = 15/81 (18%), Positives = 38/81 (46%), Gaps = 7/81 (8%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            +FVG  +  +T + L + F +YG+V+   +         R + FV ++     ++    
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG- 60

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
              + ++G ++ +S A+ + +
Sbjct: 61  -EDLIIKGISVHISNAEPKHN 80

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.2 bits (78), Expect = 0.001
 Identities = 9/48 (18%), Positives = 18/48 (37%), Gaps = 3/48 (6%)

Query: 11 RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
                R FAFVT +  +   ++          G  + ++ + +PK  
Sbjct: 36 FIPKPFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA-EPKHN 80

>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 = 58.5 bits (141), Expect = 6e-13
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 8/79 (10%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L+V      +T   L  AF  +GN+       D      R   FV Y      + A+  
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVAE 58

Query: 128 LNGVELEGRAMRVSLAQGR 146
           LNG ++E   ++V++A+ +
Sbjct: 59  LNGTQVESVQLKVNIARKQ 77

>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 = 47.3 bits (112), Expect = 1e-08
 Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 1  MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP 57
            S    + D      R  AFVT   +E  +  +  L+G +     L+VN + + +P
Sbjct: 23 AFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA-RKQP 78

>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 = 56.7 bits (136), Expect = 2e-12
 Identities = 16/71 (22%), Positives = 36/71 (50%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L++  L    T + L +  Q YG +V  + + D  + + +GYGFV + + +  + A+ +L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 129 NGVELEGRAMR 139
               ++ +  +
Sbjct: 61  KASGVQAQMAK 71

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.0 bits (77), Expect = 0.001
 Identities = 5/36 (13%), Positives = 13/36 (36%)

Query: 13 TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILR 48
          T + +G+ FV   +       +  L       ++ +
Sbjct: 36 TNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK 71

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.2 bits (137), Expect = 3e-12
 Identities = 13/85 (15%), Positives = 29/85 (34%), Gaps = 1/85 (1%)

Query: 64  ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMET 123
                  + N+ +S+T   + Q  +       A  +    +G+  G   V +  + +   
Sbjct: 6   SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 65

Query: 124 ALESLNGVELEGRAMRVSLAQGRRS 148
           +   L+  +L GR   V +      
Sbjct: 66  SER-LHRKKLNGREAFVHVVTLEDM 89

>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 = 56.3 bits (135), Expect = 4e-12
 Identities = 11/79 (13%), Positives = 25/79 (31%), Gaps = 7/79 (8%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            + V NL      + +    ++Y               R++   FV      + + A++ 
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 128 LNGVELEGRAMRVSLAQGR 146
            +     G+ + V L    
Sbjct: 60  FHQYSFRGKDLIVQLQPTD 78

>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 = 36.6 bits (84), Expect = 1e-04
 Identities = 10/45 (22%), Positives = 16/45 (35%), Gaps = 1/45 (2%)

Query: 16 SRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
          ++  AFVT+   E     I+      + G+ L V         L 
Sbjct: 39 NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ-PTDALLC 82

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.3 bits (135), Expect = 6e-12
 Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 1/77 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            L++ NL  S+  + L +   +    V +  +    SG SRG GF    +  + E  +  
Sbjct: 20  NLYISNLPLSMDEQEL-ENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 78

Query: 128 LNGVELEGRAMRVSLAQ 144
            NG  ++      +  +
Sbjct: 79  FNGKFIKTPPGVSAPTE 95

>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 = 56.2 bits (135), Expect = 7e-12
 Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 1/75 (1%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            + +         E  T+  ++YG V    V  +       G  +V +  + + E A+  
Sbjct: 29  DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVID 87

Query: 128 LNGVELEGRAMRVSL 142
           LN     G+ +   L
Sbjct: 88  LNNRWFNGQPIHAEL 102

>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 = 47.3 bits (112), Expect = 2e-08
 Identities = 9/44 (20%), Positives = 16/44 (36%)

Query: 9   YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS 52
            D       G  +V     ED    + +L+ R + G+ +    S
Sbjct: 60  CDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.1 bits (132), Expect = 2e-11
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 8/83 (9%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           +L+VG L  + +  +L + F  +G++     +          + ++ Y +    + A   
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72

Query: 128 LNGVELEG--RAMRVSLAQGRRS 148
           + G  L G  R +RV  A+   S
Sbjct: 73  MRGFPLGGPDRRLRVDFAKSGPS 95

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 3e-11
 Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           L + N+  SV+ E L   F   G VV     +     + R    +   +  E   AL  L
Sbjct: 13  LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDL 68

Query: 129 NGVEL-EGRAMRVSLAQGR 146
           +  +L E   +RVS ++  
Sbjct: 69  HNHDLGENHHLRVSFSKST 87

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.7 bits (128), Expect = 4e-11
 Identities = 13/81 (16%), Positives = 27/81 (33%), Gaps = 7/81 (8%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
           ++ V  L  S + + L    +E G+                G G V +  K +M  A+  
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGD-------VCYADVYRDGTGVVEFVRKEDMTYAVRK 54

Query: 128 LNGVELEGRAMRVSLAQGRRS 148
           L+  +        +  + +  
Sbjct: 55  LDNTKFRSHEGETAYIRVKVD 75

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.6 bits (73), Expect = 0.004
 Identities = 7/40 (17%), Positives = 12/40 (30%), Gaps = 1/40 (2%)

Query: 21 FVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
           V     ED    +  LD  ++        +  + K   P
Sbjct: 39 VVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI-RVKVDGP 77

>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 = 54.0 bits (129), Expect = 5e-11
 Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 68  KLFVGNLSWSVTTE-SLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE 126
            L V NL+    T  SL   F  YG+V   ++L+       +    V  +   + + A+ 
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF-----NKKENALVQMADGNQAQLAMS 58

Query: 127 SLNGVELEGRAMRVSLAQGRR 147
            LNG +L G+ +R++L++ + 
Sbjct: 59  HLNGHKLHGKPIRITLSKHQN 79

>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 = 42.8 bits (100), Expect = 9e-07
 Identities = 10/42 (23%), Positives = 19/42 (45%)

Query: 19 FAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLP 60
           A V M+        + +L+G +  G+ +R+  S     +LP
Sbjct: 42 NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLP 83

>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 = 53.3 bits (127), Expect = 1e-10
 Identities = 14/86 (16%), Positives = 25/86 (29%), Gaps = 11/86 (12%)

Query: 68  KLFVGNLSWSVTTE-----SLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
            L     +  V +E          F+ Y      +        +S     + +S      
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF------KSFKRVRINFSNPLSAA 60

Query: 123 TALESLNGVELEGRAMRVSLAQGRRS 148
            A   L+  E  G+ M++  AQ    
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTLHI 86

>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 = 42.5 bits (99), Expect = 1e-06
 Identities = 6/42 (14%), Positives = 13/42 (30%)

Query: 17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
               +  S           L   E+LG+ +++ F+      
Sbjct: 46 FKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIG 87

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 6e-10
 Identities = 13/89 (14%), Positives = 29/89 (32%), Gaps = 3/89 (3%)

Query: 60  PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKA 119
              + T   + +  L +  T   +   F     +        G  GR  G   V ++T  
Sbjct: 9   SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEADVEFATHE 66

Query: 120 EMETALESLNGVELEGRAMRVSLAQGRRS 148
           +   A+   +   ++ R + + L     +
Sbjct: 67  DAVAAMA-KDKANMQHRYVELFLNSTAGT 94

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 6e-10
 Identities = 8/76 (10%), Positives = 28/76 (36%), Gaps = 2/76 (2%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            +++       T + + +  ++ G V+  ++         +G  FV + +    +  +E 
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQM-RRTLHKAFKGSIFVVFDSIESAKKFVE- 65

Query: 128 LNGVELEGRAMRVSLA 143
             G + +   + +   
Sbjct: 66  TPGQKYKETDLLILFK 81

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 50.2 bits (119), Expect = 8e-10
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            LF+ NL        L+  F ++                     FV ++T+ +   A E+
Sbjct: 10  ILFLTNLPEETNEMMLSMLFNQFPGFK-----EVRLVPNRHDIAFVEFTTELQSNAAKEA 64

Query: 128 LNGVEL-EGRAMRVSLAQ 144
           L G ++    AM+++ A+
Sbjct: 65  LQGFKITPTHAMKITFAK 82

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.6 bits (118), Expect = 1e-09
 Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 9/80 (11%)

Query: 66  DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETAL 125
           D  + V     +  +  L   F +YGN++   +        +  +  + Y +K +   AL
Sbjct: 4   DTWVTVFGFPQASASYIL-LQFAQYGNILKHVM------SNTGNWMHIRYQSKLQARKAL 56

Query: 126 ESLNGVELEGRAM-RVSLAQ 144
              +G       M  V    
Sbjct: 57  S-KDGRIFGESIMIGVKPCI 75

>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 = 50.1 bits (119), Expect = 1e-09
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 7/78 (8%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           +  G L   V+   L    ++ G V    +  +      + Y F  Y T  E + A  +L
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTL 76

Query: 129 NGVEL-EGRAMRVSLAQG 145
           NG E+ +    +++L   
Sbjct: 77  NGKEVVDDLGQKITLYLN 94

>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 = 33.2 bits (75), Expect = 0.003
 Identities = 7/50 (14%), Positives = 19/50 (38%), Gaps = 1/50 (2%)

Query: 3  SKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL-GRILRVNF 51
           K  ++       ++ ++F    T E+       L+G+E +     ++  
Sbjct: 42 EKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITL 91

>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 = 2e-09
 Identities = 11/66 (16%), Positives = 22/66 (33%), Gaps = 4/66 (6%)

Query: 81  ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV 140
           E L     ++G +    +          G   V +    E +  +++L+G    GR +  
Sbjct: 34  EDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

Query: 141 SLAQGR 146
               G 
Sbjct: 90  QAWDGT 95

>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 = 49.5 bits (118), Expect = 2e-09
 Identities = 12/44 (27%), Positives = 18/44 (40%)

Query: 10 DRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD 53
                  G A V+    E+ +  I+ LDGR + GR +     D
Sbjct: 50 LLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWD 93

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (116), Expect = 5e-09
 Identities = 17/95 (17%), Positives = 42/95 (44%), Gaps = 3/95 (3%)

Query: 52  SDKPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYG 111
             + + + P   E  F +++  L +    + +   F++   V  +  +  G +G++ G G
Sbjct: 6   QKRSRSRSP--HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEG 63

Query: 112 FVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR 146
           FV +  +A+ + AL   +   +  R ++V     +
Sbjct: 64  FVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKK 97

>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 = 46.1 bits (109), Expect = 5e-08
 Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 5/59 (8%)

Query: 9   YDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDF 67
            D       G  FV  ++V DC   ++ L GR++  R++   + D        Y   DF
Sbjct: 50  VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDS-----YHRRDF 103

>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 = 45.7 bits (108), Expect = 6e-08
 Identities = 13/79 (16%), Positives = 28/79 (35%), Gaps = 2/79 (2%)

Query: 71  VGNLSWSVTTESLTQAFQEYGNVVGARVL--YDGESGRSRGYGFVCYSTKAEMETALESL 128
           + +  +    E +     +YG V    +    DG      G  FV +++  + + A++ L
Sbjct: 19  LDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 78

Query: 129 NGVELEGRAMRVSLAQGRR 147
            G +   R +         
Sbjct: 79  TGRKFANRVVVTKYCDPDS 97

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.5 bits (109), Expect = 5e-08
 Identities = 9/82 (10%), Positives = 21/82 (25%), Gaps = 6/82 (7%)

Query: 63  AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEME 122
             +   +   NL        + + F  +G++    +              V +    E  
Sbjct: 7   GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEAR 60

Query: 123 TALESLNGVELEGRAMRVSLAQ 144
            A   L   +     + +  A 
Sbjct: 61  KAFRHLAYSKFHHVPLYLEWAP 82

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.8 bits (76), Expect = 0.002
 Identities = 4/42 (9%), Positives = 11/42 (26%)

Query: 17 RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK 58
             A V      +      +L   ++    L + ++      
Sbjct: 46 GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFG 87

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.8 bits (105), Expect = 9e-08
 Identities = 10/76 (13%), Positives = 26/76 (34%), Gaps = 3/76 (3%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALES 127
            + V NL  S     + + F+  G ++   V    +  ++  +  + ++       A+  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITK 59

Query: 128 LNGVELEGRAMRVSLA 143
                +    + VS  
Sbjct: 60  -THKVVGQNEIIVSHL 74

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (107), Expect = 1e-07
 Identities = 13/78 (16%), Positives = 21/78 (26%), Gaps = 5/78 (6%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
            F G+L      E L   F  +G +     +   + G              E     +  
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIIL-----FKEKAKEALGKAKDA 68

Query: 129 NGVELEGRAMRVSLAQGR 146
           N   L+ R   V+     
Sbjct: 69  NNGNLQLRNKEVTWEVLE 86

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.1 bits (103), Expect = 2e-07
 Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 7/76 (9%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           + +  L   VT + +     +Y               + +G  FV      + E A+ + 
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYEL-------KYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 129 NGVELEGRAMRVSLAQ 144
           +   L  R + V L  
Sbjct: 54  HQSRLRERELSVQLQP 69

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.0 bits (103), Expect = 3e-07
 Identities = 11/81 (13%), Positives = 28/81 (34%), Gaps = 8/81 (9%)

Query: 69  LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL 128
           + V  L  SV    L +A +++G +    ++        +    V +      +  +   
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFA 71

Query: 129 --NGVELEGRAMRVSLAQGRR 147
               V + G+    + +  +R
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKR 92

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (100), Expect = 5e-07
 Identities = 11/82 (13%), Positives = 26/82 (31%), Gaps = 8/82 (9%)

Query: 68  KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE- 126
            L +  L   VT   +      +G V       +    + +   F+  +T+    T +  
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKV------TNILMLKGKNQAFLELATEEAAITMVNY 63

Query: 127 -SLNGVELEGRAMRVSLAQGRR 147
            S     L  + + +  +  + 
Sbjct: 64  YSAVTPHLRNQPIYIQYSNHKE 85

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.4 bits (99), Expect = 9e-07
 Identities = 12/82 (14%), Positives = 31/82 (37%), Gaps = 9/82 (10%)

Query: 69  LFVGNL-SWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE- 126
           + + +          L Q  + +G +    +L            F+  +T  + + A++ 
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDY 64

Query: 127 -SLNGVELEGRAMRVSLAQGRR 147
            +     + G+ +RV L+Q  +
Sbjct: 65  YTTTPALVFGKPVRVHLSQKYK 86

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.0 bits (92), Expect = 1e-05
 Identities = 16/94 (17%), Positives = 32/94 (34%), Gaps = 3/94 (3%)

Query: 54  KPKPKLPLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFV 113
           KP  K     E    + + NL  S  ++S      +     G    Y     +S+ +  +
Sbjct: 6   KPDQKFDQKQELGRVIHLSNLPHSGYSDSA---VLKLAEPYGKIKNYILMRMKSQAFIEM 62

Query: 114 CYSTKAEMETALESLNGVELEGRAMRVSLAQGRR 147
                A           +  +GR ++V L++  +
Sbjct: 63  ETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK 96

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	148
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.93
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.93
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.93
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.93
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.93
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.93
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.93
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.93
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.92
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.92
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.92
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.92
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.91
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.91
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.91
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.91
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.91
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.91
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.91
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.91
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.91
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.91
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.91
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.91
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.91
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.91
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.9
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.9
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.9
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.89
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.89
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.89
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.89
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.89
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.89
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.89
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.89
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.89
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.88
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.88
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.88
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.88
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.88
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.88
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.87
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.87
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.87
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.87
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.87
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.87
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.86
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.86
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.86
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.86
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.86
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.86
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.86
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.85
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.85
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.84
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.84
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.84
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.84
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.84
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.84
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.84
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.83
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.83
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.83
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.83
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.83
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.82
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.82
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.75
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.74
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.73
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.69
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.67
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.67
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.64
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.62
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.61
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.57
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.56
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.56
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.56
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.55
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.55
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.54
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.53
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.53
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.53
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.52
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.49
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.48
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.48
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.47
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.47
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.47
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.45
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.45
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.45
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.44
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.44
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.44
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.43
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.43
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.43
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.4
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.39
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.39
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.39
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.37
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.37
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.36
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.36
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.33
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.33
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.32
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.31
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.29
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.29
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.28
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.26
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.25
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.25
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.24
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.23
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.23
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.21
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.2
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.19
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.19
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.18
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.18
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.18
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.13
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.12
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.12
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.11
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.11
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.1
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.1
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.09
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.08
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.08
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.07
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.07
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.05
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.04
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.04
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.02
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.99
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	98.98
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.93
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.92
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.88
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.85
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.85
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.85
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.84
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.8
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.79
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.75
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.59
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.44
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.44
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.37
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.16
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.06
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	97.3
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.28
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	95.6

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=8.8e-30  Score=162.18  Aligned_cols=143  Identities=27%  Similarity=0.423  Sum_probs=126.6

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC-CCCCCCCCcceEEEcCCCCCCCH
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP-KLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~-~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      |+++.+++++.+|.++|||||+|.+.++|.+|+. +.+..+.++.+.+.+...... .........++|+|+|||+.+++
T Consensus        33 v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~V~~lp~~~te  111 (183)
T d1u1qa_          33 LTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEE  111 (183)
T ss_dssp             EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCCTTGGGSTTTTCCCSEEEEECCCTTCCH
T ss_pred             EEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhhcccccccccccccceeEEccCCCcCCH
Confidence            6789999999999999999999999999999998 567778888888876654433 22344556789999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ++|+++|+.||.|..+.+..++.++.++|+|||+|.+.++|++|+. +++..++|+.|+|.++.++
T Consensus       112 ~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         112 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCH
T ss_pred             HHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCc
Confidence            9999999999999999999998889999999999999999999997 7999999999999998765

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=8.1e-26  Score=127.89  Aligned_cols=85  Identities=19%  Similarity=0.409  Sum_probs=81.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||+|||.++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|+.|++.|||..++|+.|+|+++
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            45678999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 032044          144 QGRRS  148 (148)
Q Consensus       144 ~~~~~  148 (148)
                      +|+.|
T Consensus        86 kp~~n   90 (90)
T d2cq0a1          86 KPSTN   90 (90)
T ss_dssp             SCCCC
T ss_pred             eCCCC
Confidence            98865

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.93  E-value=1.8e-25  Score=125.88  Aligned_cols=83  Identities=27%  Similarity=0.483  Sum_probs=78.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||+|||.++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+..|||..++|+.|+|+|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35679999999999999999999999999999999999899999999999999999999999999999999999999999


Q ss_pred             cCC
Q 032044          144 QGR  146 (148)
Q Consensus       144 ~~~  146 (148)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            876

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.93  E-value=1e-25  Score=125.44  Aligned_cols=80  Identities=28%  Similarity=0.507  Sum_probs=77.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      +++|||+|||+++++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|++|++.|||..++|+.|+|++++|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999999988999999999999999999999999999999999999999986

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=4e-25  Score=123.04  Aligned_cols=79  Identities=32%  Similarity=0.561  Sum_probs=76.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      ++|||+|||+++++++|+++|++||.|..+.++++..++.++|+|||+|.+.++|+.|++.|||..++|+.|+|.+++|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            4799999999999999999999999999999999988899999999999999999999999999999999999999986

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=9e-26  Score=127.44  Aligned_cols=83  Identities=33%  Similarity=0.560  Sum_probs=79.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|+..|||..++|+.|+|++++
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45689999999999999999999999999999999998899999999999999999999999999999999999999999


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      +++
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            875

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=6.6e-25  Score=124.74  Aligned_cols=84  Identities=29%  Similarity=0.496  Sum_probs=79.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ..+++|||+|||+++++++|+++|++||.|.++.++.++.++.++|+|||+|.+.++|+.|++.|||..++|+.|+|+|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 032044          144 QGRR  147 (148)
Q Consensus       144 ~~~~  147 (148)
                      .+.+
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            6553

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=2.8e-25  Score=126.27  Aligned_cols=83  Identities=28%  Similarity=0.498  Sum_probs=79.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||.++++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|+.|++.|||..++|+.|+|++|+
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45799999999999999999999999999999999998999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      +++
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            875

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=9.8e-25  Score=126.02  Aligned_cols=85  Identities=28%  Similarity=0.542  Sum_probs=80.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .++++|||+|||+++++++|+++|++||.+..+.++.++.++.++|+|||+|.+.++|+.|+..|||..++|+.|+|+++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34578999999999999999999999999999999999899999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 032044          144 QGRRS  148 (148)
Q Consensus       144 ~~~~~  148 (148)
                      +++.+
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            88753

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=6.3e-25  Score=121.55  Aligned_cols=78  Identities=32%  Similarity=0.500  Sum_probs=75.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        68 ~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      .|||+|||+.+++++|+++|++||+|..+.+++++.++.++|+|||+|.++++|..|++.|||..++|++|+|+|++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999999864

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.92  E-value=1.3e-24  Score=125.04  Aligned_cols=84  Identities=24%  Similarity=0.432  Sum_probs=79.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ..+++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|+.|+..||+..++|+.|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45678999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 032044          144 QGRR  147 (148)
Q Consensus       144 ~~~~  147 (148)
                      .++.
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8764

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.92  E-value=5.3e-25  Score=122.22  Aligned_cols=79  Identities=20%  Similarity=0.303  Sum_probs=69.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      ++|||+|||+++++++|+++|++||.|..+.+..+..++.++|+|||+|.+.++|+.|++.|||..++|++|+|++++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6899999999999999999999999998888877777889999999999999999999999999999999999999986

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=4.2e-24  Score=119.03  Aligned_cols=77  Identities=36%  Similarity=0.617  Sum_probs=73.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      .++++|||+|||+++++++|+++|++||.|.++.+++++.++.++|+|||+|.+.++|+.|+..|||..++|+.|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            45679999999999999999999999999999999999888999999999999999999999999999999999986

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=8.8e-24  Score=119.11  Aligned_cols=83  Identities=25%  Similarity=0.476  Sum_probs=76.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ....+|||+|||+++++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|++|++.  +..++|+.|.|+++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            3556899999999999999999999999999999999999999999999999999999999984  55899999999999


Q ss_pred             cCCCC
Q 032044          144 QGRRS  148 (148)
Q Consensus       144 ~~~~~  148 (148)
                      .++.+
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            88754

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=1.2e-24  Score=123.15  Aligned_cols=83  Identities=37%  Similarity=0.661  Sum_probs=78.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ...+|||+|||+++++++|+++|++||.|..+.++.+..++.++|+|||+|.+.++|+.|+..|||..++|++|+|+++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999999888889999999999999999999999999999999999999987


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      ++.
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.91  E-value=2.7e-24  Score=122.38  Aligned_cols=84  Identities=25%  Similarity=0.486  Sum_probs=77.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcC-CCCCceeEEEEEecCHHHHHHHHHHh-CCceeCCeEEEEE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDG-ESGRSRGYGFVCYSTKAEMETALESL-NGVELEGRAMRVS  141 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~-~~~~~~~~~fv~f~~~~~a~~a~~~l-~~~~i~g~~l~v~  141 (148)
                      ..+.+|||+|||+++++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|+.|+..| ||..++|++|+|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            456789999999999999999999999999999998774 46889999999999999999999998 8999999999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      ||.++.
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998764

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=1.1e-24  Score=121.75  Aligned_cols=80  Identities=25%  Similarity=0.469  Sum_probs=77.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      .+|||+|||+++++++|+++|++||+|..+.+++++.++.++|+|||+|.++++|+.|+..|||..++|+.|.|+++.++
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            37999999999999999999999999999999999999999999999999999999999999999999999999999765

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=9.5e-24  Score=117.64  Aligned_cols=80  Identities=35%  Similarity=0.607  Sum_probs=75.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||+++++++|+++|++||.|..+.+++++.++.++|+|||+|.+.++|++|+. +++..|+|+.|+|+.|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            45689999999999999999999999999999999999999999999999999999999998 69999999999999875


Q ss_pred             C
Q 032044          145 G  145 (148)
Q Consensus       145 ~  145 (148)
                      +
T Consensus        84 s   84 (84)
T d1l3ka1          84 S   84 (84)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=1.1e-23  Score=119.02  Aligned_cols=83  Identities=28%  Similarity=0.432  Sum_probs=75.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .++++|||+|||.++++++|+++|++||.|..+.++.+..+  .+++|||+|.+.++|+.|+..+||..+.|+.|+|.++
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            35679999999999999999999999999999999877554  3789999999999999999999999999999999999


Q ss_pred             cCCCC
Q 032044          144 QGRRS  148 (148)
Q Consensus       144 ~~~~~  148 (148)
                      +++.+
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            87753

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.91  E-value=1.1e-23  Score=128.24  Aligned_cols=82  Identities=29%  Similarity=0.541  Sum_probs=78.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|..|+..|||..|+|+.|+|++++
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      ++
T Consensus       121 ~~  122 (139)
T d1u6fa1         121 SG  122 (139)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.91  E-value=6.4e-24  Score=118.76  Aligned_cols=79  Identities=38%  Similarity=0.650  Sum_probs=74.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEe
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG--RAMRVSL  142 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g--~~l~v~~  142 (148)
                      .+++|||+|||+++++++|+++|++||.|..+.+++++.++.++|+|||+|.+.++|++|++.|||..+.|  ++|+|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            45679999999999999999999999999999999998999999999999999999999999999999976  8899998


Q ss_pred             c
Q 032044          143 A  143 (148)
Q Consensus       143 ~  143 (148)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=7e-24  Score=118.54  Aligned_cols=79  Identities=35%  Similarity=0.655  Sum_probs=74.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEe
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG--RAMRVSL  142 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g--~~l~v~~  142 (148)
                      .+++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|++.|||..++|  ++|+|+|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            34689999999999999999999999999999999998889999999999999999999999999999987  5599988


Q ss_pred             c
Q 032044          143 A  143 (148)
Q Consensus       143 ~  143 (148)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=7e-25  Score=126.23  Aligned_cols=82  Identities=24%  Similarity=0.386  Sum_probs=77.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||+++++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|++|+. |||..++|+.|+|+++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            45789999999999999999999999999999999998899999999999999999999996 99999999999999987


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      +++
T Consensus        96 ~~~   98 (101)
T d2cq4a1          96 AEK   98 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            654

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.91  E-value=7.2e-24  Score=116.63  Aligned_cols=77  Identities=39%  Similarity=0.638  Sum_probs=73.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        68 ~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      +|||+|||+++++++|+++|++||.|..+.+..++ ++.++|+|||+|.+.++|+.|++.|||..++|+.|+|+++.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            69999999999999999999999999999998884 688899999999999999999999999999999999999864

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=3.2e-23  Score=117.72  Aligned_cols=83  Identities=29%  Similarity=0.595  Sum_probs=76.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ...+++|||+|||+.+++++|+++|++||.|..+.++.+..  .++|+|||+|.+.++|.+|+..|||..++|+.|+|++
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            44567899999999999999999999999999999987743  4689999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +.+|.
T Consensus        86 A~~r~   90 (93)
T d2cq3a1          86 ATARV   90 (93)
T ss_dssp             CCSSC
T ss_pred             cCcCC
Confidence            98873

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=4.9e-24  Score=118.77  Aligned_cols=79  Identities=28%  Similarity=0.587  Sum_probs=74.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeE-EEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCCC
Q 032044           69 LFVGNLSWSVTTESLTQAFQEYGNVVG-ARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGRR  147 (148)
Q Consensus        69 l~i~nlp~~~~~~~l~~~f~~~g~v~~-~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~~  147 (148)
                      |||+|||+++++++|+++|++||.|.. +.+++++.++.++|||||+|.+.++|++|+..++|..++|++|+|+++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            799999999999999999999999865 4788888889999999999999999999999999999999999999998875

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=3e-24  Score=124.51  Aligned_cols=83  Identities=40%  Similarity=0.713  Sum_probs=78.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|+.|++.|||..++|+.|+|+++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      ++.
T Consensus        87 ~~~   89 (104)
T d1p1ta_          87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            653

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.90  E-value=1.5e-23  Score=117.33  Aligned_cols=78  Identities=28%  Similarity=0.542  Sum_probs=72.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCC---CceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESG---RSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        69 l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~---~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      |||+|||+++++++|+++|++||.|..+.++.++.++   .++|||||+|.+.++|+.|++.+||..++|+.|+|+++++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999998876554   4689999999999999999999999999999999999865


Q ss_pred             C
Q 032044          146 R  146 (148)
Q Consensus       146 ~  146 (148)
                      +
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.90  E-value=2.2e-24  Score=118.28  Aligned_cols=76  Identities=34%  Similarity=0.647  Sum_probs=73.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      |+|||+|||+++++++|+++|++||.|..+.+++++.++.++|+|||+|.+.++|++|++ +++..++|+.|.|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999998 7999999999999886

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=9.5e-24  Score=121.77  Aligned_cols=82  Identities=35%  Similarity=0.596  Sum_probs=77.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||+++++++|+++|.+||.|..+.+++++.++.++|||||+|.+.++|+.|++ ++|..|+|+.|.|+++.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            34789999999999999999999999999999999998888999999999999999999997 89999999999999998


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      ++.
T Consensus        98 ~ke  100 (103)
T d1x4ba1          98 ARE  100 (103)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            864

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.90  E-value=5.5e-23  Score=117.97  Aligned_cols=85  Identities=27%  Similarity=0.528  Sum_probs=78.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhC------CceeCCe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLN------GVELEGR  136 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~------~~~i~g~  136 (148)
                      ....++|||+|||+++++++|+++|++||.+..+.+..+..++.++|+|||+|.+.++|.+|++.++      |..++|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3456789999999999999999999999999999999888888999999999999999999999886      6789999


Q ss_pred             EEEEEeccCCC
Q 032044          137 AMRVSLAQGRR  147 (148)
Q Consensus       137 ~l~v~~~~~~~  147 (148)
                      .|+|+++.++.
T Consensus        85 ~l~v~~a~~k~   95 (98)
T d1x4ha1          85 QLKVDLAVTRD   95 (98)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999998764

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=2e-23  Score=113.97  Aligned_cols=75  Identities=32%  Similarity=0.686  Sum_probs=71.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        68 ~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      +|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.++++|++|++ +++..++|+.|.|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            48999999999999999999999999999999999999999999999999999999998 7999999999998754

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=3e-23  Score=116.96  Aligned_cols=80  Identities=33%  Similarity=0.604  Sum_probs=74.0

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      ..+|||+|||+++++++|+++|++||.|..+.++.+..  .++|||||+|.+.++|++|+..|||..++|+.|.|.++.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            45799999999999999999999999999999987753  4689999999999999999999999999999999999988


Q ss_pred             CC
Q 032044          146 RR  147 (148)
Q Consensus       146 ~~  147 (148)
                      +.
T Consensus        86 ~~   87 (89)
T d1cvja2          86 RK   87 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            75

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=9.8e-24  Score=121.97  Aligned_cols=85  Identities=26%  Similarity=0.450  Sum_probs=79.3

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..++++|||+|||.++++++|+++|.+||.+..+.+..+..++.++|+|||+|.+.++|+.|+..|||..+.|++|+|+|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            44678999999999999999999999999999888888777888999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      ++++.
T Consensus        95 ak~k~   99 (102)
T d2cpxa1          95 GKNKK   99 (102)
T ss_dssp             CCCCS
T ss_pred             CCCcc
Confidence            98875

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=9.3e-23  Score=117.81  Aligned_cols=81  Identities=38%  Similarity=0.594  Sum_probs=75.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||+++++++|+++|++||.|.++.++.++.++.++|+|||+|.+.++|+.|++.+++ .++|+.|+|+++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            446799999999999999999999999999999999988899999999999999999999998876 7999999999986


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      ++
T Consensus        88 ~~   89 (103)
T d2cqda1          88 LG   89 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=1.3e-22  Score=115.59  Aligned_cols=82  Identities=22%  Similarity=0.465  Sum_probs=74.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..++++|||+|||+++++++|+++|++||.|..+.+...   ..++++|||+|.+.++|+.|++.|||..++|++|+|++
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            456778999999999999999999999999988877533   45689999999999999999999999999999999999


Q ss_pred             ccCCC
Q 032044          143 AQGRR  147 (148)
Q Consensus       143 ~~~~~  147 (148)
                      +++++
T Consensus        88 a~~~r   92 (95)
T d1x4aa1          88 PRSGR   92 (95)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            98765

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=1.7e-22  Score=111.46  Aligned_cols=77  Identities=23%  Similarity=0.441  Sum_probs=73.0

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .++|||+|||+++++++|+++|++||.+..+.+..++.++.++|+|||+|.+.++|++|+. ++|..|+|+.|.|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            3589999999999999999999999999999999999999999999999999999999996 8999999999999876

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=1.3e-22  Score=115.65  Aligned_cols=78  Identities=24%  Similarity=0.544  Sum_probs=72.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||..+++++|+++|++||.|.++.+..+      +|+|||+|.+.++|+.|+..|||..++|+.|+|.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4568999999999999999999999999999999854      6799999999999999999999999999999999998


Q ss_pred             CCCC
Q 032044          145 GRRS  148 (148)
Q Consensus       145 ~~~~  148 (148)
                      ++.+
T Consensus        91 ~~p~   94 (96)
T d1x4ga1          91 ESPD   94 (96)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7654

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=1.6e-23  Score=114.07  Aligned_cols=75  Identities=21%  Similarity=0.423  Sum_probs=71.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        68 ~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      +|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+. .++..++|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            58999999999999999999999999999999999999999999999999999999997 5778999999999875

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=1.2e-22  Score=117.09  Aligned_cols=83  Identities=28%  Similarity=0.483  Sum_probs=75.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCee--------EEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVV--------GARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG  135 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~--------~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g  135 (148)
                      ....+|||+|||..+++++|+++|++||.|.        .+.+..++.++.++|+|||+|.+.++|..|++.|||..++|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            3567999999999999999999999999863        45566777788999999999999999999999999999999


Q ss_pred             eEEEEEeccCC
Q 032044          136 RAMRVSLAQGR  146 (148)
Q Consensus       136 ~~l~v~~~~~~  146 (148)
                      +.|+|++++++
T Consensus        86 r~i~V~~a~~~   96 (101)
T d2cpea1          86 SKLKVSLARKK   96 (101)
T ss_dssp             EECEEECSSCC
T ss_pred             EEEEEEEcCCC
Confidence            99999999765

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.88  E-value=6.5e-23  Score=114.78  Aligned_cols=81  Identities=23%  Similarity=0.371  Sum_probs=70.5

Q ss_pred             CcceEEEcCCCCCCCH-HHHHHHHhhcCCeeEEEEEEc-CCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           65 TDFKLFVGNLSWSVTT-ESLTQAFQEYGNVVGARVLYD-GESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~-~~l~~~f~~~g~v~~~~~~~~-~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ..++|||+|||+++++ ++|+++|++||.|..+.+..+ ..++.++|+|||+|.+.++|+.|++ +||..++|+.|+|++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            4568999999999864 569999999999999998764 4678889999999999999999996 999999999999999


Q ss_pred             ccCC
Q 032044          143 AQGR  146 (148)
Q Consensus       143 ~~~~  146 (148)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9876

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=2.5e-22  Score=118.16  Aligned_cols=80  Identities=25%  Similarity=0.428  Sum_probs=73.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      +..+++|||+|||.++++++|+++|++||.|..+.+..+   +.++|+|||+|.+.++|..|+..|||..|+|+.|+|.+
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   80 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLY   80 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345679999999999999999999999999999988754   45689999999999999999999999999999999999


Q ss_pred             ccC
Q 032044          143 AQG  145 (148)
Q Consensus       143 ~~~  145 (148)
                      +.+
T Consensus        81 a~~   83 (114)
T d2f9da1          81 YNA   83 (114)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            864

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.88  E-value=6.5e-23  Score=112.11  Aligned_cols=75  Identities=31%  Similarity=0.594  Sum_probs=71.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           68 KLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        68 ~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      +|||+|||+++++++|+++|++||.+..+.+..++.++.++++|||+|.+.++|+.|++ +||..++|+.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            48999999999999999999999999999998888889999999999999999999997 9999999999999875

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.88  E-value=2.7e-23  Score=117.43  Aligned_cols=83  Identities=29%  Similarity=0.498  Sum_probs=74.7

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .+..+.+|||+|||+++++++|+++|++||.|..+.++.. .++.++|+|||+|.+.++|++|++ +||..++|+.|+|.
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            3446679999999999999999999999999888877644 568889999999999999999996 99999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++++|
T Consensus        87 ~ak~k   91 (91)
T d1fjeb1          87 KPKGR   91 (91)
T ss_dssp             CCCCS
T ss_pred             ecCCC
Confidence            99875

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.4e-22  Score=116.68  Aligned_cols=82  Identities=24%  Similarity=0.447  Sum_probs=75.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ...+++|||+|||+++++++|+++|++||.|..+.+..+ .++.++|+|||+|.+.++|++|+..|||..|.|+++.+.+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            345678999999999999999999999999999988877 5678899999999999999999999999999999998888


Q ss_pred             ccC
Q 032044          143 AQG  145 (148)
Q Consensus       143 ~~~  145 (148)
                      +.|
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            765

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.88  E-value=4.4e-22  Score=113.60  Aligned_cols=82  Identities=22%  Similarity=0.457  Sum_probs=73.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      .....++|||+|||+++++++|+++|++||.+..+.     .++.++++|||+|.+.++|+.|+..|||..++|+.|+|.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            344678999999999999999999999999876553     346789999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 032044          142 LAQGRRS  148 (148)
Q Consensus       142 ~~~~~~~  148 (148)
                      ++.++++
T Consensus        87 ~a~~k~~   93 (96)
T d1fjca_          87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EeCCCCC
Confidence            9998864

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.87  E-value=4.3e-22  Score=111.49  Aligned_cols=79  Identities=22%  Similarity=0.363  Sum_probs=70.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .+.+|+|+|||+++++++|+++|..||.+....++....++.++|+|||+|.+.++|++|++.||+..++|++|+|+++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4567999999999999999999999999876444444467889999999999999999999999999999999999874

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.87  E-value=2.7e-22  Score=112.14  Aligned_cols=78  Identities=32%  Similarity=0.536  Sum_probs=71.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||.++++++|+++|++||.|..+.+.++      +++|||+|.+.++|+.|+..|||..++|+.|+|++|.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            4467999999999999999999999999999988744      5799999999999999999999999999999999998


Q ss_pred             CCCC
Q 032044          145 GRRS  148 (148)
Q Consensus       145 ~~~~  148 (148)
                      ++.+
T Consensus        81 ~~~~   84 (86)
T d2cpja1          81 HSAS   84 (86)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            7653

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.1e-21  Score=109.42  Aligned_cols=77  Identities=10%  Similarity=0.225  Sum_probs=71.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      .++|||+|||.++++++|+++|+.||.|..+.+..+ .++.++|+|||+|.++++|++|++ ++|..+.|+.|.|+++.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~-~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee-ccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            468999999999999999999999999999999877 478899999999999999999997 79999999999999864

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=7.8e-22  Score=114.21  Aligned_cols=84  Identities=25%  Similarity=0.481  Sum_probs=73.1

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcC-CCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDG-ESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~-~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      +..++++|||+|||+++++++|+++|++|| +..+.++.+. .++.++|+|||+|.+.++|++|+. +|+..++|+.|+|
T Consensus        11 p~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V   88 (104)
T d1wi8a_          11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEE
Confidence            445678999999999999999999999998 6677666554 467889999999999999987775 9999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      .++.+++
T Consensus        89 ~~a~~~~   95 (104)
T d1wi8a_          89 DVADQAQ   95 (104)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9998764

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=4e-22  Score=110.03  Aligned_cols=75  Identities=36%  Similarity=0.564  Sum_probs=67.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCc-eeCCeEEEEEeccC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV-ELEGRAMRVSLAQG  145 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~-~i~g~~l~v~~~~~  145 (148)
                      ++|||+|||.++++++|+++|++||.+....+..      ++|||||+|.+.++|+.|++.|||. .++|++|+|+++.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999987766654      3679999999999999999999995 79999999999988


Q ss_pred             CC
Q 032044          146 RR  147 (148)
Q Consensus       146 ~~  147 (148)
                      ++
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=3.4e-21  Score=107.74  Aligned_cols=77  Identities=30%  Similarity=0.426  Sum_probs=69.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||+++++++|+++|++||.+..+.+..      ++|+|||+|.+.++|..|+..|||..++|+.|+|++++
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            456899999999999999999999999987776643      47799999999999999999999999999999999998


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      |+.
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            763

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=4.2e-22  Score=112.61  Aligned_cols=80  Identities=23%  Similarity=0.456  Sum_probs=71.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHH----HHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           65 TDFKLFVGNLSWSVTTESLTQ----AFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~----~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      ++++|||+|||+.+++++|++    +|++||.|.++.+..   ++.++|+|||+|.+.++|+.|++.+||..++|+.|+|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            467999999999999999864    579999999887753   3557899999999999999999999999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      .+++++.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9998764

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.86  E-value=1.6e-21  Score=108.39  Aligned_cols=76  Identities=22%  Similarity=0.396  Sum_probs=68.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEEe
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELE-GRAMRVSL  142 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~-g~~l~v~~  142 (148)
                      .++++|||+|||.++++++|.++|++||.|..+.+.++     .+|+|||+|.+.++|..|+..|||..+. |+.|+|.|
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            35679999999999999999999999999999988643     3679999999999999999999999984 68999999


Q ss_pred             cc
Q 032044          143 AQ  144 (148)
Q Consensus       143 ~~  144 (148)
                      |+
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            86

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.5e-21  Score=109.70  Aligned_cols=78  Identities=26%  Similarity=0.379  Sum_probs=69.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee-CCeEEEEEec
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL-EGRAMRVSLA  143 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i-~g~~l~v~~~  143 (148)
                      ++++|||+|||+++++++|+++|++||.+..+.+...    ..+++|||+|.+.++|.+|+..|||..+ +|+.|+|+|+
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            5679999999999999999999999999887766533    3467999999999999999999999998 5899999999


Q ss_pred             cCC
Q 032044          144 QGR  146 (148)
Q Consensus       144 ~~~  146 (148)
                      +++
T Consensus        85 k~~   87 (88)
T d2adca2          85 KST   87 (88)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            875

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.1e-21  Score=111.99  Aligned_cols=82  Identities=21%  Similarity=0.359  Sum_probs=73.0

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEEEcC-CCCCceeEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEEE
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGN-VVGARVLYDG-ESGRSRGYGFVCYSTKAEMETALESLNG--VELEGRAMRVS  141 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~-v~~~~~~~~~-~~~~~~~~~fv~f~~~~~a~~a~~~l~~--~~i~g~~l~v~  141 (148)
                      +++|||+|||.++++++|+++|++||. +..+.++.+. .++.++|||||+|.+.++|..|++.|++  ..++|+.|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            468999999999999999999999996 8889888764 4578899999999999999999999965  55689999999


Q ss_pred             eccCCC
Q 032044          142 LAQGRR  147 (148)
Q Consensus       142 ~~~~~~  147 (148)
                      |+.++.
T Consensus        81 ~A~p~~   86 (96)
T d2disa1          81 WAEPEI   86 (96)
T ss_dssp             ESCSSC
T ss_pred             EcCCCC
Confidence            998864

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=2.2e-21  Score=110.88  Aligned_cols=78  Identities=26%  Similarity=0.565  Sum_probs=69.4

Q ss_pred             CCCCcceEEEcCCC-CCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 032044           62 YAETDFKLFVGNLS-WSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRV  140 (148)
Q Consensus        62 ~~~~~~~l~i~nlp-~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v  140 (148)
                      +....++|||+||| ..+++++|+++|++||.|..+.+        +++||||+|.+.++|++|+..|||..++|+.|+|
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V   82 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDI   82 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456789999997 56788899999999999999987        3679999999999999999999999999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      +++.+++
T Consensus        83 ~~a~~~~   89 (98)
T d1wf2a_          83 NLAAEPK   89 (98)
T ss_dssp             EETTSCC
T ss_pred             EECCCCC
Confidence            9997654

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.86  E-value=8.3e-22  Score=110.82  Aligned_cols=77  Identities=18%  Similarity=0.330  Sum_probs=69.4

Q ss_pred             CcceEEEcCCCCCCCHHHH---HHHHhhcCCeeEEEEEEcCCCCC---ceeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 032044           65 TDFKLFVGNLSWSVTTESL---TQAFQEYGNVVGARVLYDGESGR---SRGYGFVCYSTKAEMETALESLNGVELEGRAM  138 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l---~~~f~~~g~v~~~~~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l  138 (148)
                      ..++|||+|||+++++++|   .++|++||.|..+.+++++.++.   ++|+|||+|.+.++|..|+..|||..++|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4568999999999999999   67899999999999998866544   45899999999999999999999999999999


Q ss_pred             EEE
Q 032044          139 RVS  141 (148)
Q Consensus       139 ~v~  141 (148)
                      +++
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            984

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.5e-22  Score=109.71  Aligned_cols=71  Identities=23%  Similarity=0.532  Sum_probs=68.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        69 l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      |||+|||+++++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|+.|++.|||..++|+.++
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999988999999999999999999999999999999998764

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=4.3e-21  Score=110.96  Aligned_cols=83  Identities=20%  Similarity=0.224  Sum_probs=74.6

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSL  142 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~  142 (148)
                      ...+.+|||+|||+++++++|+++|.++|.+....++....++.++|+|||+|.++++|++|+. +|+..|+|+.|+|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            4456689999999999999999999999988876666666788999999999999999999996 999999999999999


Q ss_pred             ccCC
Q 032044          143 AQGR  146 (148)
Q Consensus       143 ~~~~  146 (148)
                      +.++
T Consensus        91 ~~~~   94 (104)
T d1wg5a_          91 SSRA   94 (104)
T ss_dssp             ECTT
T ss_pred             CCHH
Confidence            8765

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2.4e-21  Score=106.64  Aligned_cols=75  Identities=25%  Similarity=0.433  Sum_probs=68.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||+|++  +++++|+++|++||.|..+.+.++      +++|||+|.+.++|..|+..|||..++|+.|+|+|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456799999986  899999999999999999988633      579999999999999999999999999999999999


Q ss_pred             cCC
Q 032044          144 QGR  146 (148)
Q Consensus       144 ~~~  146 (148)
                      +++
T Consensus        75 ~~~   77 (79)
T d2bz2a1          75 RKQ   77 (79)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            876

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.84  E-value=1.3e-20  Score=102.48  Aligned_cols=74  Identities=14%  Similarity=0.121  Sum_probs=67.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      .+|+|+|||+++++++|+++|++||.|..+.+..++..  .+++|||+|.+.++|++|+. +|+..|+|+.|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            37999999999999999999999999999999887553  45799999999999999996 8999999999999865

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=8.6e-21  Score=108.32  Aligned_cols=79  Identities=22%  Similarity=0.453  Sum_probs=70.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEE
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEG--RAMRVS  141 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g--~~l~v~  141 (148)
                      .+.++|||+|||+++++++|+++|++||.|..+.+.++      +++|||+|.+.++|+.|+..||+..+.|  ++|+|+
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            35679999999999999999999999999999888643      5689999999999999999999999976  589999


Q ss_pred             eccCCCC
Q 032044          142 LAQGRRS  148 (148)
Q Consensus       142 ~~~~~~~  148 (148)
                      |++++++
T Consensus        89 ~ak~~~~   95 (97)
T d1whya_          89 FAKSGPS   95 (97)
T ss_dssp             ECCCCCC
T ss_pred             eCCCCCC
Confidence            9988753

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=2.4e-21  Score=113.41  Aligned_cols=77  Identities=12%  Similarity=0.130  Sum_probs=69.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           64 ETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        64 ~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...++|||+|||+++++++|+++|++||.|..+.+.      ..+++|||+|.+.++|++|+..|||..+.|++|.|+|+
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEEC
Confidence            456789999999999999999999999999998774      24689999999999999999999999999999999998


Q ss_pred             cCC
Q 032044          144 QGR  146 (148)
Q Consensus       144 ~~~  146 (148)
                      ...
T Consensus        82 ~~~   84 (111)
T d1whxa_          82 PIG   84 (111)
T ss_dssp             ETT
T ss_pred             CCC
Confidence            543

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=6e-21  Score=109.94  Aligned_cols=82  Identities=15%  Similarity=0.225  Sum_probs=72.3

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ......+|||+|||+++++++|+++|..+|. ..+.++.+ .++.++|+|||+|.+.++|++|++ +|+..|+|+.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~-~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIG-PDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEES-SSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEe-cCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            3445679999999999999999999999974 56777777 457889999999999999999987 89999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      ++.++
T Consensus        88 ~s~~~   92 (102)
T d1weza_          88 LNSTA   92 (102)
T ss_dssp             EECCC
T ss_pred             EcCCC
Confidence            98765

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=8.8e-21  Score=106.35  Aligned_cols=75  Identities=16%  Similarity=0.264  Sum_probs=65.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      .+.+|||+|||+++++++|+++|++||. ..+.+      +..+++|||+|.+.++|+.|+..||+..++|+.|+|+++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCc-eeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3568999999999999999999999993 22322      2357899999999999999999999999999999999987


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      ++
T Consensus        77 ~~   78 (88)
T d1wg1a_          77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=7.5e-21  Score=110.95  Aligned_cols=76  Identities=29%  Similarity=0.504  Sum_probs=69.4

Q ss_pred             cceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           66 DFKLFVGNLSW-SVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        66 ~~~l~i~nlp~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      +.+|||+|||+ .+++++|+++|+.||.|..+.++++     .+|+|||+|.+.++|++|++.|||..++|+.|+|++++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~-----~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT-----TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec-----ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            56899999965 5999999999999999999999866     26899999999999999999999999999999999986


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      .+
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=2.3e-21  Score=113.48  Aligned_cols=85  Identities=19%  Similarity=0.301  Sum_probs=75.2

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           60 PLYAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        60 ~~~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      ..+.....+|||+|||+++++++|+++|+.+|.+..+.++....+|.++|+|||+|.+.++|++|+. +||..|+|+.|.
T Consensus        12 ~~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~   90 (112)
T d1wela1          12 RSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQ   90 (112)
T ss_dssp             SSCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBE
T ss_pred             CCCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEE
Confidence            3445567799999999999999999999999988776666666789999999999999999999997 999999999999


Q ss_pred             EEeccC
Q 032044          140 VSLAQG  145 (148)
Q Consensus       140 v~~~~~  145 (148)
                      |..+.+
T Consensus        91 V~~~~~   96 (112)
T d1wela1          91 VHPITK   96 (112)
T ss_dssp             EEEECH
T ss_pred             EEEcCh
Confidence            998754

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=5.1e-21  Score=110.51  Aligned_cols=80  Identities=16%  Similarity=0.208  Sum_probs=71.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ...+|||+|||+++++++|+++|..||.+....++....++.++|+|||+|.+.++|++|+. +|+..|+|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            45689999999999999999999999988765555555678899999999999999999996 99999999999999875


Q ss_pred             C
Q 032044          145 G  145 (148)
Q Consensus       145 ~  145 (148)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=2.8e-21  Score=108.45  Aligned_cols=76  Identities=20%  Similarity=0.382  Sum_probs=68.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      .+++|||+|||+++++++|+++|++||.|..+.+..     .+++||||+|.+.++|+.|+.  +++.|+|+.|.|+++.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            567999999999999999999999999999886642     357899999999999999986  7889999999999998


Q ss_pred             CCC
Q 032044          145 GRR  147 (148)
Q Consensus       145 ~~~  147 (148)
                      ++.
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            775

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.8e-20  Score=104.41  Aligned_cols=79  Identities=14%  Similarity=0.171  Sum_probs=70.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHh--CCceeCCeEEEE
Q 032044           63 AETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL--NGVELEGRAMRV  140 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l--~~~~i~g~~l~v  140 (148)
                      ..++++|||+|||+++++++|.++|++||.|..+.+..+      +++|||+|.+.++|+.|++.+  ++..++|++|+|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            457789999999999999999999999999999988643      569999999999999999865  578999999999


Q ss_pred             EeccCCC
Q 032044          141 SLAQGRR  147 (148)
Q Consensus       141 ~~~~~~~  147 (148)
                      +|++.+.
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9998763

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=1.8e-20  Score=107.00  Aligned_cols=78  Identities=28%  Similarity=0.359  Sum_probs=70.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ......+|||+|||+++++++|+++|++||.|..+.+..       +|+|||+|.+.++|+.|++.|||..++|+.|+|.
T Consensus        11 ~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~   83 (98)
T d1wg4a_          11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETS   83 (98)
T ss_dssp             CCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            344667899999999999999999999999999988752       4699999999999999999999999999999999


Q ss_pred             eccCC
Q 032044          142 LAQGR  146 (148)
Q Consensus       142 ~~~~~  146 (148)
                      +++.+
T Consensus        84 ~~~~~   88 (98)
T d1wg4a_          84 YIRVY   88 (98)
T ss_dssp             EEEEE
T ss_pred             EEecC
Confidence            97654

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.7e-21  Score=109.12  Aligned_cols=73  Identities=22%  Similarity=0.287  Sum_probs=65.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      ++|||+|||+++++++|+++|++||.|..+.+..       .|+|||+|.+.++|+.|+..|||..++|+.++|.+++.+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            3699999999999999999999999999998753       369999999999999999999999999999888776543

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=2.9e-20  Score=101.11  Aligned_cols=71  Identities=20%  Similarity=0.346  Sum_probs=63.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccCC
Q 032044           69 LFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQGR  146 (148)
Q Consensus        69 l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~~  146 (148)
                      |||+|||+++++++|+++|++|| +..+.+      +.++|+|||+|.+.++|++|+..|||..++|++|+|+++..+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999998 444333      245789999999999999999999999999999999999765

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.3e-20  Score=108.56  Aligned_cols=78  Identities=21%  Similarity=0.348  Sum_probs=70.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee--CCeEEEEEe
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL--EGRAMRVSL  142 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i--~g~~l~v~~  142 (148)
                      +..+|+|+|||+++++++|+++|++||.|..+.+..++    .+|+|||+|.+.++|+.|+..|||..+  .|++|++.+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            45679999999999999999999999999999988763    478999999999999999999999988  578999999


Q ss_pred             ccCC
Q 032044          143 AQGR  146 (148)
Q Consensus       143 ~~~~  146 (148)
                      ++++
T Consensus        82 s~~~   85 (108)
T d2adba1          82 SKLT   85 (108)
T ss_dssp             CSSC
T ss_pred             cCCc
Confidence            8764

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=3.2e-20  Score=106.18  Aligned_cols=81  Identities=15%  Similarity=0.270  Sum_probs=70.9

Q ss_pred             CCCCCcceEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHH--HhCCceeCCeE
Q 032044           61 LYAETDFKLFVGNLSWS-VTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALE--SLNGVELEGRA  137 (148)
Q Consensus        61 ~~~~~~~~l~i~nlp~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~--~l~~~~i~g~~  137 (148)
                      .....+++|||+|||.+ +++++|.++|++||.|..+.+.++      +++|||+|.+.++|..|+.  .+++..++|+.
T Consensus        13 ~~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~   86 (99)
T d1x4fa1          13 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRC   86 (99)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSC
T ss_pred             cCCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEE
Confidence            33456789999999985 899999999999999999988744      5799999999999999998  46888999999


Q ss_pred             EEEEeccCCC
Q 032044          138 MRVSLAQGRR  147 (148)
Q Consensus       138 l~v~~~~~~~  147 (148)
                      |+|.+++.++
T Consensus        87 l~V~~s~~~~   96 (99)
T d1x4fa1          87 VKVDLSEKYK   96 (99)
T ss_dssp             CEEEEECSCS
T ss_pred             EEEEEcCCcc
Confidence            9999997664

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=1.5e-19  Score=104.40  Aligned_cols=80  Identities=14%  Similarity=0.176  Sum_probs=70.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHh--CCceeCCeEEE
Q 032044           62 YAETDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL--NGVELEGRAMR  139 (148)
Q Consensus        62 ~~~~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l--~~~~i~g~~l~  139 (148)
                      ...++.+|||+|||..+++++|.++|++||.|..+.+.+.      +++|||+|.+.++|+.|+..+  ++..++|++|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            3456789999999999999999999999999999988633      668999999999999999977  56778999999


Q ss_pred             EEeccCCC
Q 032044          140 VSLAQGRR  147 (148)
Q Consensus       140 v~~~~~~~  147 (148)
                      |.|++.++
T Consensus        85 v~~s~~~~   92 (104)
T d1wexa_          85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEcCCCc
Confidence            99997653

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=2e-19  Score=100.84  Aligned_cols=78  Identities=18%  Similarity=0.232  Sum_probs=69.1

Q ss_pred             CCCcceEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHh--CCceeCCeEEE
Q 032044           63 AETDFKLFVGNLSWS-VTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL--NGVELEGRAMR  139 (148)
Q Consensus        63 ~~~~~~l~i~nlp~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l--~~~~i~g~~l~  139 (148)
                      ..++++|||+|||.. .+++||.++|++||.|..+.+..+      +++|||+|.+.++|..|+..+  ++..++|++|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            456779999999986 789999999999999999988754      458999999999999999966  67899999999


Q ss_pred             EEeccCC
Q 032044          140 VSLAQGR  146 (148)
Q Consensus       140 v~~~~~~  146 (148)
                      |.|+++.
T Consensus        79 V~~s~~~   85 (89)
T d1x4da1          79 VHLSQKY   85 (89)
T ss_dssp             EEEECCC
T ss_pred             EEECCCc
Confidence            9999764

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=1.5e-18  Score=99.88  Aligned_cols=77  Identities=17%  Similarity=0.129  Sum_probs=67.8

Q ss_pred             CcceEEEcCCCCCC-CH----HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 032044           65 TDFKLFVGNLSWSV-TT----ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMR  139 (148)
Q Consensus        65 ~~~~l~i~nlp~~~-~~----~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~  139 (148)
                      .+.+|||.||+.++ ++    ++|+++|++||.|..+.+.+      .+++|||+|.+.++|.+|+..|||..++|+.|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            45689999999986 33    46999999999999998873      366899999999999999999999999999999


Q ss_pred             EEeccCCC
Q 032044          140 VSLAQGRR  147 (148)
Q Consensus       140 v~~~~~~~  147 (148)
                      |.|++++.
T Consensus        78 v~~a~~~~   85 (104)
T d1weya_          78 LYFAQTLH   85 (104)
T ss_dssp             EECCCCSS
T ss_pred             EeecccCC
Confidence            99997663

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=3.2e-19  Score=102.69  Aligned_cols=76  Identities=18%  Similarity=0.209  Sum_probs=70.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ..+++.+++..+++++|+++|++||.|..+.++.+ .++.++|+|||+|.+.++|.+|+..|||.+++|++|.|+++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            35788889999999999999999999999999876 57889999999999999999999999999999999999985

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=3.7e-20  Score=104.31  Aligned_cols=77  Identities=17%  Similarity=0.455  Sum_probs=66.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-----EEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARV-----LYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVS  141 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~-----~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~  141 (148)
                      ++|||+|||+++++++|+++|++||.+..+.+     ..+..++.++|||||+|.+.++|+.|++ |||..++|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            47999999999999999999999998665543     2344566788999999999999999986 99999999999997


Q ss_pred             ecc
Q 032044          142 LAQ  144 (148)
Q Consensus       142 ~~~  144 (148)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            644

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.1e-16  Score=91.25  Aligned_cols=81  Identities=15%  Similarity=0.290  Sum_probs=68.7

Q ss_pred             CCCcceEEEcCC--CCCC---------CHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCc
Q 032044           63 AETDFKLFVGNL--SWSV---------TTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGV  131 (148)
Q Consensus        63 ~~~~~~l~i~nl--p~~~---------~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~  131 (148)
                      ...+++|+|.|+  |.++         .+++|++.|++||.|..+.+..+    .++|+|||+|.+.++|.+|+..|||.
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCc
Confidence            446779999999  5432         12689999999999999987644    35789999999999999999999999


Q ss_pred             eeCCeEEEEEeccCCC
Q 032044          132 ELEGRAMRVSLAQGRR  147 (148)
Q Consensus       132 ~i~g~~l~v~~~~~~~  147 (148)
                      .++|+.|.|.+..++.
T Consensus        81 ~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          81 WFGGRQITAQAWDGTT   96 (99)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCEEEEEEEeCCcC
Confidence            9999999999987764

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=2e-16  Score=90.35  Aligned_cols=65  Identities=28%  Similarity=0.358  Sum_probs=57.1

Q ss_pred             CCCcceEEEcC--CCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCcee
Q 032044           63 AETDFKLFVGN--LSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVEL  133 (148)
Q Consensus        63 ~~~~~~l~i~n--lp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i  133 (148)
                      ..+..+++|.|  ||.++++++|+++|++||.|..+.+..+      +++|||+|.+.++|..|+..|||..+
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            34556788855  9999999999999999999999877643      56999999999999999999999987

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=6.7e-16  Score=97.29  Aligned_cols=81  Identities=36%  Similarity=0.619  Sum_probs=73.0

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      ..++|||+|||+++++++|+++|++||.|..+.++.+..++.++|+|||+|.+.++|+.|+. +++..++++.+.+....
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhh
Confidence            34799999999999999999999999999999999998999999999999999999999998 67777888888887654


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      ++
T Consensus        84 ~~   85 (183)
T d1u1qa_          84 SR   85 (183)
T ss_dssp             CT
T ss_pred             hc
Confidence            43

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=4.8e-16  Score=85.06  Aligned_cols=73  Identities=16%  Similarity=0.235  Sum_probs=61.5

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCe-EEEEEecc
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGR-AMRVSLAQ  144 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~-~l~v~~~~  144 (148)
                      .+-|+|.|+|++.+++ +.++|++||.|.++.+.      ..+++|||+|.++++|++|++ +||..++|+ .|.|.++.
T Consensus         4 ~~wV~V~G~p~~~~~~-il~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASY-ILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHH-HHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHH-HHHHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            4569999999998865 55689999999998764      236799999999999999996 999999997 56798886


Q ss_pred             CC
Q 032044          145 GR  146 (148)
Q Consensus       145 ~~  146 (148)
                      .+
T Consensus        76 ~k   77 (81)
T d1wwha1          76 DK   77 (81)
T ss_dssp             CH
T ss_pred             Ch
Confidence            54

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=3.6e-16  Score=89.85  Aligned_cols=81  Identities=16%  Similarity=0.213  Sum_probs=68.2

Q ss_pred             CcceEEEcCC--CCCCC--------HHHHHHHHhhcCCeeEEEEEEcCCCC--CceeEEEEEecCHHHHHHHHHHhCCce
Q 032044           65 TDFKLFVGNL--SWSVT--------TESLTQAFQEYGNVVGARVLYDGESG--RSRGYGFVCYSTKAEMETALESLNGVE  132 (148)
Q Consensus        65 ~~~~l~i~nl--p~~~~--------~~~l~~~f~~~g~v~~~~~~~~~~~~--~~~~~~fv~f~~~~~a~~a~~~l~~~~  132 (148)
                      ++++|.|.|+  |..+.        .++|++.|++||.|..+.++++....  ...|++||+|.+.++|.+|+..|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            5678999999  44433        35799999999999999998765443  346899999999999999999999999


Q ss_pred             eCCeEEEEEeccC
Q 032044          133 LEGRAMRVSLAQG  145 (148)
Q Consensus       133 i~g~~l~v~~~~~  145 (148)
                      ++|+.|.+.+...
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999764

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=5.5e-16  Score=90.35  Aligned_cols=72  Identities=19%  Similarity=0.206  Sum_probs=61.4

Q ss_pred             cceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCH-HHHHHHHHHhCCceeCCeEEEEEec
Q 032044           66 DFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTK-AEMETALESLNGVELEGRAMRVSLA  143 (148)
Q Consensus        66 ~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~-~~a~~a~~~l~~~~i~g~~l~v~~~  143 (148)
                      ...+||+|||+++|+++|+++|++||.|.++.++.+      +++|||.|.++ ++|..|+..+++..+.++.+.|.+.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            345689999999999999999999999999998743      67999999885 7899999999998887766555554

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=3.5e-15  Score=81.71  Aligned_cols=53  Identities=23%  Similarity=0.365  Sum_probs=50.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|.+|+|++++.+|+++|||||+|.+.++|..|++.|++..+.|++|.|.|+.
T Consensus        26 ~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1          26 PILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             CEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            37899999999999999999999999999999999999999999999999985

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.56  E-value=3.4e-15  Score=83.21  Aligned_cols=54  Identities=30%  Similarity=0.492  Sum_probs=51.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      .|++|++++++.+|+++|||||+|.+.++|+.|+..+++..+.|++|.|+|+..
T Consensus        33 ~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_          33 EIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV   86 (88)
T ss_dssp             CEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             CcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecC
Confidence            478999999999999999999999999999999999999999999999999854

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=4.8e-15  Score=82.78  Aligned_cols=56  Identities=36%  Similarity=0.640  Sum_probs=52.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|++|++++++.+|+++|||||+|.+.++|+.|+..+++..+.|++|.|.++.+.+
T Consensus        31 ~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~~   86 (89)
T d2cqba1          31 DITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR   86 (89)
T ss_dssp             CCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             eEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            47899999999999999999999999999999999999999999999999997554

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=7.5e-15  Score=82.13  Aligned_cols=55  Identities=31%  Similarity=0.549  Sum_probs=51.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .|.++++++++.+|.++|||||+|.+.++|..|++.|++..+.|++|.|+|+.+.
T Consensus        34 ~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~   88 (90)
T d2cq0a1          34 SISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS   88 (90)
T ss_dssp             CEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCC
T ss_pred             ccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCC
Confidence            4789999999999999999999999999999999999999999999999999754

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.55  E-value=5.7e-15  Score=81.24  Aligned_cols=54  Identities=26%  Similarity=0.450  Sum_probs=51.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      .|+++++++++.+|+++|||||+|.+.++|+.|++.|++..+.|++|.|.|+.+
T Consensus        28 ~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          28 PINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            478999999999999999999999999999999999999999999999999864

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=6.1e-15  Score=81.63  Aligned_cols=56  Identities=23%  Similarity=0.348  Sum_probs=52.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|+++++++|+.||+++|||||+|.++++|+.|+..+++..+.|++|.|.++....
T Consensus        27 ~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~   82 (85)
T d2u2fa_          27 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             CEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             ccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            47899999999999999999999999999999999999999999999999997544

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=6.6e-15  Score=82.83  Aligned_cols=56  Identities=27%  Similarity=0.411  Sum_probs=52.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.++++++++.+|.++|||||+|.+.++|+.|+..|++..+.|++|.|.++.+..
T Consensus        35 ~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          35 PVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   90 (93)
T ss_dssp             CEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             CccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            47899999999999999999999999999999999999999999999999997654

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=2.2e-14  Score=80.62  Aligned_cols=56  Identities=21%  Similarity=0.377  Sum_probs=52.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|++|++++++.+|.++|||||+|.+.++|..|+..|++..+.|++|.|.|+....
T Consensus        33 ~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~~~   88 (93)
T d1h2vz_          33 DIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK   88 (93)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCC
T ss_pred             CcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            47899999999999999999999999999999999999999999999999986544

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=2.6e-14  Score=81.27  Aligned_cols=58  Identities=34%  Similarity=0.425  Sum_probs=53.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .|.++++++++.+|+++|||||+|.+.++|+.|+..|++..+.|++|.|.++..+...
T Consensus        34 ~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~~   91 (99)
T d1whwa_          34 PLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             CEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTT
T ss_pred             CceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCcc
Confidence            4789999999999999999999999999999999999999999999999998876543

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=2.2e-14  Score=78.85  Aligned_cols=54  Identities=22%  Similarity=0.458  Sum_probs=50.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|+.|+..+++..+.|++|.|.|+.+
T Consensus        28 ~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          28 EIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            478999999999999999999999999999999999999999999999999864

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=2.7e-14  Score=81.62  Aligned_cols=57  Identities=21%  Similarity=0.331  Sum_probs=52.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|.++++++++.+|+++|||||+|.+.++|+.|+..|++..+.|++|.|+|+.++..
T Consensus        44 ~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~~  100 (102)
T d2cpza1          44 NVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  100 (102)
T ss_dssp             CCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             cccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCCCC
Confidence            367899999999999999999999999999999999999999999999999876654

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=5.2e-14  Score=77.47  Aligned_cols=55  Identities=25%  Similarity=0.555  Sum_probs=49.4

Q ss_pred             cce-eEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            2 LSK-LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         2 i~~-i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      |.+ +++++++.+|+++|||||+|.+.++|+.|++.+++..+.|++|.|.++.++.
T Consensus        25 i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1          25 ILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             BSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             eeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            434 4788999999999999999999999999999999999999999999987543

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=3e-14  Score=81.74  Aligned_cols=55  Identities=35%  Similarity=0.681  Sum_probs=51.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      +|.+|++++++.+|+++|||||+|.+.++|..|++.|++..+.|++|.|.++...
T Consensus        34 ~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_          34 PVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             CCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             cccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            4789999999999999999999999999999999999999999999999998654

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.48  E-value=8.5e-14  Score=83.88  Aligned_cols=57  Identities=26%  Similarity=0.497  Sum_probs=52.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      +|++|++++++.||+++|||||+|.+.++|..|++.|++..|.|++|.|.++.....
T Consensus        68 ~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~~  124 (139)
T d1u6fa1          68 PIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ  124 (139)
T ss_dssp             CEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCC
T ss_pred             cccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            478999999999999999999999999999999999999999999999999865543

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=8e-14  Score=75.79  Aligned_cols=52  Identities=31%  Similarity=0.438  Sum_probs=48.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|.++++.+++ +|+++|||||+|.+.++|+.|++.+|+..++|++|.|+++.
T Consensus        26 ~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_          26 TLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             CEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            47899999996 89999999999999999999999999999999999999874

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.47  E-value=5.8e-14  Score=77.61  Aligned_cols=52  Identities=31%  Similarity=0.455  Sum_probs=48.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecC--cEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG--RILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~--~~i~v~~~   52 (148)
                      +|.++++++++.+|+++|||||+|.+.++|.+|++.+++..+.|  ++|.|.|+
T Consensus        32 ~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          32 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            47899999999999999999999999999999999999999876  88999875

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=9e-14  Score=78.24  Aligned_cols=56  Identities=27%  Similarity=0.435  Sum_probs=50.3

Q ss_pred             CcceeEeeecCC-CCCcccEEEEEeCCHHHHHHHHHHh-CCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRE-TGRSRGFAFVTMSTVEDCNAVIENL-DGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~-~~~~~g~afv~f~~~~~a~~a~~~l-~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.++++++++. +|+++|||||+|.+.++|.+|+..| ++..+.|++|.|.|+....
T Consensus        34 ~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~~   91 (94)
T d2cpha1          34 ELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV   91 (94)
T ss_dssp             CEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCC
T ss_pred             CceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCCC
Confidence            478899998854 7999999999999999999999988 8999999999999997654

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.45  E-value=9.2e-14  Score=76.11  Aligned_cols=53  Identities=25%  Similarity=0.339  Sum_probs=42.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      |.++.++++..+|+++|||||+|.+.++|++|++.|++..+.|++|.|.++.+
T Consensus        28 v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          28 VALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             EEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            56778888888999999999999999999999999999999999999999864

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=9.8e-14  Score=76.66  Aligned_cols=52  Identities=27%  Similarity=0.484  Sum_probs=47.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecC--cEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG--RILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~--~~i~v~~~   52 (148)
                      +|+++++++++.+|+++|||||+|.+.++|+.|++.||+..+.|  ++|.|.|+
T Consensus        32 ~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          32 RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            47899999999999999999999999999999999999999987  55888875

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=1e-13  Score=77.47  Aligned_cols=57  Identities=37%  Similarity=0.648  Sum_probs=52.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      +|.++.+++++.+|.++|||||+|.+.++|+.|+..|++..+.|++|.|+++.+...
T Consensus        31 ~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~~~   87 (90)
T d1x5sa1          31 QISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   87 (90)
T ss_dssp             CCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             cccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            478899999999999999999999999999999999999999999999999866544

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=1.3e-13  Score=75.90  Aligned_cols=49  Identities=39%  Similarity=0.708  Sum_probs=46.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEE
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRV   49 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v   49 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|..|+..+++..+.|++|.|
T Consensus        35 ~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          35 PIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4789999999999999999999999999999999999999999999986

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.44  E-value=5e-14  Score=76.35  Aligned_cols=51  Identities=25%  Similarity=0.353  Sum_probs=47.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      +|+++++++|+.||+++|||||+|.+.++|++|++ +++..++|++|.|..+
T Consensus        26 ~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          26 EVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            47899999999999999999999999999999997 7999999999999865

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=2.7e-13  Score=75.53  Aligned_cols=55  Identities=24%  Similarity=0.334  Sum_probs=49.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|.+|+|++|+.+|+++|||||+|.+.++|++|++  +...+.|+.|.|.++.+++.
T Consensus        34 ~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~--~~~~l~Gr~i~v~~a~~k~~   88 (90)
T d2cqga1          34 EVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPNSKQS   88 (90)
T ss_dssp             CEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECCCTTCC
T ss_pred             ccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh--cCCccCCEEeEEEeCCCCCC
Confidence            47899999999999999999999999999999998  44588999999999876543

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.43  E-value=1.8e-13  Score=75.55  Aligned_cols=54  Identities=24%  Similarity=0.412  Sum_probs=48.8

Q ss_pred             CcceeEeeecCCCC---CcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            1 MLSKLTVLYDRETG---RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         1 ~i~~i~~~~~~~~~---~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      .|+++++++++.++   .++|||||+|.+.++|++|++.+++..++|++|.|+++..
T Consensus        24 ~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1          24 AIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             CEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            47899999987765   5789999999999999999999999999999999999854

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=8.8e-14  Score=79.22  Aligned_cols=52  Identities=27%  Similarity=0.494  Sum_probs=48.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|.+|++++++.+|+++|||||+|.+.++|++|+. +++..+.|++|.|.++.
T Consensus        44 ~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          44 KVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             CEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             eEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            47899999999999999999999999999999996 99999999999999864

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=2.8e-13  Score=77.44  Aligned_cols=55  Identities=29%  Similarity=0.414  Sum_probs=49.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|+++++++++.+|+++|||||+|.+.++|+.|++.+++ .+.|++|.|.++....
T Consensus        36 ~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~~~   90 (103)
T d2cqda1          36 DIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGA   90 (103)
T ss_dssp             CEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTTC
T ss_pred             cccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCCCC
Confidence            478999999999999999999999999999999997765 7999999999986543

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.40  E-value=6.2e-13  Score=73.16  Aligned_cols=52  Identities=35%  Similarity=0.503  Sum_probs=47.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      +|.++++++|+.+|+++|||||+|.+.++|++|+. +++..+.|+.|.|..+.
T Consensus        32 ~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          32 TLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             cccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            47899999999999999999999999999999997 68999999999998763

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=1e-12  Score=73.25  Aligned_cols=55  Identities=20%  Similarity=0.467  Sum_probs=48.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .|.+|++++++.+  .+|||||+|.+.++|..|+..+++..+.|++|.|.|+.++..
T Consensus        34 ~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~   88 (90)
T d2cqia1          34 PCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS   88 (90)
T ss_dssp             CEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTC
T ss_pred             CceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            3788999998755  489999999999999999999999999999999999976543

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=2.9e-13  Score=72.93  Aligned_cols=50  Identities=28%  Similarity=0.452  Sum_probs=46.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEee
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF   51 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~   51 (148)
                      .|.++++++++.+|+++|||||+|.+.++|++|+. +++..+.|+.|.|..
T Consensus        25 ~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_          25 EVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             cccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            47899999999999999999999999999999997 788999999998864

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=3.5e-13  Score=77.05  Aligned_cols=51  Identities=18%  Similarity=0.297  Sum_probs=47.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      .|++|+|+++ .+|+++|||||+|.+.++|.+|+..|+|..+.|++|.|+++
T Consensus        53 ~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          53 EVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             CEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             CEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4789999877 58999999999999999999999999999999999999986

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.37  E-value=5.5e-13  Score=73.72  Aligned_cols=54  Identities=15%  Similarity=0.279  Sum_probs=45.6

Q ss_pred             CcceeEeeec-CCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYD-RETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~-~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .|++|++.++ +.+|+++|||||+|.+.++|..|++ +++..+.|++|.|.++.++
T Consensus        31 ~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a~~k   85 (86)
T d2ghpa3          31 SIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADKK   85 (86)
T ss_dssp             CEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEECCCC
T ss_pred             hccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEcCCC
Confidence            4788998774 5689999999999999999999996 9999999999999998653

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=1e-12  Score=74.97  Aligned_cols=55  Identities=27%  Similarity=0.429  Sum_probs=50.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.++.|++++.++.++|||||+|.+.++|+.|+. +++..|.|+.|.|.++.++.
T Consensus        46 ~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~ke  100 (103)
T d1x4ba1          46 KLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVARE  100 (103)
T ss_dssp             CCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSCC
T ss_pred             cccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcccC
Confidence            47899999999999999999999999999999996 79999999999999887554

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=1.4e-12  Score=74.20  Aligned_cols=55  Identities=29%  Similarity=0.559  Sum_probs=49.7

Q ss_pred             ceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            3 SKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         3 ~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      ..+.+.+++.+|+++|||||+|.+.++|..|+..+++..+.|++|.|.++....+
T Consensus        44 ~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          44 PMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP   98 (101)
T ss_dssp             BSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCC
T ss_pred             ceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            3567788888999999999999999999999999999999999999999876543

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=5.2e-13  Score=76.20  Aligned_cols=56  Identities=27%  Similarity=0.426  Sum_probs=51.2

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      |.++.++.+..+|.++|||||+|.+.++|..|+..|++..+.|++|.|.|+.+++.
T Consensus        45 v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~~  100 (102)
T d2cpxa1          45 KKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ  100 (102)
T ss_dssp             SSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             eeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCccc
Confidence            56788888888999999999999999999999999999999999999999976543

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=7.6e-13  Score=73.62  Aligned_cols=54  Identities=26%  Similarity=0.345  Sum_probs=48.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.+++++.++.  .++|||||+|.+.++|++|+..|++..+.|++|.|.++.+++
T Consensus        34 ~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2          34 NILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             CEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            377899999863  478999999999999999999999999999999999987654

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=3.6e-12  Score=71.40  Aligned_cols=54  Identities=26%  Similarity=0.471  Sum_probs=48.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.+|++++++.  .++|||||+|.+.++|..|+..+++..+.|++|.|+++.++.
T Consensus        37 ~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~   90 (93)
T d2cq3a1          37 KILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV   90 (93)
T ss_dssp             CEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             eeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCC
Confidence            478899999864  479999999999999999999999999999999999997653

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=4.9e-13  Score=71.94  Aligned_cols=50  Identities=18%  Similarity=0.294  Sum_probs=45.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEee
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNF   51 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~   51 (148)
                      .|.++++++++.+|+++|||||+|.+.++|++|++ .++..++|+.+.|+.
T Consensus        25 ~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~   74 (75)
T d1x0fa1          25 EVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKV   74 (75)
T ss_dssp             CEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEEC
T ss_pred             CcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEE
Confidence            47899999999999999999999999999999997 577789999988875

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.31  E-value=3.4e-12  Score=70.88  Aligned_cols=50  Identities=22%  Similarity=0.241  Sum_probs=44.7

Q ss_pred             CcceeEeeecCCCCCc---ccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEe
Q 032044            1 MLSKLTVLYDRETGRS---RGFAFVTMSTVEDCNAVIENLDGREYLGRILRVN   50 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~---~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~   50 (148)
                      +|++|.+++++.++.+   +|||||+|.+.++|.+|++.|||..+.|++|++.
T Consensus        37 ~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          37 KIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             CEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            4789999999877654   4899999999999999999999999999999873

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.29  E-value=6.4e-12  Score=71.00  Aligned_cols=56  Identities=25%  Similarity=0.363  Sum_probs=49.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhC------CCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLD------GREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~------~~~~~~~~i~v~~~~~~~   56 (148)
                      .|.++.++.++.++.++|||||+|.+.++|..|+..++      +..+.|++|.|.++.++.
T Consensus        34 ~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          34 DLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD   95 (98)
T ss_dssp             CEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCC
T ss_pred             cceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCCC
Confidence            36789999999999999999999999999999999876      567889999999987543

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.29  E-value=2.6e-12  Score=69.11  Aligned_cols=51  Identities=24%  Similarity=0.441  Sum_probs=47.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      +|.++.+++++.+|.++|||||+|.+.++|+.|++ +++..+.|++|.|+++
T Consensus        25 ~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          25 KVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            46788999999999999999999999999999997 9999999999999864

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.28  E-value=6.1e-12  Score=68.31  Aligned_cols=51  Identities=24%  Similarity=0.422  Sum_probs=46.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      .|.+++++.++.++.++|||||+|.+.++|++|+. +++..+.|++|.|+.+
T Consensus        28 ~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          28 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             cccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            36789999999999999999999999999999996 8999999999999865

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=8.9e-12  Score=70.16  Aligned_cols=57  Identities=18%  Similarity=0.262  Sum_probs=48.0

Q ss_pred             cceeEeeecCC-CCCcccEEEEEeCCHHHHHHHHHHhCC--CeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRE-TGRSRGFAFVTMSTVEDCNAVIENLDG--REYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~-~~~~~g~afv~f~~~~~a~~a~~~l~~--~~~~~~~i~v~~~~~~~~~   58 (148)
                      |+++.++++.. +|+++|||||+|.+.++|..|+..|++  ..+.|++|.|.|+.+....
T Consensus        29 i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~~~   88 (96)
T d2disa1          29 VLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDV   88 (96)
T ss_dssp             EEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCST
T ss_pred             ceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCCCC
Confidence            67889998854 689999999999999999999998864  4567999999999765543

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.25  E-value=1.9e-12  Score=72.24  Aligned_cols=51  Identities=25%  Similarity=0.457  Sum_probs=45.5

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      |.+++++.+ .+|+++|||||+|.+.++|++|++ +++..++|++|.|.++..
T Consensus        40 i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          40 KNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             HHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             EEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            566777765 589999999999999999999996 999999999999998864

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=1.4e-11  Score=69.57  Aligned_cols=49  Identities=31%  Similarity=0.577  Sum_probs=42.4

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |.+|++        ++|||||+|.+.++|++|+..|++..+.|++|.|+++..+...
T Consensus        43 i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~~   91 (98)
T d1wf2a_          43 IVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVN   91 (98)
T ss_dssp             EEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCCCC
T ss_pred             EEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            556665        4689999999999999999999999999999999999765443

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=8.6e-12  Score=68.61  Aligned_cols=51  Identities=20%  Similarity=0.324  Sum_probs=46.0

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|.+|++++++ +|+++|||||+|.+.++|++|++ +++..+.|++|.|.+..
T Consensus        32 ~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2          32 QVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             CEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             ccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            37789998885 89999999999999999999996 79999999999998753

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=1.7e-11  Score=70.59  Aligned_cols=51  Identities=18%  Similarity=0.469  Sum_probs=45.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      +|++|++++++     +|||||+|.+.++|.+|++.+++..+.|++|.|.|+....
T Consensus        29 ~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1          29 DVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             ccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            47889998874     6899999999999999999999999999999999986543

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.23  E-value=1e-11  Score=68.52  Aligned_cols=47  Identities=21%  Similarity=0.414  Sum_probs=41.4

Q ss_pred             eEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            5 LTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         5 i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      +.+..+ .+|+++|+|||+|.+.++|+.|+..+++..+.|++|+|.++
T Consensus        40 ~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          40 VCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             EEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            344444 68999999999999999999999999999999999999763

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.21  E-value=2.1e-11  Score=68.53  Aligned_cols=49  Identities=20%  Similarity=0.491  Sum_probs=43.9

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      .|++|+++++      +|||||+|.+.++|..|+..|++..+.|++|+|.|+.+.
T Consensus        44 ~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          44 QIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             CEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            3678888865      589999999999999999999999999999999998653

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.20  E-value=2.4e-12  Score=68.72  Aligned_cols=47  Identities=13%  Similarity=0.359  Sum_probs=43.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEE
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRIL   47 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i   47 (148)
                      .|.++++++++.++.++|||||+|.+.++|+.|+..|||..+.|+.+
T Consensus        24 ~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1          24 KIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             CEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             cccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            36789999999999999999999999999999999999999988765

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=1.6e-11  Score=69.78  Aligned_cols=55  Identities=20%  Similarity=0.211  Sum_probs=48.2

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      +.++.++++. +|+++|||||+|.+.++|++|++ +++..|.|+.|.|.++......
T Consensus        41 ~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~~~~   95 (102)
T d1weza_          41 PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTS   95 (102)
T ss_dssp             CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCCC
T ss_pred             cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCCCCCC
Confidence            4578888885 78999999999999999999996 8999999999999998766543

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=3.3e-11  Score=69.89  Aligned_cols=76  Identities=21%  Similarity=0.278  Sum_probs=57.4

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCCCCCCCCCcceEEEcCCCCCCCH
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPKLPLYAETDFKLFVGNLSWSVTT   80 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~i~nlp~~~~~   80 (148)
                      +|++|++..   ++.++|||||+|.+.++|..|+..|+|..+.|++|.|.++.......             .......+
T Consensus        33 ~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~~~-------------~~~~~~~~   96 (114)
T d2f9da1          33 PIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQ-------------KMDTKKKE   96 (114)
T ss_dssp             CEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHHHTT-------------TSCHHHHH
T ss_pred             CeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCchhh-------------hhHHHHHH
Confidence            467777765   45678999999999999999999999999999999999975432211             11222345


Q ss_pred             HHHHHHHhhcCC
Q 032044           81 ESLTQAFQEYGN   92 (148)
Q Consensus        81 ~~l~~~f~~~g~   92 (148)
                      +++..+.+++|.
T Consensus        97 ~~~~~~~~~~g~  108 (114)
T d2f9da1          97 EQLKLLKEKYGI  108 (114)
T ss_dssp             HHHHHHHHHHCC
T ss_pred             HHHHHHHHHhCC
Confidence            677788888874

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.18  E-value=4e-11  Score=68.37  Aligned_cols=56  Identities=16%  Similarity=0.382  Sum_probs=46.9

Q ss_pred             cceeEeeecC-CCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            2 LSKLTVLYDR-ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         2 i~~i~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      |.++.++.++ .+++++|||||+|.+.++|++|+. +++..+.|++|.|.++.+....
T Consensus        41 ~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~a~~~~~~   97 (104)
T d1wi8a_          41 ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEECCCCCCC
T ss_pred             cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEECCCCCCC
Confidence            4567777765 478999999999999999987775 9999999999999998766543

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.18  E-value=7.4e-12  Score=69.78  Aligned_cols=51  Identities=18%  Similarity=0.417  Sum_probs=44.0

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      |.+|++.   .+++++|||||+|.+.++|..|+..+++..+.|++|.|.|+..+
T Consensus        34 i~~i~~~---~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~~   84 (91)
T d1nu4a_          34 ILDILVS---RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD   84 (91)
T ss_dssp             EEEEECC---HHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSC
T ss_pred             ccceEEe---eeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCCC
Confidence            4555553   35678999999999999999999999999999999999998654

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.18  E-value=7.8e-12  Score=71.03  Aligned_cols=52  Identities=27%  Similarity=0.411  Sum_probs=46.1

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|.++.++.+. ++.++|||||+|.+.++|++|++.|||..+.|+++.+.++.
T Consensus        44 ~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          44 QVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             cccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            36778888884 88999999999999999999999999999999998887654

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.13  E-value=7e-11  Score=63.98  Aligned_cols=48  Identities=27%  Similarity=0.414  Sum_probs=42.1

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      |.+|++.+      .+|||||+|.+.++|..|+..+++..+.|++|.|.|+.++
T Consensus        30 I~~v~~~~------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1          30 IIDLSMDP------PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CSCEEEET------TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             cceeeecc------CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            66777654      4589999999999999999999999999999999999654

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.12  E-value=1.2e-10  Score=66.32  Aligned_cols=50  Identities=14%  Similarity=0.149  Sum_probs=43.4

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      |.++++++      ++|||||+|.+.++|.+|+..|++..+.|++|.|.|+.....
T Consensus        37 i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~   86 (104)
T d1weya_          37 DTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHI   86 (104)
T ss_dssp             SCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSSC
T ss_pred             ceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccCCC
Confidence            56676663      568999999999999999999999999999999999876544

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.12  E-value=9.1e-11  Score=66.86  Aligned_cols=55  Identities=20%  Similarity=0.181  Sum_probs=46.1

Q ss_pred             ceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044            3 SKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus         3 ~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      .+..++++..++.++|||||+|.++++|++|+. +++..|.++.|.|.++...+..
T Consensus        43 ~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~~~~~~   97 (104)
T d1wg5a_          43 PNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVR   97 (104)
T ss_dssp             EEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEECTTTSC
T ss_pred             eEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECCHHHhc
Confidence            344455565789999999999999999999996 8999999999999998766543

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.11  E-value=7e-11  Score=65.02  Aligned_cols=50  Identities=24%  Similarity=0.375  Sum_probs=44.3

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      +|.+|++.++      +|||||+|.+.++|+.|+..|++..+.|++|.|+|+....
T Consensus        34 ~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1          34 KAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            4678888755      5899999999999999999999999999999999987654

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=2e-10  Score=64.32  Aligned_cols=51  Identities=25%  Similarity=0.418  Sum_probs=42.9

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      |..+.+.   .++.++|||||+|.+.++|+.|++.|++..+.|++|.|+|+...
T Consensus        41 v~~~~~~---~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          41 IRDIDLK---NRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             EEEEEEC---CSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             eEEEEec---ccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            4445543   34567899999999999999999999999999999999998653

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.10  E-value=5.8e-11  Score=66.71  Aligned_cols=46  Identities=22%  Similarity=0.479  Sum_probs=42.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCC
Q 032044           12 ETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKP   57 (148)
Q Consensus        12 ~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~   57 (148)
                      .++.++|||||+|.+.++|+.|+..|++..+.|++|.|.|+.++..
T Consensus        48 ~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          48 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            4788999999999999999999999999999999999999976654

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.10  E-value=6.2e-11  Score=63.53  Aligned_cols=43  Identities=26%  Similarity=0.346  Sum_probs=39.3

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044           13 TGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus        13 ~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      +++++|||||+|.+.++|++|+..||+..+.|++|.|+++...
T Consensus        29 ~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1          29 VDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             ecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            4568899999999999999999999999999999999998543

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.09  E-value=5.7e-11  Score=64.48  Aligned_cols=43  Identities=33%  Similarity=0.499  Sum_probs=38.3

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCC-eecCcEEEEeecCCCCC
Q 032044           15 RSRGFAFVTMSTVEDCNAVIENLDGR-EYLGRILRVNFSDKPKP   57 (148)
Q Consensus        15 ~~~g~afv~f~~~~~a~~a~~~l~~~-~~~~~~i~v~~~~~~~~   57 (148)
                      .++|||||+|.+.++|+.|++.++|. .+.|++|.|+|+.+++.
T Consensus        35 ~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1          35 LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             cccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            45799999999999999999999985 69999999999986553

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.08  E-value=2.3e-10  Score=64.54  Aligned_cols=51  Identities=27%  Similarity=0.393  Sum_probs=43.7

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKP   55 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~   55 (148)
                      +|.+|++..+    ..+|+|||+|.+.++|..|+..|+|..+.|++|.|.++...
T Consensus        45 ~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          45 QIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGT   95 (99)
T ss_dssp             CCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSC
T ss_pred             cEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCc
Confidence            3667766554    36799999999999999999999999999999999998644

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.08  E-value=7.1e-11  Score=67.20  Aligned_cols=51  Identities=18%  Similarity=0.191  Sum_probs=43.1

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      |..+.++....+|+++|||||+|.+.++|+.|+. +++..|.|++|.|.++.
T Consensus        35 i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1          35 DENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             EEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            3344445555699999999999999999999996 89999999999998764

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.07  E-value=1.5e-10  Score=63.93  Aligned_cols=43  Identities=23%  Similarity=0.325  Sum_probs=39.3

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044           14 GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus        14 ~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      +.++|||||+|.+.++|+.|+..|++..+.|++|.|+++....
T Consensus        37 ~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_          37 DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            4678999999999999999999999999999999999986544

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.07  E-value=1.4e-10  Score=63.79  Aligned_cols=43  Identities=26%  Similarity=0.441  Sum_probs=38.9

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044           14 GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus        14 ~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      ++++|||||+|.+.++|..|+..|++..+.|++|.|.|+.++.
T Consensus        41 ~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1          41 KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            3567999999999999999999999999999999999987543

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=2.1e-10  Score=65.78  Aligned_cols=54  Identities=17%  Similarity=0.198  Sum_probs=45.8

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCee--cCcEEEEeecCCCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREY--LGRILRVNFSDKPKPK   58 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~--~~~~i~v~~~~~~~~~   58 (148)
                      .|++|.+++++    ++|||||+|.+.++|+.|+..|++..+  .+.++.+.|+......
T Consensus        33 ~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~~~   88 (108)
T d2adba1          33 TVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLN   88 (108)
T ss_dssp             CEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCSCC
T ss_pred             cEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCcccc
Confidence            47788898875    579999999999999999999999988  5788999998765443

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.04  E-value=3.8e-10  Score=60.34  Aligned_cols=49  Identities=12%  Similarity=0.036  Sum_probs=42.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      .|+++++++++..  .++||||+|.++++|++|+. +++..++|++|.|...
T Consensus        26 ~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          26 PIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             ceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            4788999998643  45799999999999999996 8999999999999854

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.04  E-value=2e-10  Score=62.67  Aligned_cols=47  Identities=21%  Similarity=0.392  Sum_probs=40.8

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeec-CcEEEEeecC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL-GRILRVNFSD   53 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~-~~~i~v~~~~   53 (148)
                      |++++++++     .+|||||+|.+.++|..|+..|+|..+. |++|.|.|+.
T Consensus        35 i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          35 FKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             EEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             EEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            677888755     3689999999999999999999999884 6899999985

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.02  E-value=3.4e-10  Score=65.11  Aligned_cols=49  Identities=10%  Similarity=0.063  Sum_probs=41.7

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      |.+|.|.      .++|||||+|.+.++|++|+..||+..|.|++|.|+|+....
T Consensus        37 I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_          37 LGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             ccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            5566553      357999999999999999999999999999999999985543

>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=98.99  E-value=4.4e-10  Score=63.93  Aligned_cols=53  Identities=21%  Similarity=0.483  Sum_probs=46.5

Q ss_pred             CcceeEeeecCCCC--CcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            1 MLSKLTVLYDRETG--RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         1 ~i~~i~~~~~~~~~--~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .|++|.|.+++.+.  ...|++||+|.+.++|.+|+..|+|..+.|++|.+.+..
T Consensus        40 ~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~   94 (104)
T d1o0pa_          40 LVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   94 (104)
T ss_dssp             CEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEEC
T ss_pred             ceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcC
Confidence            47889998876543  456899999999999999999999999999999999875

>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=98.98  E-value=6.2e-10  Score=61.36  Aligned_cols=41  Identities=27%  Similarity=0.474  Sum_probs=36.7

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCCee-cCcEEEEeecCC
Q 032044           14 GRSRGFAFVTMSTVEDCNAVIENLDGREY-LGRILRVNFSDK   54 (148)
Q Consensus        14 ~~~~g~afv~f~~~~~a~~a~~~l~~~~~-~~~~i~v~~~~~   54 (148)
                      ++++|||||+|.+.++|.+|+..|++..+ .|++|.|.|+..
T Consensus        45 ~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2          45 QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            34678999999999999999999999988 589999999864

>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=98.93  E-value=2.8e-10  Score=65.61  Aligned_cols=49  Identities=16%  Similarity=0.173  Sum_probs=42.3

Q ss_pred             eeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            4 KLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         4 ~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .+.++.+..+|.++|||||+|.+.++|++|+. +++..|+|+.|.|.++.
T Consensus        47 ~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          47 DSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             TTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             cceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            33455555799999999999999999999996 99999999999998764

>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=98.92  E-value=2.3e-10  Score=62.99  Aligned_cols=46  Identities=17%  Similarity=0.221  Sum_probs=39.3

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDK   54 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~   54 (148)
                      |.+++++++       |||||+|.+.++|+.|+..|++..+.|+.+.+.+...
T Consensus        27 v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1          27 VCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             EEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             ccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            566666543       8999999999999999999999999999998887643

>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=98.88  E-value=4.6e-09  Score=59.59  Aligned_cols=53  Identities=11%  Similarity=0.146  Sum_probs=42.4

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHh--CCCeecCcEEEEeecCCCCCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENL--DGREYLGRILRVNFSDKPKPKLP   60 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l--~~~~~~~~~i~v~~~~~~~~~~~   60 (148)
                      |+++++.+      .+|+|||+|.+.++|+.|+..+  ++..+.|++|.|.|+...+...+
T Consensus        42 I~~~~~~~------~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~~~~~   96 (104)
T d1wexa_          42 ICYVMMMP------FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRP   96 (104)
T ss_dssp             EEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCCCS
T ss_pred             ceEEEEEe------cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCccCCC
Confidence            56676654      4589999999999999999877  55678899999999976654443

>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=98.85  E-value=2.8e-09  Score=59.91  Aligned_cols=50  Identities=26%  Similarity=0.396  Sum_probs=42.2

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHH--HhCCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIE--NLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~--~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      +|.++.++++      +|||||+|.+.++|..|+.  .+++..+.|++|.|.++...+
T Consensus        45 ~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~~   96 (99)
T d1x4fa1          45 KIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK   96 (99)
T ss_dssp             CCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCS
T ss_pred             ceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCcc
Confidence            3677777754      4899999999999999997  478889999999999997554

>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=98.85  E-value=1.2e-09  Score=61.44  Aligned_cols=48  Identities=15%  Similarity=0.178  Sum_probs=40.7

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~   56 (148)
                      |+++++.       .+|||||+|.+.++|++|++.||+..+.|+.|.+.+.....
T Consensus        42 v~~~~i~-------~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          42 VCYADVQ-------KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             EEEEEEE-------TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             ccccccc-------ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            5566654       34899999999999999999999999999999999875433

>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=98.85  E-value=3.5e-09  Score=59.32  Aligned_cols=48  Identities=21%  Similarity=0.427  Sum_probs=40.6

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecC--cEEEEeecCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLG--RILRVNFSDKP   55 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~--~~i~v~~~~~~   55 (148)
                      |+++++.++      ++||||+|.+.++|..|+..|++..+.|  ++|+|.|+...
T Consensus        44 i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          44 IRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             EEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             cceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            566776654      5799999999999999999999999976  57999998754

>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=98.84  E-value=7.6e-09  Score=56.85  Aligned_cols=49  Identities=12%  Similarity=0.268  Sum_probs=40.7

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHh--CCCeecCcEEEEeecCCCC
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENL--DGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l--~~~~~~~~~i~v~~~~~~~   56 (148)
                      |.+++++.+      +|||||+|.+.++|..|+..+  ++..+.|++|.|.|+..+.
T Consensus        35 i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          35 VTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   85 (88)
T ss_dssp             EEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             ccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCCC
Confidence            566776644      479999999999999999864  6778999999999997654

>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=98.80  E-value=1.9e-10  Score=63.78  Aligned_cols=46  Identities=17%  Similarity=0.452  Sum_probs=39.9

Q ss_pred             eeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044            7 VLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus         7 ~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      .+.+..+++++|||||+|.+.++|+.|+. |++..+.|+.|.|..+.
T Consensus        38 ~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~r~k   83 (90)
T d1u2fa_          38 PVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPH   83 (90)
T ss_dssp             SEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCBCTT
T ss_pred             eeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEECCCC
Confidence            34566678999999999999999999995 99999999999997543

>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=98.79  E-value=9e-09  Score=56.66  Aligned_cols=50  Identities=30%  Similarity=0.423  Sum_probs=41.6

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHh--CCCeecCcEEEEeecCCCC
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENL--DGREYLGRILRVNFSDKPK   56 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l--~~~~~~~~~i~v~~~~~~~   56 (148)
                      +|.+|.++.++      ++|||+|.+.++|..|+..+  ++..+.|++|.|.|+...+
T Consensus        35 ~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~~   86 (89)
T d1x4da1          35 VISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   86 (89)
T ss_dssp             CEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             CeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCcc
Confidence            46777777654      68999999999999999855  6778999999999987543

>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=98.75  E-value=5.3e-09  Score=57.49  Aligned_cols=43  Identities=16%  Similarity=0.202  Sum_probs=36.8

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecCCCCCC
Q 032044           14 GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSDKPKPK   58 (148)
Q Consensus        14 ~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~   58 (148)
                      +.++|||||+|.+.++|+.|+.  ++..+.|++|.|.++.++...
T Consensus        39 ~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~~   81 (88)
T d1wf0a_          39 KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCCC
T ss_pred             eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCCC
Confidence            3578999999999999999996  788899999999998765443

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.59  E-value=6.1e-08  Score=52.20  Aligned_cols=40  Identities=13%  Similarity=0.190  Sum_probs=34.0

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCCeecCcE-EEEeecCC
Q 032044           14 GRSRGFAFVTMSTVEDCNAVIENLDGREYLGRI-LRVNFSDK   54 (148)
Q Consensus        14 ~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~-i~v~~~~~   54 (148)
                      ++++|||||+|.++++|++|++ +||..++|+. +.|.+..+
T Consensus        36 ~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1          36 SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             cCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            3567999999999999999996 9999999975 56877654

>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=98.44  E-value=2.3e-07  Score=52.01  Aligned_cols=36  Identities=19%  Similarity=0.406  Sum_probs=30.0

Q ss_pred             cceeEeeecCCCCCcccEEEEEeCCHHHHHHHHHHhCCCeec
Q 032044            2 LSKLTVLYDRETGRSRGFAFVTMSTVEDCNAVIENLDGREYL   43 (148)
Q Consensus         2 i~~i~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~   43 (148)
                      |++|+++.+      +|||||+|.+.++|..|+..|+|..+.
T Consensus        47 i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          47 VDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             EEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             ccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            556666544      579999999999999999999999873

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.44  E-value=1.2e-06  Score=47.73  Aligned_cols=77  Identities=13%  Similarity=0.135  Sum_probs=61.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCc--eeEEEEEecCHHHHHHHHHHhCCceeCC-----eEEE
Q 032044           67 FKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRS--RGYGFVCYSTKAEMETALESLNGVELEG-----RAMR  139 (148)
Q Consensus        67 ~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~--~~~~fv~f~~~~~a~~a~~~l~~~~i~g-----~~l~  139 (148)
                      ++|.|+.||++++++++.+.+...|.+.......+..+..+  ..-|||.|.+.++.......++|+.+-+     .+..
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            47899999999999999999999998888777766444332  3568999999999999999999987732     2456


Q ss_pred             EEec
Q 032044          140 VSLA  143 (148)
Q Consensus       140 v~~~  143 (148)
                      |++|
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            6665

>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=98.37  E-value=4.6e-06  Score=42.54  Aligned_cols=61  Identities=21%  Similarity=0.226  Sum_probs=50.9

Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecc
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQ  144 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~  144 (148)
                      +-|.+.|.++|.|.++.+....+   ....|-|...+.++|+-|+..||-++|++++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d---g~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD---YQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS---TTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC---CcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            44567889999999998864422   23368899999999999999999999999999999875

>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=98.16  E-value=5e-06  Score=44.60  Aligned_cols=56  Identities=23%  Similarity=0.446  Sum_probs=48.6

Q ss_pred             HHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEeccC
Q 032044           81 ESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESLNGVELEGRAMRVSLAQG  145 (148)
Q Consensus        81 ~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~i~g~~l~v~~~~~  145 (148)
                      .+|.+.|..||.|.-+++..+        --.|+|.+-+.|..|++ ++|.+++|+.|.+....+
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~~   94 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPSS   94 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCCC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCCC
Confidence            467788899999988888744        47899999999999999 999999999999987543

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.06  E-value=1.2e-06  Score=50.00  Aligned_cols=46  Identities=4%  Similarity=0.032  Sum_probs=36.5

Q ss_pred             CcceeEeeecCCCCCcccEEEEEeCCH-HHHHHHHHHhCCCeecCcEEEEeec
Q 032044            1 MLSKLTVLYDRETGRSRGFAFVTMSTV-EDCNAVIENLDGREYLGRILRVNFS   52 (148)
Q Consensus         1 ~i~~i~~~~~~~~~~~~g~afv~f~~~-~~a~~a~~~l~~~~~~~~~i~v~~~   52 (148)
                      .|.+|+|+++      +|||||.|.++ ++|..|+..+++..+.++.+.+.+.
T Consensus        37 ~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          37 EIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             ChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            3678888754      58999999985 7899999999999887766666554

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.30  E-value=0.00098  Score=36.11  Aligned_cols=56  Identities=20%  Similarity=0.262  Sum_probs=45.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEEEcCCCCCceeEEEEEecCHHHHHHHHHHh
Q 032044           65 TDFKLFVGNLSWSVTTESLTQAFQEYGNVVGARVLYDGESGRSRGYGFVCYSTKAEMETALESL  128 (148)
Q Consensus        65 ~~~~l~i~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l  128 (148)
                      ....+|.-..|..+...||.++|++||.|.-..| -+  +     .|||...+.++++.+++.+
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd--T-----Sa~V~L~~~e~~~~v~~~~   69 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD--T-----SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET--T-----EEEEECSCHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC--c-----eEEEEecCHHHHHHHHHHh
Confidence            4457888999999999999999999998654333 22  1     5999999999999988754

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.28  E-value=0.014  Score=29.44  Aligned_cols=39  Identities=15%  Similarity=0.178  Sum_probs=35.3

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044           15 RSRGFAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus        15 ~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      ...-.|-|...+.++|..|+..|+...++++.|.|.++.
T Consensus        33 dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          33 DYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             STTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            345579999999999999999999999999999999874

>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=95.60  E-value=0.014  Score=30.98  Aligned_cols=34  Identities=21%  Similarity=0.382  Sum_probs=30.6

Q ss_pred             EEEEEeCCHHHHHHHHHHhCCCeecCcEEEEeecC
Q 032044           19 FAFVTMSTVEDCNAVIENLDGREYLGRILRVNFSD   53 (148)
Q Consensus        19 ~afv~f~~~~~a~~a~~~l~~~~~~~~~i~v~~~~   53 (148)
                      ...|.|.+.++|..|+. +++..+.|+.+.+....
T Consensus        60 ~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          60 QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCC
Confidence            38999999999999998 89999999999997543