Citrus Sinensis ID: 029166

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------20
Protein Sequence
MEKRRHCCERKGEREERTLLYKLCFHRNSSYCQFNIVFLLVLIGGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQVS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccHHHHHHHccccEEEcccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEccccEEEEEEccHHHHHHHHHHHcccEEccEEEEEEEcccccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHccHccccccHHHHHHHHHHHHcccccEccccccEEEEEcccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEcccccEEEEEccHHHHHHHHHHHcccEccccEEEEEEcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccc
Coil and Loop (DISEMBL)
mekrrhccerkgerEERTLLYKLCFhrnssycqFNIVFLLVLIGgyasngapgqgpqsegdssnttifvggldpnvtdedlrqpfsqygeiasvkipvgkgcgfvqfANRENAEEALHKLNgtvigkqsvrlswgrnpankqfradygnqwsgayyggqvydgygyaipppndpsMYAAAAAAYgaypvygshqqqvs
Flexible Loop (DISEMBL)
mekrrhccerkgereerTLLYKLCFHRNSSYCQFNIVFLLVLIGGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKlngtvigkqsvrlswgrnpaNKQFRADYGNQWSGAYYGGQVYDGYGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQVS
Low Complexity Region (SEG)
MEKRRHCCERKGEREERTLLYKLCFHRNSSYCQFNIVFLLVLIGGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSgayyggqvydgygyAIPPPNDPSMyaaaaaaygayPVYGSHQQQVS
Disordered region (IsUnstruct)
****************RTLLYKLCFHRNSSYCQFNIVFLLVLIGGYA*******************IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIPPPNDPSMYAAAAAAYGAYPVY********
Disordered Region (DISOPRED)
***RR****RKG******************************************************IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRL****************************************************GA************
Disordered Region (DISEMBL)
*************REERTLLYKLCFHRNSSYCQFNIVFLLVLIGGYASNG************SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIPPPNDPSMYAAAAAAYGAYPVY********
Disordered Region (DISPRO)
************EREERTLLYKLCFHRNSSYCQFNIVFLLVLIGG****************SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA********GNQWSGAYYGGQVYDGYGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQ****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEKRRHCCERKGEREERTLLYKLCFHRNSSYCQFNIVFLLVLIGGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQVS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	198	2.2.26 [Sep-21-2011]
Q9SX80	434	Polyadenylate-binding pro	yes	no	0.742	0.338	0.722	9e-57
Q9SX79	432	Polyadenylate-binding pro	no	no	0.742	0.340	0.709	9e-56
Q9LEB3	428	Polyadenylate-binding pro	N/A	no	0.757	0.350	0.635	8e-54
Q0WW84	435	Polyadenylate-binding pro	no	no	0.580	0.264	0.689	2e-43
F4I3B3	445	Polyadenylate-binding pro	no	no	0.712	0.316	0.602	1e-41
Q9LEB4	409	Polyadenylate-binding pro	N/A	no	0.686	0.332	0.528	1e-29
Q93W34	415	Polyadenylate-binding pro	no	no	0.606	0.289	0.548	3e-28
Q9FPJ8	387	Polyadenylate-binding pro	no	no	0.570	0.291	0.561	3e-28
Q9SAB3	405	Polyadenylate-binding pro	no	no	0.565	0.276	0.547	6e-27
Q8VXZ9	425	Polyadenylate-binding pro	no	no	0.691	0.322	0.478	2e-24

>sp|Q9SX80|R47CP_ARATH Polyadenylate-binding protein RBP47C' OS=Arabidopsis thaliana GN=RBP47C' PE=2 SV=1

 Score =  219 bits (558), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 112/155 (72%), Positives = 123/155 (79%), Gaps = 8/155 (5%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG 103
           GGY  +GA     +SEGD+ NTTIFVGGLD +VTDEDL+QPFS++GEI SVKIPVGKGCG
Sbjct: 288 GGYMPSGA---FTRSEGDTINTTIFVGGLDSSVTDEDLKQPFSEFGEIVSVKIPVGKGCG 344

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDG 163
           FVQF NR NAEEAL KLNGTVIGKQ+VRLSWGRNPANKQ R  YGNQW   YYGGQ Y+G
Sbjct: 345 FVQFVNRPNAEEALEKLNGTVIGKQTVRLSWGRNPANKQPRDKYGNQWVDPYYGGQFYNG 404

Query: 164 YGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQVS 198
           YGY +P P DP MY AA      YP+YG HQQQVS
Sbjct: 405 YGYMVPQP-DPRMYPAAP----YYPMYGGHQQQVS 434

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9SX79|RB47C_ARATH Polyadenylate-binding protein RBP47C OS=Arabidopsis thaliana GN=RBP47C PE=2 SV=1

 Score =  216 bits (549), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 110/155 (70%), Positives = 120/155 (77%), Gaps = 8/155 (5%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG 103
           GGY  NG   +    EGD  NTTIFVGGLD +VTDEDL+QPF+++GEI SVKIPVGKGCG
Sbjct: 286 GGYMPNGTLTR---PEGDIMNTTIFVGGLDSSVTDEDLKQPFNEFGEIVSVKIPVGKGCG 342

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDG 163
           FVQF NR NAEEAL KLNGTVIGKQ+VRLSWGRNPANKQ R  YGNQW   YYGGQ Y+G
Sbjct: 343 FVQFVNRPNAEEALEKLNGTVIGKQTVRLSWGRNPANKQPRDKYGNQWVDPYYGGQFYNG 402

Query: 164 YGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQVS 198
           YGY +P P DP MY AA      YP+YG HQQQVS
Sbjct: 403 YGYMVPQP-DPRMYPAAP----YYPMYGGHQQQVS 432

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LEB3|RBP47_NICPL Polyadenylate-binding protein RBP47 OS=Nicotiana plumbaginifolia GN=RBP47 PE=1 SV=1

 Score =  209 bits (533), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 101/159 (63%), Positives = 121/159 (76%)

Query: 40  LVLIGGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG 99
           ++L GGYASNGA   G QS+GDSSNTTIFVGGLD  VTDE+LRQ F+Q+GE+ SVKIP G
Sbjct: 270 VILSGGYASNGAATHGSQSDGDSSNTTIFVGGLDSEVTDEELRQSFNQFGEVVSVKIPAG 329

Query: 100 KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQ 159
           KGCGFVQF++R +A+EA+ KL+G +IGKQ+VRLSWGR+PANKQ R D G+QW+G Y G Q
Sbjct: 330 KGCGFVQFSDRSSAQEAIQKLSGAIIGKQAVRLSWGRSPANKQMRTDSGSQWNGGYNGRQ 389

Query: 160 VYDGYGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQVS 198
            Y GYGY      D  MYA  AA   +   YG+HQQ VS
Sbjct: 390 NYGGYGYGASQNQDSGMYATGAAYGASSNRYGNHQQPVS 428

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Nicotiana plumbaginifolia (taxid: 4092)

>sp|Q0WW84|RB47B_ARATH Polyadenylate-binding protein RBP47B OS=Arabidopsis thaliana GN=RBP47B PE=2 SV=1

 Score =  175 bits (443), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 80/116 (68%), Positives = 100/116 (86%), Gaps = 1/116 (0%)

Query: 40  LVLIGGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG 99
           ++L GG+ SNG+ G G QS+G+S+N TIFVGG+DP+V DEDLRQPFSQ+GE+ SVKIPVG
Sbjct: 296 VILAGGHGSNGSMGYGSQSDGESTNATIFVGGIDPDVIDEDLRQPFSQFGEVVSVKIPVG 355

Query: 100 KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAY 155
           KGCGFVQFA+R++AE+A+  LNGTVIGK +VRLSWGR+P NKQ+R D G QW+G Y
Sbjct: 356 KGCGFVQFADRKSAEDAIESLNGTVIGKNTVRLSWGRSP-NKQWRGDSGQQWNGGY 410

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|F4I3B3|RB47A_ARATH Polyadenylate-binding protein RBP47A OS=Arabidopsis thaliana GN=RBP47A PE=2 SV=1

 Score =  169 bits (428), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 91/151 (60%), Positives = 113/151 (74%), Gaps = 10/151 (6%)

Query: 27  RNSSYCQFNIVFLLVLIGGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFS 86
           R ++Y Q N    L L GG+  NG+      S+G+S+N+TIFVGGLD +VT+EDL QPFS
Sbjct: 294 RAAAYGQQNGSQALTLAGGHGGNGS-----MSDGESNNSTIFVGGLDADVTEEDLMQPFS 348

Query: 87  QYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRAD 146
            +GE+ SVKIPVGKGCGFVQFANR++AEEA+  LNGTVIGK +VRLSWGR+P NKQ+R+D
Sbjct: 349 DFGEVVSVKIPVGKGCGFVQFANRQSAEEAIGNLNGTVIGKNTVRLSWGRSP-NKQWRSD 407

Query: 147 YGNQWSGAYYGGQVYDGYGYAIPPPNDPSMY 177
            GNQW+G Y  GQ Y+  GYA     D +MY
Sbjct: 408 SGNQWNGGYSRGQGYNN-GYA---NQDSNMY 434

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LEB4|RBP45_NICPL Polyadenylate-binding protein RBP45 OS=Nicotiana plumbaginifolia GN=RBP45 PE=1 SV=1

 Score =  129 bits (325), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 75/142 (52%), Positives = 88/142 (61%), Gaps = 6/142 (4%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENA 113
           Q  Q E D +NTTIFVGGLDP V +E LRQ FS YGE+  VKI  GK CGFVQF  R +A
Sbjct: 271 QATQGESDPNNTTIFVGGLDPTVAEEHLRQVFSPYGELVHVKIVAGKRCGFVQFGTRASA 330

Query: 114 EEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIPPPND 173
           E+AL  LNGT +G QS+RLSWGR+P++KQ          GAYYG           PP  D
Sbjct: 331 EQALSSLNGTQLGGQSIRLSWGRSPSSKQTDQTQWGGSGGAYYGYGQGYEAYGYAPPAQD 390

Query: 174 PSMYAAAAAAYGAYPVYGSHQQ 195
           P+MY      YG YP Y ++QQ
Sbjct: 391 PNMY------YGNYPGYANYQQ 406

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Nicotiana plumbaginifolia (taxid: 4092)

>sp|Q93W34|RP45C_ARATH Polyadenylate-binding protein RBP45C OS=Arabidopsis thaliana GN=RBP45C PE=2 SV=1

 Score =  125 bits (313), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 68/124 (54%), Positives = 84/124 (67%), Gaps = 4/124 (3%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENA 113
           QG   E D +NTTIFVG +D +VT++DL+  F Q+GE+  VKIP GK CGFVQ+ANR  A
Sbjct: 267 QGNSGESDPTNTTIFVGAVDQSVTEDDLKSVFGQFGELVHVKIPAGKRCGFVQYANRACA 326

Query: 114 EEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG---NQWSGAYYGGQVYDGYGYAIPP 170
           E+AL  LNGT +G QS+RLSWGR+P+NKQ + D            Y  Q Y+ YGYA PP
Sbjct: 327 EQALSVLNGTQLGGQSIRLSWGRSPSNKQTQPDQAQYGGGGGYYGYPPQGYEAYGYA-PP 385

Query: 171 PNDP 174
           P DP
Sbjct: 386 PQDP 389

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FPJ8|RB45A_ARATH Polyadenylate-binding protein RBP45A OS=Arabidopsis thaliana GN=RBP45A PE=2 SV=1

 Score =  124 bits (312), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 68/121 (56%), Positives = 85/121 (70%), Gaps = 8/121 (6%)

Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALH 118
           + D +NTTIFVGGLD NVTD++L+  F Q+GE+  VKIP GK CGFVQ+AN+ +AE AL 
Sbjct: 254 DNDPNNTTIFVGGLDANVTDDELKSIFGQFGELLHVKIPPGKRCGFVQYANKASAEHALS 313

Query: 119 KLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWS-GAYYG--GQVYDGYGYAI-PPPNDP 174
            LNGT +G QS+RLSWGR+P  +  +A    QW+ G YYG   Q   GYGYA  PP  DP
Sbjct: 314 VLNGTQLGGQSIRLSWGRSPNKQSDQA----QWNGGGYYGYPPQPQGGYGYAAQPPTQDP 369

Query: 175 S 175
           +
Sbjct: 370 N 370

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SAB3|RB45B_ARATH Polyadenylate-binding protein RBP45B OS=Arabidopsis thaliana GN=RBP45B PE=1 SV=1

 Score =  120 bits (301), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 63/115 (54%), Positives = 79/115 (68%), Gaps = 3/115 (2%)

Query: 55  GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 114
           G  ++ D +NTT+FVGGLD +VTD+ L+  FSQYGEI  VKIP GK CGFVQF+ +  AE
Sbjct: 251 GVTTDNDPNNTTVFVGGLDASVTDDHLKNVFSQYGEIVHVKIPAGKRCGFVQFSEKSCAE 310

Query: 115 EALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIP 169
           EAL  LNG  +G  +VRLSWGR+P+NKQ   D    + G Y  GQ  + YGY +P
Sbjct: 311 EALRMLNGVQLGGTTVRLSWGRSPSNKQ-SGDPSQFYYGGY--GQGQEQYGYTMP 362

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8VXZ9|R47BP_ARATH Polyadenylate-binding protein RBP47B' OS=Arabidopsis thaliana GN=RBP47B' PE=2 SV=1

 Score =  112 bits (280), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 68/142 (47%), Positives = 88/142 (61%), Gaps = 5/142 (3%)

Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALH 118
           E D + TTI V  LD NVT+E+L++ FSQ GE+  VKIP  KG G+VQF  R +AEEA+ 
Sbjct: 231 ESDVTCTTISVANLDQNVTEEELKKAFSQLGEVIYVKIPATKGYGYVQFKTRPSAEEAVQ 290

Query: 119 KLNGTVIGKQSVRLSWGRNPANKQF--RADYGNQWSGAYYGGQVYDGYGYAIPPPNDPSM 176
           ++ G VIG+Q+VR+SW +NP    +  +AD  NQW+G Y  GQ YD Y Y      DPS+
Sbjct: 291 RMQGQVIGQQAVRISWSKNPGQDGWVTQAD-PNQWNGYYGYGQGYDAYAYGA--TQDPSV 347

Query: 177 YAAAAAAYGAYPVYGSHQQQVS 198
           YA     Y  YP  G   Q +S
Sbjct: 348 YAYGGYGYPQYPQQGEGTQDIS 369

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

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	198
302142363	324	unnamed protein product [Vitis vinifera]	0.752	0.459	0.858	3e-71
359492060	418	PREDICTED: uncharacterized RNA-binding p	0.752	0.356	0.858	4e-71
255538402	443	nuclear acid binding protein, putative [	0.767	0.343	0.839	4e-71
224137382	429	predicted protein [Populus trichocarpa]	0.742	0.342	0.883	1e-69
359492062	409	PREDICTED: uncharacterized RNA-binding p	0.702	0.339	0.880	1e-68
224067280	429	predicted protein [Populus trichocarpa]	0.767	0.354	0.819	4e-68
147856810	536	hypothetical protein VITISV_008697 [Viti	0.742	0.274	0.829	4e-68
449446975	426	PREDICTED: polyadenylate-binding protein	0.757	0.352	0.818	3e-66
356562301	401	PREDICTED: RNA-binding post-transcriptio	0.722	0.356	0.808	2e-63
356552180	425	PREDICTED: uncharacterized RNA-binding p	0.722	0.336	0.808	7e-63

>gi|302142363|emb|CBI19566.3| unnamed protein product [Vitis vinifera]

 Score =  273 bits (697), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 133/155 (85%), Positives = 142/155 (91%), Gaps = 6/155 (3%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG 103
           GGYASNGA     QS+GDS NTTIFVGGLDPNV+DEDLRQPFSQYGEI SVKIPVGKGCG
Sbjct: 176 GGYASNGA---SVQSDGDSMNTTIFVGGLDPNVSDEDLRQPFSQYGEIVSVKIPVGKGCG 232

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDG 163
           FVQFANR NAE+AL KLNGTVIGKQ+VRLSWGRNPANKQ RAD+GNQWSGAYYGGQVYDG
Sbjct: 233 FVQFANRNNAEDALQKLNGTVIGKQTVRLSWGRNPANKQMRADFGNQWSGAYYGGQVYDG 292

Query: 164 YGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQVS 198
           YGYA+PPP+DP+MY   AAAYGAYPVYG+HQQQVS
Sbjct: 293 YGYALPPPHDPTMY---AAAYGAYPVYGNHQQQVS 324

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359492060|ref|XP_003634360.1| PREDICTED: uncharacterized RNA-binding protein C23E6.01c-like isoform 2 [Vitis vinifera]

 Score =  273 bits (697), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 133/155 (85%), Positives = 142/155 (91%), Gaps = 6/155 (3%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG 103
           GGYASNGA     QS+GDS NTTIFVGGLDPNV+DEDLRQPFSQYGEI SVKIPVGKGCG
Sbjct: 270 GGYASNGA---SVQSDGDSMNTTIFVGGLDPNVSDEDLRQPFSQYGEIVSVKIPVGKGCG 326

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDG 163
           FVQFANR NAE+AL KLNGTVIGKQ+VRLSWGRNPANKQ RAD+GNQWSGAYYGGQVYDG
Sbjct: 327 FVQFANRNNAEDALQKLNGTVIGKQTVRLSWGRNPANKQMRADFGNQWSGAYYGGQVYDG 386

Query: 164 YGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQVS 198
           YGYA+PPP+DP+MY   AAAYGAYPVYG+HQQQVS
Sbjct: 387 YGYALPPPHDPTMY---AAAYGAYPVYGNHQQQVS 418

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255538402|ref|XP_002510266.1| nuclear acid binding protein, putative [Ricinus communis] gi|223550967|gb|EEF52453.1| nuclear acid binding protein, putative [Ricinus communis]

 Score =  272 bits (696), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 131/156 (83%), Positives = 142/156 (91%), Gaps = 4/156 (2%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG 103
           GGY SNGA GQ  Q++GDS+NTTIFVGGLDPNVTDEDL+QPFSQYGEI SVKIPVGKGCG
Sbjct: 291 GGYVSNGASGQAFQADGDSTNTTIFVGGLDPNVTDEDLKQPFSQYGEIVSVKIPVGKGCG 350

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANK-QFRADYGNQWSGAYYGGQVYD 162
           FVQFA+R NAEEAL KLNGTVIGKQ+VRLSWGRNPANK Q R+D+GNQW GAYYGGQ+YD
Sbjct: 351 FVQFASRSNAEEALQKLNGTVIGKQTVRLSWGRNPANKQQLRSDFGNQWGGAYYGGQIYD 410

Query: 163 GYGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQVS 198
           GYGYA+PPP+DPSMY   AA YGAYPVYGSHQQQVS
Sbjct: 411 GYGYALPPPHDPSMY---AAPYGAYPVYGSHQQQVS 443

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224137382|ref|XP_002327112.1| predicted protein [Populus trichocarpa] gi|222835427|gb|EEE73862.1| predicted protein [Populus trichocarpa]

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 137/155 (88%), Positives = 148/155 (95%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG 103
           GGY SNGA  QG QS+GDS+NTTIFVGGLDPNVTDEDL+QPFSQYGEI SVKIPVGKGCG
Sbjct: 275 GGYGSNGASAQGFQSDGDSNNTTIFVGGLDPNVTDEDLKQPFSQYGEIVSVKIPVGKGCG 334

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDG 163
           FVQFANR+NAEEAL KLNGTVIGKQ+VRLSWGRNPANKQFRAD+G+ W+GAYYGGQVYDG
Sbjct: 335 FVQFANRDNAEEALQKLNGTVIGKQTVRLSWGRNPANKQFRADFGSPWNGAYYGGQVYDG 394

Query: 164 YGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQVS 198
           YGYA+PPP+DPSMYAAAAAAYGAYP+YGSHQQQVS
Sbjct: 395 YGYALPPPHDPSMYAAAAAAYGAYPIYGSHQQQVS 429

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359492062|ref|XP_002284337.2| PREDICTED: uncharacterized RNA-binding protein C23E6.01c-like isoform 1 [Vitis vinifera]

 Score =  265 bits (676), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 125/142 (88%), Positives = 134/142 (94%), Gaps = 3/142 (2%)

Query: 57  QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEA 116
           QS+GDS NTTIFVGGLDPNV+DEDLRQPFSQYGEI SVKIPVGKGCGFVQFANR NAE+A
Sbjct: 271 QSDGDSMNTTIFVGGLDPNVSDEDLRQPFSQYGEIVSVKIPVGKGCGFVQFANRNNAEDA 330

Query: 117 LHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIPPPNDPSM 176
           L KLNGTVIGKQ+VRLSWGRNPANKQ RAD+GNQWSGAYYGGQVYDGYGYA+PPP+DP+M
Sbjct: 331 LQKLNGTVIGKQTVRLSWGRNPANKQMRADFGNQWSGAYYGGQVYDGYGYALPPPHDPTM 390

Query: 177 YAAAAAAYGAYPVYGSHQQQVS 198
           Y   AAAYGAYPVYG+HQQQVS
Sbjct: 391 Y---AAAYGAYPVYGNHQQQVS 409

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224067280|ref|XP_002302445.1| predicted protein [Populus trichocarpa] gi|222844171|gb|EEE81718.1| predicted protein [Populus trichocarpa]

 Score =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 127/155 (81%), Positives = 138/155 (89%), Gaps = 3/155 (1%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG 103
           GGY SNGA  QG QS+GDSSN TIFVGGLDPNVTDEDL+QPFSQYGEI SVKIPV KGCG
Sbjct: 278 GGYGSNGASSQGFQSDGDSSNATIFVGGLDPNVTDEDLKQPFSQYGEIVSVKIPVSKGCG 337

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDG 163
           FVQFANR NAEEAL KLNGTVIGKQ+VRLSWGRNP +KQ RAD+ + W+GAYYGGQVYDG
Sbjct: 338 FVQFANRNNAEEALQKLNGTVIGKQTVRLSWGRNPGHKQHRADFSSPWNGAYYGGQVYDG 397

Query: 164 YGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQVS 198
           YGYA+PPP+DPS Y   AAAYGAYP+YG+HQQQVS
Sbjct: 398 YGYALPPPHDPSTY---AAAYGAYPMYGNHQQQVS 429

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147856810|emb|CAN81343.1| hypothetical protein VITISV_008697 [Vitis vinifera]

 Score =  262 bits (670), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 131/158 (82%), Positives = 140/158 (88%), Gaps = 11/158 (6%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG 103
           GGYASNGA     QS+GDS NTTIFVGGLDPNV+DEDLRQPFSQYGEI SVKIPVGKGCG
Sbjct: 158 GGYASNGA---SVQSDGDSMNTTIFVGGLDPNVSDEDLRQPFSQYGEIVSVKIPVGKGCG 214

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ-----FRADYGNQWSGAYYGG 158
           FVQFANR NAE+AL KLNGTVIGKQ+VRLSWGRNPANKQ      RAD+GNQWSGAYYGG
Sbjct: 215 FVQFANRNNAEDALQKLNGTVIGKQTVRLSWGRNPANKQANSLFMRADFGNQWSGAYYGG 274

Query: 159 QVYDGYGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQ 196
           QVYDGYGYA+PPP+DP+MY   AAAYGAYPVYG+HQQQ
Sbjct: 275 QVYDGYGYALPPPHDPTMY---AAAYGAYPVYGNHQQQ 309

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446975|ref|XP_004141245.1| PREDICTED: polyadenylate-binding protein RBP47C-like [Cucumis sativus] gi|449498692|ref|XP_004160607.1| PREDICTED: polyadenylate-binding protein RBP47C-like [Cucumis sativus]

 Score =  256 bits (655), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 126/154 (81%), Positives = 137/154 (88%), Gaps = 4/154 (2%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG 103
           GGY++NG   QG QSEGDS+NTTIFVGGLDPNVTDEDLRQPFSQYGEI SVKIPVGKGCG
Sbjct: 271 GGYSTNGYFSQGLQSEGDSANTTIFVGGLDPNVTDEDLRQPFSQYGEIVSVKIPVGKGCG 330

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDG 163
           FVQFANR +AEEAL KLNGTVIGKQ+VRLSWGRNPANKQFR D+GNQW+GAYYGG +YDG
Sbjct: 331 FVQFANRNDAEEALQKLNGTVIGKQTVRLSWGRNPANKQFR-DFGNQWNGAYYGGHIYDG 389

Query: 164 YGYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQV 197
           YGY +  P+DPSMY    AAYGAY VYG+HQQQV
Sbjct: 390 YGYGLASPHDPSMY---HAAYGAYTVYGNHQQQV 420

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356562301|ref|XP_003549410.1| PREDICTED: RNA-binding post-transcriptional regulator csx1-like [Glycine max]

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 118/146 (80%), Positives = 129/146 (88%), Gaps = 3/146 (2%)

Query: 53  GQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANREN 112
           G   QSE DS+NTTIFVGGLDPNV+DEDLRQPFSQYGEI SVKIPVGKGCGFVQFANR N
Sbjct: 259 GTANQSEADSTNTTIFVGGLDPNVSDEDLRQPFSQYGEIVSVKIPVGKGCGFVQFANRNN 318

Query: 113 AEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIPPPN 172
           AEEAL KLNGT IGKQ+VRLSWGRNPANKQFR D+G+ W+GAYYG  +YDGYGYA+PP +
Sbjct: 319 AEEALQKLNGTTIGKQTVRLSWGRNPANKQFRMDFGSPWTGAYYGAPMYDGYGYALPPRH 378

Query: 173 DPSMYAAAAAAYGAYPVYGSHQQQVS 198
           DPS+Y   AAAYGAYP+YG HQQQVS
Sbjct: 379 DPSIY---AAAYGAYPLYGGHQQQVS 401

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552180|ref|XP_003544447.1| PREDICTED: uncharacterized RNA-binding protein C23E6.01c-like [Glycine max]

 Score =  245 bits (625), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 118/146 (80%), Positives = 128/146 (87%), Gaps = 3/146 (2%)

Query: 53  GQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANREN 112
           G   QSE DS+NTTIFVGGLDPNV+DEDLRQPFSQYGEI SVKIPVGKGCGFVQFANR N
Sbjct: 283 GTANQSEADSTNTTIFVGGLDPNVSDEDLRQPFSQYGEIVSVKIPVGKGCGFVQFANRNN 342

Query: 113 AEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIPPPN 172
           AEEAL KLNGT IGKQ+VRLSWGRNPANKQFR D+GN W+GAYYG  +YDGYGYA+ P +
Sbjct: 343 AEEALQKLNGTSIGKQTVRLSWGRNPANKQFRMDFGNPWTGAYYGAPMYDGYGYALTPRH 402

Query: 173 DPSMYAAAAAAYGAYPVYGSHQQQVS 198
           DPS+Y   AAAYGAYP+YG HQQQVS
Sbjct: 403 DPSIY---AAAYGAYPLYGGHQQQVS 425

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	198
TAIR|locus:2015398	434	RBP47C' "RNA-binding protein 4	0.742	0.338	0.632	1.5e-44
UNIPROTKB|Q9LEB3	428	RBP47 "Polyadenylate-binding p	0.803	0.371	0.553	1.3e-43
TAIR|locus:2015403	432	RBP47C "RNA-binding protein 47	0.742	0.340	0.625	1.3e-43
TAIR|locus:2094098	435	RBP47B "RNA-binding protein 47	0.565	0.257	0.690	7.5e-41
TAIR|locus:2012211	445	RBP47A "RNA-binding protein 47	0.606	0.269	0.634	5.5e-38
TAIR|locus:2116322	415	ATRBP45C [Arabidopsis thaliana	0.691	0.330	0.468	3.1e-28
UNIPROTKB|Q9LEB4	409	RBP45 "Polyadenylate-binding p	0.616	0.298	0.516	8.2e-28
TAIR|locus:2160210	387	RBP45A "RNA-binding protein 45	0.671	0.343	0.466	4e-26
TAIR|locus:2027372	405	RBP45B [Arabidopsis thaliana (	0.474	0.232	0.587	1.1e-25
TAIR|locus:2150215	425	AT5G19350 [Arabidopsis thalian	0.691	0.322	0.401	2.2e-20

TAIR|locus:2015398 RBP47C' "RNA-binding protein 47C'" [Arabidopsis thaliana (taxid:3702)]

 Score = 469 (170.2 bits), Expect = 1.5e-44, P = 1.5e-44
 Identities = 98/155 (63%), Positives = 108/155 (69%)

Query:    44 GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG 103
             GGY  +GA     +SEGD+ NTTIFVGGLD +VTDEDL+QPFS++GEI SVKIPVGKGCG
Sbjct:   288 GGYMPSGA---FTRSEGDTINTTIFVGGLDSSVTDEDLKQPFSEFGEIVSVKIPVGKGCG 344

Query:   104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSXXXXXXXXXXX 163
             FVQF NR NAEEAL KLNGTVIGKQ+VRLSWGRNPANKQ R  YGNQW            
Sbjct:   345 FVQFVNRPNAEEALEKLNGTVIGKQTVRLSWGRNPANKQPRDKYGNQWVDPYYGGQFYNG 404

Query:   164 XXXAIPPPNDPSMXXXXXXXXXXXPVYGSHQQQVS 198
                 +P P DP M           P+YG HQQQVS
Sbjct:   405 YGYMVPQP-DPRMYPAAPYY----PMYGGHQQQVS 434

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0008143 "poly(A) RNA binding" evidence=ISS

UNIPROTKB|Q9LEB3 RBP47 "Polyadenylate-binding protein RBP47" [Nicotiana plumbaginifolia (taxid:4092)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 88/159 (55%), Positives = 107/159 (67%)

Query:    40 LVLIGGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG 99
             ++L GGYASNGA   G QS+GDSSNTTIFVGGLD  VTDE+LRQ F+Q+GE+ SVKIP G
Sbjct:   270 VILSGGYASNGAATHGSQSDGDSSNTTIFVGGLDSEVTDEELRQSFNQFGEVVSVKIPAG 329

Query:   100 KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSXXXXXXX 159
             KGCGFVQF++R +A+EA+ KL+G +IGKQ+VRLSWGR+PANKQ R D G+QW+       
Sbjct:   330 KGCGFVQFSDRSSAQEAIQKLSGAIIGKQAVRLSWGRSPANKQMRTDSGSQWNGGYNGRQ 389

Query:   160 XXXXXXXAIPPPNDPSMXXXXXXXXXXXPVYGSHQQQVS 198
                          D  M             YG+HQQ VS
Sbjct:   390 NYGGYGYGASQNQDSGMYATGAAYGASSNRYGNHQQPVS 428

GO:0005634 "nucleus" evidence=IDA

GO:0008143 "poly(A) RNA binding" evidence=IDA

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0034605 "cellular response to heat" evidence=IDA

TAIR|locus:2015403 RBP47C "RNA-binding protein 47C" [Arabidopsis thaliana (taxid:3702)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 97/155 (62%), Positives = 106/155 (68%)

Query:    44 GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG 103
             GGY  NG   + P  EGD  NTTIFVGGLD +VTDEDL+QPF+++GEI SVKIPVGKGCG
Sbjct:   286 GGYMPNGTLTR-P--EGDIMNTTIFVGGLDSSVTDEDLKQPFNEFGEIVSVKIPVGKGCG 342

Query:   104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSXXXXXXXXXXX 163
             FVQF NR NAEEAL KLNGTVIGKQ+VRLSWGRNPANKQ R  YGNQW            
Sbjct:   343 FVQFVNRPNAEEALEKLNGTVIGKQTVRLSWGRNPANKQPRDKYGNQWVDPYYGGQFYNG 402

Query:   164 XXXAIPPPNDPSMXXXXXXXXXXXPVYGSHQQQVS 198
                 +P P DP M           P+YG HQQQVS
Sbjct:   403 YGYMVPQP-DPRMYPAAPYY----PMYGGHQQQVS 432

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0009507 "chloroplast" evidence=ISM

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0008143 "poly(A) RNA binding" evidence=ISS

TAIR|locus:2094098 RBP47B "RNA-binding protein 47B" [Arabidopsis thaliana (taxid:3702)]

 Score = 434 (157.8 bits), Expect = 7.5e-41, P = 7.5e-41
 Identities = 78/113 (69%), Positives = 98/113 (86%)

Query:    40 LVLIGGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG 99
             ++L GG+ SNG+ G G QS+G+S+N TIFVGG+DP+V DEDLRQPFSQ+GE+ SVKIPVG
Sbjct:   296 VILAGGHGSNGSMGYGSQSDGESTNATIFVGGIDPDVIDEDLRQPFSQFGEVVSVKIPVG 355

Query:   100 KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWS 152
             KGCGFVQFA+R++AE+A+  LNGTVIGK +VRLSWGR+P NKQ+R D G QW+
Sbjct:   356 KGCGFVQFADRKSAEDAIESLNGTVIGKNTVRLSWGRSP-NKQWRGDSGQQWN 407

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0008143 "poly(A) RNA binding" evidence=ISS

GO:0005829 "cytosol" evidence=IDA

GO:0042991 "transcription factor import into nucleus" evidence=RCA

TAIR|locus:2012211 RBP47A "RNA-binding protein 47A" [Arabidopsis thaliana (taxid:3702)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 80/126 (63%), Positives = 100/126 (79%)

Query:    27 RNSSYCQFNIVFLLVLIGGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFS 86
             R ++Y Q N    L L GG+  NG+      S+G+S+N+TIFVGGLD +VT+EDL QPFS
Sbjct:   294 RAAAYGQQNGSQALTLAGGHGGNGS-----MSDGESNNSTIFVGGLDADVTEEDLMQPFS 348

Query:    87 QYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRAD 146
              +GE+ SVKIPVGKGCGFVQFANR++AEEA+  LNGTVIGK +VRLSWGR+P NKQ+R+D
Sbjct:   349 DFGEVVSVKIPVGKGCGFVQFANRQSAEEAIGNLNGTVIGKNTVRLSWGRSP-NKQWRSD 407

Query:   147 YGNQWS 152
              GNQW+
Sbjct:   408 SGNQWN 413

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2116322 ATRBP45C [Arabidopsis thaliana (taxid:3702)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 68/145 (46%), Positives = 86/145 (59%)

Query:    54 QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENA 113
             QG   E D +NTTIFVG +D +VT++DL+  F Q+GE+  VKIP GK CGFVQ+ANR  A
Sbjct:   267 QGNSGESDPTNTTIFVGAVDQSVTEDDLKSVFGQFGELVHVKIPAGKRCGFVQYANRACA 326

Query:   114 EEALHKLNGTVIGKQSVRLSWGRNPANKQFRAD---YGNQWSXXXXXXXXXXXXXXAIPP 170
             E+AL  LNGT +G QS+RLSWGR+P+NKQ + D   YG                  A PP
Sbjct:   327 EQALSVLNGTQLGGQSIRLSWGRSPSNKQTQPDQAQYGGGGGYYGYPPQGYEAYGYA-PP 385

Query:   171 PNDPSMXXXXXXXXXXXPVYGSHQQ 195
             P DP+              YG++QQ
Sbjct:   386 PQDPNAYYGGYAGGG----YGNYQQ 406

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005829 "cytosol" evidence=IDA

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

UNIPROTKB|Q9LEB4 RBP45 "Polyadenylate-binding protein RBP45" [Nicotiana plumbaginifolia (taxid:4092)]

 Score = 311 (114.5 bits), Expect = 8.2e-28, P = 8.2e-28
 Identities = 64/124 (51%), Positives = 77/124 (62%)

Query:    54 QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENA 113
             Q  Q E D +NTTIFVGGLDP V +E LRQ FS YGE+  VKI  GK CGFVQF  R +A
Sbjct:   271 QATQGESDPNNTTIFVGGLDPTVAEEHLRQVFSPYGELVHVKIVAGKRCGFVQFGTRASA 330

Query:   114 EEALHKLNGTVIGKQSVRLSWGRNPANKQF-RADYGNQWSXXXXXXXXXXXXXXAIPPPN 172
             E+AL  LNGT +G QS+RLSWGR+P++KQ  +  +G                  A PP  
Sbjct:   331 EQALSSLNGTQLGGQSIRLSWGRSPSSKQTDQTQWGGSGGAYYGYGQGYEAYGYA-PPAQ 389

Query:   173 DPSM 176
             DP+M
Sbjct:   390 DPNM 393

GO:0005634 "nucleus" evidence=IDA

GO:0008143 "poly(A) RNA binding" evidence=IDA

TAIR|locus:2160210 RBP45A "RNA-binding protein 45A" [Arabidopsis thaliana (taxid:3702)]

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 69/148 (46%), Positives = 88/148 (59%)

Query:    54 QGPQS-EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANREN 112
             QG  + + D +NTTIFVGGLD NVTD++L+  F Q+GE+  VKIP GK CGFVQ+AN+ +
Sbjct:   248 QGANAGDNDPNNTTIFVGGLDANVTDDELKSIFGQFGELLHVKIPPGKRCGFVQYANKAS 307

Query:   113 AEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSXXXXXXX----XXXXXXXAI 168
             AE AL  LNGT +G QS+RLSWGR+P NKQ  +D   QW+                  A 
Sbjct:   308 AEHALSVLNGTQLGGQSIRLSWGRSP-NKQ--SDQA-QWNGGGYYGYPPQPQGGYGYAAQ 363

Query:   169 PPPNDPSMXXXXXXXXXXXPVYGSHQQQ 196
             PP  DP+              YG++QQQ
Sbjct:   364 PPTQDPNAYYGGYTG------YGNYQQQ 385

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0008143 "poly(A) RNA binding" evidence=ISS

GO:0005829 "cytosol" evidence=IDA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

TAIR|locus:2027372 RBP45B [Arabidopsis thaliana (taxid:3702)]

 Score = 291 (107.5 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 57/97 (58%), Positives = 71/97 (73%)

Query:    46 YASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFV 105
             Y S+ A   G  ++ D +NTT+FVGGLD +VTD+ L+  FSQYGEI  VKIP GK CGFV
Sbjct:   245 YQSSAA---GVTTDNDPNNTTVFVGGLDASVTDDHLKNVFSQYGEIVHVKIPAGKRCGFV 301

Query:   106 QFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
             QF+ +  AEEAL  LNG  +G  +VRLSWGR+P+NKQ
Sbjct:   302 QFSEKSCAEEALRMLNGVQLGGTTVRLSWGRSPSNKQ 338

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0005634 "nucleus" evidence=ISS

GO:0008143 "poly(A) RNA binding" evidence=ISS

GO:0010193 "response to ozone" evidence=IEP

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

TAIR|locus:2150215 AT5G19350 [Arabidopsis thaliana (taxid:3702)]

 Score = 245 (91.3 bits), Expect = 2.2e-20, P = 2.2e-20
 Identities = 57/142 (40%), Positives = 77/142 (54%)

Query:    59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALH 118
             E D + TTI V  LD NVT+E+L++ FSQ GE+  VKIP  KG G+VQF  R +AEEA+ 
Sbjct:   231 ESDVTCTTISVANLDQNVTEEELKKAFSQLGEVIYVKIPATKGYGYVQFKTRPSAEEAVQ 290

Query:   119 KLNGTVIGKQSVRLSWGRNPANKQF--RADYGNQWSXXXXXXXXXXXXXXAIPPPNDPSM 176
             ++ G VIG+Q+VR+SW +NP    +  +AD  NQW+              A     DPS+
Sbjct:   291 RMQGQVIGQQAVRISWSKNPGQDGWVTQAD-PNQWNGYYGYGQGYDAY--AYGATQDPSV 347

Query:   177 XXXXXXXXXXXPVYGSHQQQVS 198
                        P  G   Q +S
Sbjct:   348 YAYGGYGYPQYPQQGEGTQDIS 369

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0008143 "poly(A) RNA binding" evidence=ISS

GO:0010048 "vernalization response" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9SX80	R47CP_ARATH	No assigned EC number	0.7225	0.7424	0.3387	yes	no

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

Fail to connect to STRING server

---

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	198
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	7e-40
smart00360	73	smart00360, RRM, RNA recognition motif	4e-23
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-22
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-22
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-21
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-20
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-19
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	5e-18
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-16
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-16
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-15
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	7e-15
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-14
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-14
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-14
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-14
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	4e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-14
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-14
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	9e-14
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-13
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-13
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-13
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	8e-13
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	9e-13
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-12
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-12
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	1e-12
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	2e-12
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-12
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-12
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-12
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	3e-12
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	5e-12
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-12
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	9e-12
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-11
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	1e-11
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	3e-11
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	3e-11
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-11
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	4e-11
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	4e-11
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	5e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	6e-11
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	6e-11
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	6e-11
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	6e-11
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	6e-11
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	9e-11
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	1e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-10
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-10
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-10
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	2e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-10
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-10
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	3e-10
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-10
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-10
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-10
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	3e-10
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-10
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	4e-10
cd12462	79	cd12462, RRM_SCAF8, RNA recognition motif in SR-re	4e-10
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	4e-10
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	4e-10
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	5e-10
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	6e-10
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	6e-10
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	8e-10
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	8e-10
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	9e-10
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-09
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	1e-09
cd12461	81	cd12461, RRM_SCAF4, RNA recognition motif found in	1e-09
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-09
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-09
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-09
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-09
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-09
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	2e-09
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-09
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	3e-09
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	3e-09
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	3e-09
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	4e-09
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-09
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	4e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	5e-09
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	5e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	6e-09
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	8e-09
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	9e-09
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-08
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	1e-08
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	1e-08
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	1e-08
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	1e-08
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	1e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-08
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	1e-08
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-08
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-08
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-08
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-08
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-08
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	3e-08
cd12426	79	cd12426, RRM4_PTBPH3, RNA recognition motif 4 in p	3e-08
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-08
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-08
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	4e-08
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-08
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	4e-08
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-08
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	4e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-08
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	5e-08
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	5e-08
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	6e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	7e-08
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	7e-08
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	7e-08
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	8e-08
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	8e-08
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	8e-08
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	8e-08
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	8e-08
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	9e-08
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	9e-08
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	9e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-07
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	1e-07
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-07
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-07
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	1e-07
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-07
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	1e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-07
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	1e-07
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-07
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	2e-07
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-07
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	2e-07
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	2e-07
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-07
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-07
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	2e-07
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	2e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	3e-07
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	3e-07
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	3e-07
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	3e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	4e-07
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	4e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-07
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	5e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	5e-07
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-07
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	6e-07
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	6e-07
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	7e-07
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	7e-07
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	8e-07
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	8e-07
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	8e-07
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	1e-06
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-06
pfam08777	102	pfam08777, RRM_3, RNA binding motif	1e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-06
cd12331	79	cd12331, RRM_NRD1_SEB1_like, RNA recognition motif	1e-06
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	1e-06
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	2e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-06
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	2e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	2e-06
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	2e-06
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	3e-06
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	3e-06
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	3e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	3e-06
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	4e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	4e-06
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	4e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-06
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	5e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	5e-06
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	6e-06
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	6e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	7e-06
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	8e-06
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	8e-06
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	8e-06
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	8e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	9e-06
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	9e-06
cd12441	73	cd12441, RRM_Nup53_like, RNA recognition motif in	1e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-05
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	1e-05
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	1e-05
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	1e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	1e-05
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	1e-05
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	1e-05
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	1e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	1e-05
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-05
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	1e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	2e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	2e-05
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	2e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-05
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	2e-05
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-05
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	2e-05
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-05
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	3e-05
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	3e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-05
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	3e-05
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-05
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	3e-05
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	4e-05
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	4e-05
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	4e-05
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	4e-05
cd12520	74	cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA	4e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	4e-05
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	5e-05
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	5e-05
cd12259	76	cd12259, RRM_SRSF11_SREK1, RNA recognition motif i	6e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	6e-05
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	6e-05
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	6e-05
cd12292	75	cd12292, RRM2_La_like, RNA recognition motif 2 in	6e-05
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	8e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	8e-05
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	8e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	9e-05
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	9e-05
cd12558	76	cd12558, RRM3_RBM15B, RNA recognition motif 3 in p	9e-05
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	9e-05
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	1e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	1e-04
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	1e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-04
cd12541	76	cd12541, RRM2_La, RNA recognition motif 2 in La au	1e-04
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	1e-04
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	1e-04
cd12425	76	cd12425, RRM4_PTBP1_like, RNA recognition motif 4	1e-04
cd12605	69	cd12605, RRM_RALYL, RNA recognition motif in verte	1e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	1e-04
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	2e-04
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-04
cd12274	71	cd12274, RRM2_NEFsp, RNA recognition motif 2 in ve	2e-04
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-04
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	2e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	2e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	2e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	2e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	2e-04
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	2e-04
cd12443	73	cd12443, RRM_MCM3A_like, RNA recognition motif in	2e-04
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	2e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-04
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	3e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-04
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	3e-04
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	3e-04
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	4e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	4e-04
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	4e-04
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	4e-04
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	4e-04
cd12452	88	cd12452, RRM_ARP_like, RNA recognition motif in ye	5e-04
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	5e-04
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	6e-04
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	6e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	6e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	6e-04
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	6e-04
cd12281	92	cd12281, RRM1_TatSF1_like, RNA recognition motif 1	8e-04
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	8e-04
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	9e-04
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	0.001
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.001
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	0.001
cd12626	77	cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in	0.001
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	0.001
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	0.001
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	0.001
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	0.001
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	0.001
cd12435	71	cd12435, RRM_GW182_like, RNA recognition motif in	0.001
cd12228	84	cd12228, RRM_ENOX, RNA recognition motif (RRM) in	0.001
cd12248	74	cd12248, RRM_RBM44, RNA recognition motif in RNA-b	0.001
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	0.002
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.002
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	0.002
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.002
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.002
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	0.002
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	0.002
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	0.002
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	0.003
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.003
cd12410	93	cd12410, RRM2_RRT5, RNA recognition motif 2 in yea	0.003
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	0.004
cd12682	76	cd12682, RRM_RBPMS, RNA recognition motif in verte	0.004
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	0.004

>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 =  130 bits (328), Expect = 7e-40
 Identities = 45/72 (62%), Positives = 55/72 (76%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
           NTT+FVGGLDP VT+++LR  F  +GEI  VKIP GKGCGFVQF +R  AE A+ +L GT
Sbjct: 1   NTTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGT 60

Query: 124 VIGKQSVRLSWG 135
           +IG   +RLSWG
Sbjct: 61  IIGGSRIRLSWG 72

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|214636 smart00360, RRM, RNA recognition motif

 Score = 87.3 bits (217), Expect = 4e-23
 Identities = 28/73 (38%), Positives = 48/73 (65%), Gaps = 6/73 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 119
           T+FVG L P+ T+E+LR+ FS++G++ SV++         KG  FV+F + E+AE+AL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 120 LNGTVIGKQSVRL 132
           LNG  +  + +++
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>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 = 85.0 bits (211), Expect = 4e-22
 Identities = 30/72 (41%), Positives = 46/72 (63%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTV 124
           TT++VG L   +T+E+L++ FS +G I  V++   KG  FV+F   E A  A+  +NGT 
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTS 60

Query: 125 IGKQSVRLSWGR 136
           I  Q+V+ SWG+
Sbjct: 61  INGQTVKCSWGK 72

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

 Score = 84.3 bits (209), Expect = 7e-22
 Identities = 32/72 (44%), Positives = 48/72 (66%), Gaps = 5/72 (6%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENAEEALHKLN 121
           +FVG L P+ T+EDLR+ FS++GEI SV+I        KG  FV+F + E+AE+AL  LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 122 GTVIGKQSVRLS 133
           G  +  + +++S
Sbjct: 61  GKELDGRKLKVS 72

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

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

 Score = 83.8 bits (208), Expect = 1e-21
 Identities = 33/73 (45%), Positives = 47/73 (64%), Gaps = 1/73 (1%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL-NGT 123
           TT++VGGL   VT++DLR  F Q+GEI S+ +   + C FV F  RE AE+A  +L N  
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKAAERLFNKL 61

Query: 124 VIGKQSVRLSWGR 136
           +I  + ++L WGR
Sbjct: 62  IINGRRLKLKWGR 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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 80.8 bits (200), Expect = 2e-20
 Identities = 34/82 (41%), Positives = 49/82 (59%), Gaps = 9/82 (10%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--P-------VGKGCGFVQFANRENAEE 115
           T ++VG L+P VT+E L Q F ++G +ASVKI  P         + CGFV F NR +AE 
Sbjct: 2   TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER 61

Query: 116 ALHKLNGTVIGKQSVRLSWGRN 137
           AL +L+G  +    ++L WG+ 
Sbjct: 62  ALDELDGKDVMGYELKLGWGKA 83

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 78.4 bits (194), Expect = 1e-19
 Identities = 29/65 (44%), Positives = 42/65 (64%), Gaps = 5/65 (7%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLN 121
           +FVG L P+ T+EDL+  FS++G I S++I        KG  FV+F + E+AE+AL  LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 122 GTVIG 126
           G  +G
Sbjct: 61  GKELG 65

(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|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 = 74.3 bits (183), Expect = 5e-18
 Identities = 26/74 (35%), Positives = 44/74 (59%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTV 124
           TT+++G L   VT+EDL+  F +YGEI S+ +   +GC +V    R++A  AL KL    
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLRNVK 62

Query: 125 IGKQSVRLSWGRNP 138
           +  + ++++W  N 
Sbjct: 63  LAGKKIKVAWAPNK 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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 70.9 bits (174), Expect = 1e-16
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 6/74 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKL 120
           IFVG L P +  E LR  F+ +GEI+  ++         KG GFV F  +E+AE A+  +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 121 NGTVIGKQSVRLSW 134
           NG  +G +++R +W
Sbjct: 62  NGQWLGGRAIRTNW 75

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

 Score = 69.5 bits (171), Expect = 4e-16
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 7/78 (8%)

Query: 68  FVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK---GCGFVQFANRENAEEALHKLN 121
           +VG L P+VT+  L + FS  G + S+++    + +   G  +V F N  +AE AL  LN
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 122 GTVIGKQSVRLSWG-RNP 138
             VI  + +R+ W  R+P
Sbjct: 63  FDVIKGKPIRIMWSQRDP 80

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

 Score = 68.1 bits (167), Expect = 1e-15
 Identities = 25/63 (39%), Positives = 43/63 (68%), Gaps = 1/63 (1%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI- 125
           +FVG L  ++T+E+ ++ FS+YGE++ V +   KG GF++   R NAE+A  +L+G +  
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIMRK 63

Query: 126 GKQ 128
           G+Q
Sbjct: 64  GRQ 66

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

 Score = 66.1 bits (162), Expect = 7e-15
 Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 11/72 (15%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----------GCGFVQFANRENA 113
           TT+FV  L+   T+E L++ F + G + SV I   K           G GFV+F ++E A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 114 EEALHKLNGTVI 125
           ++AL +L GTV+
Sbjct: 61  QKALKRLQGTVL 72

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

 Score = 65.0 bits (159), Expect = 2e-14
 Identities = 27/57 (47%), Positives = 37/57 (64%), Gaps = 5/57 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI-----PVGKGCGFVQFANRENAEEAL 117
            IFVGG+ P+ T+E+LR  FS++G +  VKI      V KG GFV F  +E+AE+ L
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKIL 60

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 64.5 bits (158), Expect = 2e-14
 Identities = 30/69 (43%), Positives = 47/69 (68%), Gaps = 4/69 (5%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP----VGKGCGFVQFANRENAEEALHKLNG 122
           ++V  L P+VT+EDLR+ FS YG++  V++       +G  FV+FA+ E+AE AL KLNG
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 123 TVIGKQSVR 131
            V+  +++R
Sbjct: 61  LVLDGRTLR 69

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

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

 Score = 69.6 bits (169), Expect = 3e-14
 Identities = 30/108 (27%), Positives = 56/108 (51%), Gaps = 8/108 (7%)

Query: 48  SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KG 101
              +     + +    N T+FVG L  +VT+EDLR+ F ++G +  V++         +G
Sbjct: 99  FRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRG 158

Query: 102 CGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGN 149
             FV+F + E+AE+A+ +LNG  +  + +R+   +     Q R++  N
Sbjct: 159 FAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP--ASQPRSELSN 204

Length = 306

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

 Score = 64.2 bits (157), Expect = 4e-14
 Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 2/68 (2%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           ++V  L  + T+E LR+ FS+YGE+  VK    K   FV F  R++A +A+ ++NG  + 
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKI--KDYAFVHFEERDDAVKAMEEMNGKELE 61

Query: 127 KQSVRLSW 134
              + +S 
Sbjct: 62  GSPIEVSL 69

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

 Score = 64.2 bits (157), Expect = 4e-14
 Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 5/65 (7%)

Query: 75  NVTDEDLRQPFSQYGEIASVKIP---VGKGCGF--VQFANRENAEEALHKLNGTVIGKQS 129
             T+ DL++ FS +G +  V IP    GK  GF  VQF ++ +AE+A+  +NG  I  + 
Sbjct: 10  KCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRP 69

Query: 130 VRLSW 134
           V + W
Sbjct: 70  VAVDW 74

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

 Score = 64.2 bits (157), Expect = 4e-14
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 9/80 (11%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI-------PVGK--GCGFVQFANRENAEEA 116
            +++G LD  +T+  L + FS+YG+I              G+  G  FV F  +E AE+A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 117 LHKLNGTVIGKQSVRLSWGR 136
           L  LNG     + + + W  
Sbjct: 61  LKSLNGKTALGKKLVVRWAH 80

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

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

 Score = 64.2 bits (157), Expect = 4e-14
 Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 6/72 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 119
            ++VG L  NVT+EDL+  F Q+GE+ S ++         +G GFV+    E A  A+ K
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 120 LNGTVIGKQSVR 131
           LNGT  G +++ 
Sbjct: 61  LNGTDFGGRTLT 72

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

 Score = 63.8 bits (156), Expect = 6e-14
 Identities = 27/69 (39%), Positives = 41/69 (59%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK---------GCGFVQFANRENAEEAL 117
           I+V  LD  + ++DLR  FS++GE+ S++IP  +         G  FV F +  +AE AL
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 118 HKLNGTVIG 126
            +LNGT +G
Sbjct: 63  -QLNGTELG 70

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

 Score = 68.7 bits (168), Expect = 9e-14
 Identities = 36/159 (22%), Positives = 59/159 (37%), Gaps = 29/159 (18%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI-----PVGKGCGFVQFANRENAEEALHKLN 121
           ++V  LD  VTDE LR+ FS+ GEI S K+      V +G GFV F+N E A  A+ +++
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMH 347

Query: 122 GTVIG---------------KQSVRLSWGRN----PANKQFRADYGNQWSGAYYG---GQ 159
           G ++G               +  ++  + +               G      YYG    Q
Sbjct: 348 GRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQ 407

Query: 160 VYDGY--GYAIPPPNDPSMYAAAAAAYGAYPVYGSHQQQ 196
            ++G   G+         M               + +  
Sbjct: 408 QFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAP 446

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

 Score = 63.0 bits (154), Expect = 1e-13
 Identities = 27/62 (43%), Positives = 41/62 (66%), Gaps = 6/62 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKL 120
           ++VG L  N+T++DLR  F  +GEI  V++         KG GF+QFA+ E+A++AL +L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 121 NG 122
           NG
Sbjct: 61  NG 62

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

 Score = 62.6 bits (153), Expect = 2e-13
 Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 7/74 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHK 119
           ++FVG L  ++ +E+LR+ F   G++ +V+I       +GKG G+V F  +++   AL K
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-K 59

Query: 120 LNGTVIGKQSVRLS 133
           LNG  +  + +R+ 
Sbjct: 60  LNGIKLKGRKIRVK 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|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 = 2e-13
 Identities = 27/64 (42%), Positives = 37/64 (57%), Gaps = 6/64 (9%)

Query: 68  FVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKLN 121
           FVG L    T+ED+R  F +YG I  V I         KGC FV+F++RE A++A+  L+
Sbjct: 3   FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALH 62

Query: 122 GTVI 125
           G V 
Sbjct: 63  GKVT 66

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

 Score = 60.7 bits (148), Expect = 8e-13
 Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PV---GKGCGFVQFANRENAEEAL--- 117
           +F+GGL  + T+E LR+ FS+YGE+    I   P+    +G GFV FA+  + ++ L   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 118 -HKLNGTVI 125
            H L+G  I
Sbjct: 61  PHVLDGREI 69

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

 Score = 60.7 bits (148), Expect = 9e-13
 Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI----PVGKGCGFVQFANRENAEEALHKLNG 122
           ++VG L P  T  +L   F +YG + SV +    P   G  FV+F +  +AE+A+  L+G
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP---GFAFVEFEDPRDAEDAVRALDG 58

Query: 123 TVIGKQSVRLSWGRN 137
             I    VR+   R 
Sbjct: 59  RRICGNRVRVELSRG 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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 60.7 bits (148), Expect = 1e-12
 Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 6/58 (10%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVG---KGCGFVQFANRENAEEAL 117
           T+F+  L  + T+E+L++ FSQ+GE+   +I    +    KG  FV+F  +E+A++ L
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59

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

 Score = 60.1 bits (146), Expect = 1e-12
 Identities = 27/72 (37%), Positives = 45/72 (62%), Gaps = 6/72 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           +FVG L  +  ++ + + F +YGEI+SV++P        KG G+V+F+++E A+ AL  L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 121 NGTVIGKQSVRL 132
            GT +  + VRL
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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 60.1 bits (146), Expect = 1e-12
 Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 5/79 (6%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI-----PVGKGCGFVQFANRENAEEAL 117
           +  T+FVG L+  +T+E+LR+ F +YG +  V I       G    FV+F N + A  A 
Sbjct: 1   ATRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAK 60

Query: 118 HKLNGTVIGKQSVRLSWGR 136
             ++G  IG+  +++ +G+
Sbjct: 61  VAMSGQYIGRNQIKIGYGK 79

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 59.5 bits (145), Expect = 2e-12
 Identities = 29/65 (44%), Positives = 40/65 (61%), Gaps = 3/65 (4%)

Query: 67  IFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
           +FVG L+ + V+ EDL + FS+YG+I    I + KG GFVQF N E+A  A+   NG  I
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILG--ISLHKGYGFVQFDNEEDARAAVAGENGREI 60

Query: 126 GKQSV 130
             Q +
Sbjct: 61  AGQKL 65

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

>gnl|CDD|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 = 59.9 bits (146), Expect = 2e-12
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK---GCGFVQFANRENAEEALH 118
             +FV GL    T+++L   FS++G +  V +   P      G GFV F + E+A+ A+ 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 119 KLNGTVI-GKQ 128
            LNG  + G+ 
Sbjct: 62  DLNGKELEGRV 72

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

 Score = 59.6 bits (145), Expect = 2e-12
 Identities = 31/78 (39%), Positives = 45/78 (57%), Gaps = 8/78 (10%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALHK 119
           T+++G L+P + +  +   F++ GE+ SVKI   K      G GFV+FA  E AE+AL  
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 120 LNGTVI--GKQSVRLSWG 135
           LNG  I   +Q  RL+W 
Sbjct: 61  LNGKPIPNTQQRFRLNWA 78

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

 Score = 59.4 bits (144), Expect = 3e-12
 Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 6/74 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKL 120
           IFVG L P VTD  L   FS +   +  ++         +G GFV F ++++AE A++++
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 121 NGTVIGKQSVRLSW 134
           NG  +G + +R +W
Sbjct: 62  NGKWLGSRPIRCNW 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|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins

 Score = 59.5 bits (144), Expect = 3e-12
 Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 5/75 (6%)

Query: 67  IFVG-----GLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
           +++G     G + N+ +++LR+   +YGEI S++I   K C F+ F N  NA  AL  LN
Sbjct: 5   VYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILREKACAFINFMNIPNAIAALQTLN 64

Query: 122 GTVIGKQSVRLSWGR 136
           G       VR+++G+
Sbjct: 65  GKKPYDTIVRINYGK 79

This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 82

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

 Score = 58.4 bits (142), Expect = 5e-12
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 2/74 (2%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
              T++V G    +T+E L++ FS +G I ++ +   K CGFV F   E+A+ A+ +LNG
Sbjct: 3   KGNTLYVHGY--GLTEEILKKAFSPFGNIINISMEKEKNCGFVTFEKMESADRAIAELNG 60

Query: 123 TVIGKQSVRLSWGR 136
           T +    +++S  R
Sbjct: 61  TTVQGVQLKVSLAR 74

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

 Score = 58.5 bits (142), Expect = 5e-12
 Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI----PVGKGCGFVQFANRENAEEALHKLN 121
           +IFVG L P+VT E+L + FS++G+I  V +           F++F   + A  A+   N
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESEN 64

Query: 122 GTVIGKQSVR 131
            +++  +++ 
Sbjct: 65  HSMLKNKTMH 74

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

 Score = 58.3 bits (141), Expect = 9e-12
 Identities = 28/60 (46%), Positives = 37/60 (61%), Gaps = 5/60 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI-----PVGKGCGFVQFANRENAEEALHKLN 121
           IFVGG+D    + DLR+ FSQYG +  VKI      V KG GFV F  +E+A++ L + N
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEAN 64

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

 Score = 58.0 bits (141), Expect = 1e-11
 Identities = 26/71 (36%), Positives = 42/71 (59%), Gaps = 5/71 (7%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK--GCGFVQFANRENAEEALHK 119
           T ++V  L  ++ DE L++ F +YG+I S K+     GK  G GFV F N E A++A+ +
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61

Query: 120 LNGTVIGKQSV 130
           LNG  +  + +
Sbjct: 62  LNGKEVNGKKL 72

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

>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 58.2 bits (141), Expect = 1e-11
 Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 12/86 (13%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
           S  + F+ G++ ++ +  +R  F Q+G+  SV +     CGFV+F  RE AE+    ++ 
Sbjct: 1   SIKSFFLFGVEDDLPEYKIRDYFEQFGKSKSVIVNHRAKCGFVRFETREAAEKFAAAISE 60

Query: 123 T------------VIGKQSVRLSWGR 136
                        V+    +R++WG+
Sbjct: 61  NGLNAGLSRGGLLVLEGCPLRVAWGK 86

This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities. . Length = 86

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

 Score = 56.9 bits (138), Expect = 3e-11
 Identities = 26/65 (40%), Positives = 40/65 (61%), Gaps = 5/65 (7%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI-----PVGKGCGFVQFANRENAEEALHKLN 121
           ++V  LD ++ DE LR+ FS +G I S K+        KG GFV F++ E A +A+ ++N
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMN 63

Query: 122 GTVIG 126
           G +IG
Sbjct: 64  GRIIG 68

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

 Score = 56.9 bits (138), Expect = 3e-11
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 6/64 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKL 120
           ++V GL   +T ++L   FS YG I + +I       + +G GF++F  R  AE A+  L
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 121 NGTV 124
           NGT+
Sbjct: 63  NGTI 66

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

 Score = 56.5 bits (137), Expect = 3e-11
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 6/62 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 120
           ++VGGL   V ++ L   F  +G+I  ++IP+       +G  FV+F   E+A  A+  +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 121 NG 122
           N 
Sbjct: 61  NE 62

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

 Score = 56.3 bits (136), Expect = 4e-11
 Identities = 22/73 (30%), Positives = 36/73 (49%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTV 124
           TT++VG + P  T  DL   F  +G I   +    +G  FV+    E A  A+ +L G  
Sbjct: 1   TTVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFP 60

Query: 125 IGKQSVRLSWGRN 137
           +  + +R  WG++
Sbjct: 61  VHGRPLRCGWGKD 73

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|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 56.2 bits (135), Expect = 4e-11
 Identities = 24/71 (33%), Positives = 44/71 (61%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
           T++ GG+   +T++ +RQ FS +G+I  +++   KG  F++F+  E+A  A+  +NGT I
Sbjct: 2   TVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEKGYSFIRFSTHESAAHAIVSVNGTTI 61

Query: 126 GKQSVRLSWGR 136
               V+  WG+
Sbjct: 62  EGHVVKCYWGK 72

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

 Score = 56.1 bits (136), Expect = 5e-11
 Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 10/67 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL--- 117
           +FVGGL  +VT+EDLR+ FSQYG + SV+I   K      G  FV F + +  ++ +   
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61

Query: 118 -HKLNGT 123
            H +NG 
Sbjct: 62  YHTINGH 68

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|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 = 56.0 bits (135), Expect = 6e-11
 Identities = 23/72 (31%), Positives = 43/72 (59%), Gaps = 6/72 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKL 120
           +F+GGL  +  ++ L Q FS+YG+I+ V +         +G GFV F N ++A++A+  +
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 121 NGTVIGKQSVRL 132
           NG  +  + +R+
Sbjct: 63  NGKSVDGRQIRV 74

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

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

 Score = 55.7 bits (135), Expect = 6e-11
 Identities = 29/72 (40%), Positives = 41/72 (56%), Gaps = 10/72 (13%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG--------KGCGFVQFANRENAEEA 116
           T IFVGGL  + TD+ LR+ FSQ+GEI   +  V         +G GFV F ++E+AE A
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEI--EEAVVITDRQTGKSRGYGFVTFKDKESAERA 58

Query: 117 LHKLNGTVIGKQ 128
               N  + G++
Sbjct: 59  CKDPNPIIDGRK 70

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 56.2 bits (136), Expect = 6e-11
 Identities = 30/89 (33%), Positives = 47/89 (52%), Gaps = 16/89 (17%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGE-IASVKIPVGK------GCGFVQFANRENAEEALH 118
           ++++G L+P + +  +++ F+  GE + SVKI   K      G  FV+FA+   AE  LH
Sbjct: 1   SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60

Query: 119 KLNGTVIGKQSVRLSWGRNPANKQFRADY 147
           KLNG  I         G NP  K+F+ + 
Sbjct: 61  KLNGKPIP--------GSNP-PKRFKLNR 80

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

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

 Score = 56.1 bits (136), Expect = 6e-11
 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGKGC---GFVQFANRENAEEALHK 119
           T+FV  L  + TDE L + FS+ G I     VK    K C   G+V FA  E+A+ AL +
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 120 LNGTVIGKQSVRL 132
              T  G + + +
Sbjct: 61  KKKTKFGGRKIHV 73

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

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

 Score = 55.6 bits (135), Expect = 6e-11
 Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 6/62 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           + VG L  NV  + L++ FS YG +  V +P+       +G  +V+F + E+AE+A+  +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 121 NG 122
           +G
Sbjct: 61  DG 62

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|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 55.5 bits (133), Expect = 9e-11
 Identities = 26/71 (36%), Positives = 44/71 (61%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
           T++ GG+   +T++ +RQ FS +G+I  V++   KG  FV+F + E+A  A+  +NGT I
Sbjct: 2   TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAIVSVNGTTI 61

Query: 126 GKQSVRLSWGR 136
               V+  WG+
Sbjct: 62  EGHVVKCYWGK 72

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

 Score = 55.0 bits (133), Expect = 1e-10
 Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL 117
              IFV  L P+  +  L Q FS +G + +VK+         KG GFV   N E A  A+
Sbjct: 1   GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

Query: 118 HKLNGTVIGKQSVRLS 133
             LNG  +G + +++S
Sbjct: 61  ASLNGYRLGGRVLQVS 76

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

 Score = 59.1 bits (143), Expect = 2e-10
 Identities = 27/81 (33%), Positives = 45/81 (55%), Gaps = 7/81 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALHK 119
           +++VG LDP+VT+  L   F  +G + SV++          G G+V F N  +AE AL  
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 120 LNGTVIGKQSVRLSWG-RNPA 139
           +N   +G + +R+ W  R+P+
Sbjct: 62  MNFKRLGGKPIRIMWSQRDPS 82

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

 Score = 54.9 bits (133), Expect = 2e-10
 Identities = 24/63 (38%), Positives = 34/63 (53%), Gaps = 6/63 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHK 119
           TI V  L  +  ++DLR+ F  +G I+ V +         +G  FV F  RE+AE A+ K
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 120 LNG 122
           LNG
Sbjct: 61  LNG 63

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

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

 Score = 54.5 bits (132), Expect = 2e-10
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 5/74 (6%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK--GCGFVQFANRENAEEALHK 119
           T + V  L  +VT+EDL + F + GE+  VKI     G+  G   V F  RE+AE A+ +
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60

Query: 120 LNGTVIGKQSVRLS 133
            NG ++  Q +++ 
Sbjct: 61  FNGVLLDGQPMQVE 74

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

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

 Score = 54.6 bits (131), Expect = 2e-10
 Identities = 24/66 (36%), Positives = 43/66 (65%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           +FVG L  ++T+ED ++ F +YGE + V I   +G GF++  +R  AE A  +L+GT++ 
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 63

Query: 127 KQSVRL 132
            + +R+
Sbjct: 64  NRPLRI 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 53.7 bits (130), Expect = 2e-10
 Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 81  LRQPFSQYGEIASVKI-PVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW 134
           L + FS +G +  +K+     G  FV+F+  E AE+A+  LNG + G + +R+ +
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

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

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

 Score = 54.2 bits (131), Expect = 2e-10
 Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 6/69 (8%)

Query: 69  VGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKLNG 122
           V  L    T +DLR+ F +YGE+  V IP        +G  FV+F ++ +AE+A+  ++G
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 123 TVIGKQSVR 131
             +  + +R
Sbjct: 63  KELDGRELR 71

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

 Score = 54.3 bits (131), Expect = 3e-10
 Identities = 26/69 (37%), Positives = 37/69 (53%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASV---KIPVGK---GCGFVQFANRENAEEAL--- 117
           +F+GGL    TD+ L+  FSQ+GEI      K P  K   G GFV FA+    + A+   
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNAR 61

Query: 118 -HKLNGTVI 125
            HK++G  +
Sbjct: 62  PHKVDGREV 70

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|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 = 3e-10
 Identities = 23/59 (38%), Positives = 36/59 (61%), Gaps = 5/59 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEALHK 119
           T+FV  LD +V +++LR+ FS+ GEI  V++        KG  +V+F N E+ +EAL  
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKL 59

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|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 = 53.8 bits (130), Expect = 3e-10
 Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 6/65 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 120
           +FV  L    T+E+LR+ F  +GEI+ V +P+       KG  FV F   E+A +A  +L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 121 NGTVI 125
           +G++ 
Sbjct: 62  DGSIF 66

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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 58.0 bits (140), Expect = 3e-10
 Identities = 29/95 (30%), Positives = 51/95 (53%), Gaps = 12/95 (12%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GK 100
           A+   PG  P      +   ++VG L  N+T+++LRQ F  +G+I  V++         K
Sbjct: 175 AATHQPGDIP------NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSK 228

Query: 101 GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG 135
           G GF+QF + E A+EAL  +NG  +  + +++ + 
Sbjct: 229 GFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYA 263

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

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

 Score = 53.7 bits (129), Expect = 3e-10
 Identities = 25/68 (36%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVK-IPVGKGCGFVQFANRENAEEALHKLNGTV 124
           T+ V  LDP+V+++DL Q F  YGEI  ++  P  +   F++F +  +AE AL  LN + 
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSE 62

Query: 125 IGKQSVRL 132
           I  + ++L
Sbjct: 63  IAGKRIKL 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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 54.0 bits (130), Expect = 4e-10
 Identities = 27/80 (33%), Positives = 47/80 (58%), Gaps = 10/80 (12%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENAEEALHKL 120
            +FV GL  +VT E+L + F ++G + SV++        KG  +V++ N  +A +A+ K+
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 121 NGTVIGKQ--SVRLSWGRNP 138
           +GT I ++  SV +S   NP
Sbjct: 64  DGTEIKEKTISVAIS---NP 80

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

>gnl|CDD|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 = 53.9 bits (130), Expect = 4e-10
 Identities = 30/82 (36%), Positives = 50/82 (60%), Gaps = 15/82 (18%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG---------FVQFANRENAEEA 116
           TI VGG+D +++++DL++ FS  GE+  V++     CG         FV+FA+ E+A  A
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRL-----CGDRQHSARFAFVEFADAESALSA 56

Query: 117 LHKLNGTVIGKQSVRLSWGRNP 138
           L  L+GT++G   +R+S  + P
Sbjct: 57  L-NLSGTLLGGHPLRVSPSKTP 77

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 53.9 bits (129), Expect = 4e-10
 Identities = 25/76 (32%), Positives = 46/76 (60%), Gaps = 2/76 (2%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
           +TT++VG +D   T +DL   F ++G+I S+ +   +GC +V   +R++A  AL KL+  
Sbjct: 2   STTLWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAYRALQKLSSG 61

Query: 124 V--IGKQSVRLSWGRN 137
              IG + ++++W  N
Sbjct: 62  SYKIGSKVIKIAWALN 77

This subgroup corresponds to the RRM of SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8), 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. 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, together with SCAF4, represents a new class of SCAFs (SR-like CTD-associated factors). They contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 79

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

 Score = 53.9 bits (129), Expect = 4e-10
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 6/75 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKL 120
           +FVG L P +T ED++  F+ +G+I+  ++         KG GFV F N+ +AE A+  +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 121 NGTVIGKQSVRLSWG 135
            G  +G + +R +W 
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

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

 Score = 53.7 bits (129), Expect = 4e-10
 Identities = 28/73 (38%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENAEEALHKLN 121
           ++VG LDP VT++ L+Q F   G + +VKI   K       GFV++    +AE AL  LN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 122 GTVIGKQSVRLSW 134
           G  I    +R++W
Sbjct: 61  GRQIENNEIRVNW 73

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

 Score = 53.4 bits (129), Expect = 5e-10
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 7/75 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQ-YGEIASVKI---PV---GKGCGFVQFANRENAEEALH 118
           +IFVG L P+VTD  L++ F   Y  +   K+   PV    KG GFV+F + +  + AL 
Sbjct: 3   SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62

Query: 119 KLNGTVIGKQSVRLS 133
           ++NG     + +R+S
Sbjct: 63  EMNGVYCSSRPMRVS 77

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|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 = 53.2 bits (128), Expect = 6e-10
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 66  TIFVGGLDPNVT-DEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTV 124
           T+FV G DP  T +ED+ + F  +G +    I   K   FV+F + E+A +AL  L+G+ 
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIR--KTFAFVEFEDSEDATKALEALHGSR 58

Query: 125 IGKQSVRLSWGR 136
           I    + + + +
Sbjct: 59  IDGSVLTVEFVK 70

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

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

 Score = 52.9 bits (128), Expect = 6e-10
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLN 121
           IF+  LD ++ ++ L   FS +G I S K+        KG GFV F   E A  A+ K+N
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64

Query: 122 GTVIGKQSV 130
           G ++  + V
Sbjct: 65  GMLLNDKKV 73

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

 Score = 53.1 bits (128), Expect = 8e-10
 Identities = 26/70 (37%), Positives = 42/70 (60%), Gaps = 10/70 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASV--------KIPVGKGCGFVQFANRENAEEALH 118
           IFVGGL PNVT+ DLR+ FSQ+G +  V        K P  +G GF+ F + ++ ++ ++
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRP--RGFGFITFESEDSVDQVVN 62

Query: 119 KLNGTVIGKQ 128
           +    + GK+
Sbjct: 63  EHFHDINGKK 72

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

 Score = 53.0 bits (128), Expect = 8e-10
 Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 6/67 (8%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI----PVGK--GCGFVQFANRENAEEALH 118
             +FV  L+P  TDEDL   FS++G+I S ++      G      F++F  +E+ EEA  
Sbjct: 4   NVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYF 63

Query: 119 KLNGTVI 125
           K++  +I
Sbjct: 64  KMDNVLI 70

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

 Score = 52.8 bits (127), Expect = 9e-10
 Identities = 26/52 (50%), Positives = 32/52 (61%), Gaps = 4/52 (7%)

Query: 78  DEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNGTVI 125
           D DLRQ F Q+G I  V+I       KG GFV FAN  +A+ A  KL+GTV+
Sbjct: 14  DPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLHGTVV 65

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

 Score = 52.8 bits (127), Expect = 9e-10
 Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 119
           T+FVG L  +V DE L+  F ++G +   ++         +G G+V F + E+A++A+  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 120 LNGTVIGKQSVRL 132
           ++G  +  + + +
Sbjct: 61  MDGKELDGRPINV 73

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

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

 Score = 56.7 bits (137), Expect = 1e-09
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 5/74 (6%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEA 116
           S    IFV  LD +V ++ L   FS++G I S K+        +G GFV F   E+A+ A
Sbjct: 86  SGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAA 145

Query: 117 LHKLNGTVIGKQSV 130
           + K+NG ++  + V
Sbjct: 146 IQKVNGMLLNDKEV 159

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|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 52.4 bits (126), Expect = 1e-09
 Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 14/83 (16%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
            +++G +D ++T+E LR  FSQYGEI SV     K C FV F N  NA +A+  +     
Sbjct: 5   NVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAIKAIDGVK---- 60

Query: 126 GKQSVRLSWGRNPANKQFRADYG 148
                      +P  K+F+  YG
Sbjct: 61  ----------SHPLFKKFKISYG 73

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins

 Score = 52.7 bits (126), Expect = 1e-09
 Identities = 22/76 (28%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
           +TT++VG LD   T +D+     ++G I S+ +   +GC ++   +R++A  AL KL+  
Sbjct: 4   STTLWVGQLDKRTTQQDVTSLLEEFGPIESINMIPPRGCAYIVMVHRQDAYRALQKLSRG 63

Query: 124 V--IGKQSVRLSWGRN 137
              + ++S++++W  N
Sbjct: 64  NVKVNQKSIKIAWALN 79

The CD corresponds to the RRM of SCAF4 (also termed splicing factor, arginine/serine-rich 15 or SFR15, or CTD-binding SR-like protein RA4) that belongs to a new class of SCAFs (SR-like CTD-associated factors). Although its biological function remains unclear, SCAF4 shows high sequence similarity to SCAF8 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) and may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF4 and SCAF8 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 81

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

 Score = 52.3 bits (126), Expect = 1e-09
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 6/71 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKL 120
           ++V GL       DL+Q FS+YG++   KI      P  +  GFV  A+ E A + +  L
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 121 NGTVIGKQSVR 131
           + T +  + + 
Sbjct: 62  HRTELHGRVIS 72

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

 Score = 51.9 bits (125), Expect = 1e-09
 Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 3/71 (4%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC---GFVQFANRENAEEALHKLNGT 123
           ++VG LD  VT++ L + FSQ G I S K+    G     FV++ +  +A  AL  +NG 
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60

Query: 124 VIGKQSVRLSW 134
           +I  Q ++++W
Sbjct: 61  LILGQEIKVNW 71

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

 Score = 56.4 bits (136), Expect = 2e-09
 Identities = 29/79 (36%), Positives = 47/79 (59%), Gaps = 7/79 (8%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVG--KGCGFVQFANRENAEEALHK 119
           T ++V  LDP+V ++ LR+ F+++GEI S  +     G  +G  FV F   E+A +A+ +
Sbjct: 179 TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEE 238

Query: 120 LNGTVIG--KQSVRLSWGR 136
           +NG  IG  K+  +L  GR
Sbjct: 239 MNGKKIGLAKEGKKLYVGR 257

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

 Score = 51.9 bits (125), Expect = 2e-09
 Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENAEEALH 118
           + T+FVG LD  VT+E L + F Q G +  VKIP       K   FV F +  +   A+ 
Sbjct: 1   DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQ 60

Query: 119 KLNGTVIGKQSVRLS 133
            LNG  +  + +R+ 
Sbjct: 61  LLNGIRLFGRELRIK 75

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

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

 Score = 51.9 bits (125), Expect = 2e-09
 Identities = 19/71 (26%), Positives = 42/71 (59%), Gaps = 6/71 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           I+V  + P+++++D++  F  +G+I S  +         KG GF+++ N ++A++A+  +
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 121 NGTVIGKQSVR 131
           N   +G Q +R
Sbjct: 63  NLFDLGGQQLR 73

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

 Score = 51.5 bits (124), Expect = 2e-09
 Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
           +FVG L    T E+LR  F +YG +   +  V K  GFV     E+AE+A+  LNG   
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTV--TECDVVKNYGFVHMEEEEDAEDAIKALNGYEF 58

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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 51.9 bits (124), Expect = 2e-09
 Identities = 27/79 (34%), Positives = 47/79 (59%), Gaps = 5/79 (6%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-VGKG----CGFVQFANRENAEEAL 117
           +N T+F+G LD  VT+ DLR+ F ++G I  V I   G+G     GF++F N + A  A 
Sbjct: 6   ANRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAK 65

Query: 118 HKLNGTVIGKQSVRLSWGR 136
             ++G V+ +  +++ +G+
Sbjct: 66  LAMSGKVLRRNPIKIGYGK 84

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

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

 Score = 51.5 bits (123), Expect = 3e-09
 Identities = 26/64 (40%), Positives = 37/64 (57%), Gaps = 6/64 (9%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALH 118
             ++V GL   +T ++L Q FSQYG I + +I       V +G GF++F  R  AEEA+ 
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 119 KLNG 122
            LNG
Sbjct: 61  GLNG 64

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

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

 Score = 51.6 bits (123), Expect = 3e-09
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 6/75 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKL 120
           +FVG L P +T +D++  F+ +G I+  ++         KG GFV F N+ +AE A+ ++
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 121 NGTVIGKQSVRLSWG 135
            G  +G + +R +W 
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 51.1 bits (123), Expect = 3e-09
 Identities = 26/61 (42%), Positives = 36/61 (59%), Gaps = 4/61 (6%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEAL---HKLNG 122
           +FVG L  ++T+EDLRQ FSQ+GE+  V IP   +   FV FA+ E A+      H + G
Sbjct: 3   VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFADPEVAQSLCGEDHIIKG 62

Query: 123 T 123
            
Sbjct: 63  V 63

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

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

 Score = 51.2 bits (123), Expect = 3e-09
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           IFVGGL P  T+E +R+ F ++G I  +++P+       +G  F+ F + E  ++ L   
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILETQ 61

Query: 121 NGTVIGKQ 128
              + GK+
Sbjct: 62  FHVIGGKK 69

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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 50.9 bits (122), Expect = 4e-09
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 3/70 (4%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGKGCGFVQFANRENAEEALHKLNG 122
           T+F+G L+   T  DLR+ F ++GEI  + I          F+Q+A+  +  +A+ K++G
Sbjct: 4   TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDG 63

Query: 123 TVIGKQSVRL 132
             +G   V+L
Sbjct: 64  EYLGNNRVKL 73

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

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

 Score = 50.8 bits (122), Expect = 4e-09
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 8/69 (11%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 120
           IFVG +D   T E+L++ F   G I  + I         KG  +++F ++ + E AL  L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LL 60

Query: 121 NGTVI-GKQ 128
           N +   G+Q
Sbjct: 61  NESEFRGRQ 69

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

 Score = 50.7 bits (122), Expect = 4e-09
 Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 11/83 (13%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           ++VGGL P  +  +L + F ++G I  +    G+   ++++ + E A+ A   L G  +G
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQAAKEALRGFPLG 60

Query: 127 KQSVRLSWGRNPANKQFRADYGN 149
                         ++ R D+ +
Sbjct: 61  G-----------PGRRLRVDFAD 72

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

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

 Score = 50.7 bits (122), Expect = 5e-09
 Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 6/69 (8%)

Query: 69  VGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNG 122
           V GL    T+ DLR+ FS+YG I  V++         +G GFV F + E+A+EA  +LNG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

Query: 123 TVIGKQSVR 131
             I  + +R
Sbjct: 64  MEIDGRRIR 72

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

 Score = 50.3 bits (121), Expect = 5e-09
 Identities = 26/67 (38%), Positives = 37/67 (55%), Gaps = 6/67 (8%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALH 118
           T +++ GL PN TDEDL +    +G+I S K  +       KG GFV F + E A +A+ 
Sbjct: 1   TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 119 KLNGTVI 125
            LNG  +
Sbjct: 61  GLNGRGV 67

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

 Score = 50.6 bits (121), Expect = 6e-09
 Identities = 29/75 (38%), Positives = 36/75 (48%), Gaps = 6/75 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGK---GCGFVQFANRENAEEALHK 119
           T+FV  L  +VT EDL   FS    I     V  P      G GFV FA  E+A+EAL K
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 120 LNGTVIGKQSVRLSW 134
           L    +  + +RL  
Sbjct: 61  LKNKKLHGRILRLDI 75

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

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

 Score = 50.4 bits (121), Expect = 8e-09
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKL 120
           T+FVG L  +   +DL + F + GE+  V+I        KG G V+FA  E A++AL + 
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EK 59

Query: 121 NGTVIGKQSVRL 132
           +G  +  + +R+
Sbjct: 60  SGEELLGREIRV 71

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

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

 Score = 50.1 bits (120), Expect = 9e-09
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 6/68 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALHKL 120
           IFVGGL P+VT+E+ ++ FSQ+G++   ++          G GFV F +    E      
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 121 NGTVIGKQ 128
              + GKQ
Sbjct: 62  MLELGGKQ 69

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

 Score = 50.1 bits (120), Expect = 1e-08
 Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 6/78 (7%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALH 118
           T+++V  +      +DLR+ F +YG I  V IP+       +G  +VQF +  +AE+AL+
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 119 KLNGTVIGKQSVRLSWGR 136
            L+ T    + + + + +
Sbjct: 61  YLDRTRFLGREIEIQFAQ 78

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

 Score = 49.6 bits (119), Expect = 1e-08
 Identities = 23/67 (34%), Positives = 31/67 (46%), Gaps = 6/67 (8%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF--VQFANRENAEEAL---HK 119
            T+ V  L  + T+  +RQ F   GEI  VKI   +G     ++F   + A  AL   HK
Sbjct: 1   LTVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLVAVIEFETEDEALAALTKDHK 60

Query: 120 -LNGTVI 125
            L G  I
Sbjct: 61  RLGGNEI 67

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

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

 Score = 50.2 bits (119), Expect = 1e-08
 Identities = 29/86 (33%), Positives = 46/86 (53%), Gaps = 8/86 (9%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
           +  ++V GL   +T ++L Q FSQYG I + +I V       +G GF++F  R  AEEA+
Sbjct: 5   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64

Query: 118 HKLNGTVI--GKQSVRLSWGRNPANK 141
             LNG       + + + +  NP+ K
Sbjct: 65  KGLNGQKPPGATEPITVKFANNPSQK 90

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

 Score = 49.5 bits (119), Expect = 1e-08
 Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVK-IPVGKGCGFVQFANRENAEEALHKLNGTV 124
           T+ V  LD  ++D++LR  FSQ+GE+  ++  P+     FV+F +   AE AL  LNG  
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNGRP 62

Query: 125 I-GKQ 128
             G +
Sbjct: 63  FLGGR 67

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

>gnl|CDD|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 = 49.7 bits (119), Expect = 1e-08
 Identities = 23/62 (37%), Positives = 37/62 (59%), Gaps = 5/62 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVG--KGCGFVQFANRENAEEALHKLN 121
           +FVG L    T++D+R+ F  +G I    I   P G  KGC FV+F++   A+ A++ L+
Sbjct: 4   LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63

Query: 122 GT 123
           G+
Sbjct: 64  GS 65

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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 49.5 bits (118), Expect = 1e-08
 Identities = 24/63 (38%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI- 125
           +FVG L P++T+E++R+ F +YG+   + I   KG GF++   R  AE A  +L+   + 
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLAEIAKAELDNMPLR 63

Query: 126 GKQ 128
           GKQ
Sbjct: 64  GKQ 66

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

 Score = 49.9 bits (120), Expect = 1e-08
 Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 6/66 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVK----IPVG--KGCGFVQFANRENAEEALHK 119
           T+FVG L    T+E LR+ FS+YG+I  ++    I  G  KG  FV++ +  +A  A   
Sbjct: 5   TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

Query: 120 LNGTVI 125
            +  VI
Sbjct: 65  AHKLVI 70

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

 Score = 49.4 bits (118), Expect = 1e-08
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVK-IPVGKGCGFVQFANRENAEEALHKLNGTV 124
           T+ +  LDP V+ E LR  F  YG++  ++  P  +   FV+F +  +A +AL  +NG  
Sbjct: 3   TLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNGKE 62

Query: 125 IGKQSVRL 132
           I  + V +
Sbjct: 63  ISGKPVVI 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|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 49.7 bits (118), Expect = 2e-08
 Identities = 26/65 (40%), Positives = 38/65 (58%), Gaps = 6/65 (9%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL 117
           +  ++V GL   +T ++L Q FSQYG I + +I       V +G GF++F  R  AEEA+
Sbjct: 2   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61

Query: 118 HKLNG 122
             LNG
Sbjct: 62  KGLNG 66

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

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 26/76 (34%), Positives = 45/76 (59%), Gaps = 6/76 (7%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 118
           T + V  L  N+T +++R  FS  GEI S K+   K      G GFV + + E+AE+A++
Sbjct: 2   TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61

Query: 119 KLNGTVIGKQSVRLSW 134
            LNG  +  +++++S+
Sbjct: 62  TLNGLRLQNKTIKVSY 77

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

 Score = 49.1 bits (117), Expect = 2e-08
 Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
           +FVG L P  T++++R  F QYG++    I   K  GFV   ++  A+EA+  L+
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDII--KNYGFVHMDDKTAADEAIRNLH 55

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

 Score = 49.1 bits (118), Expect = 2e-08
 Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 6/63 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALHKL 120
           ++VG LD  VT+E L + F Q G + +V IP  +      G GFV+F + E+A+ A+  +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 121 NGT 123
           N  
Sbjct: 61  NMI 63

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

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK--GCGFVQFANRENAEEALHK 119
           + + V  L   + ++ LR+ F  +G I  V++     GK    GFV +   E A++AL  
Sbjct: 1   SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKH 60

Query: 120 LNGTVIGKQSVRL 132
            N + I    + +
Sbjct: 61  FNNSFIDTSKITV 73

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

 Score = 48.7 bits (117), Expect = 3e-08
 Identities = 26/65 (40%), Positives = 38/65 (58%), Gaps = 7/65 (10%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQ-FA--NRENAEEALHK---- 119
           +FVGGL P+VT+ DL + FS++G ++ V+I   K  G  + FA  +   +E  L K    
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 120 LNGTV 124
           LNGT 
Sbjct: 62  LNGTK 66

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|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3)

 Score = 48.6 bits (116), Expect = 3e-08
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--PVGKGCGFVQFANRENAEEALHKLNGT 123
            I V  L  +VT+ED+    +++G I +VK+    GK    V+FA  E A EAL   + +
Sbjct: 9   MIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKKQALVEFATEEQATEALACKHAS 68

Query: 124 VIGKQSVRLSW 134
            +   ++RL++
Sbjct: 69  SLNGSTIRLAF 79

This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

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

 Score = 50.0 bits (119), Expect = 3e-08
 Identities = 30/111 (27%), Positives = 52/111 (46%), Gaps = 8/111 (7%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
           +T +F+GGL     D  LR  F+ +G++   K+ V       +G GFV F +   A  A+
Sbjct: 34  STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93

Query: 118 HKLNGTVIGKQSVRLSWG--RNPANKQFRADYGNQWSGAYYGGQVYDGYGY 166
            +++G  +  + +R++    R  A + +    G    G  YGG    G G+
Sbjct: 94  SEMDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGGGDGGGGF 144

Length = 144

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 48.4 bits (116), Expect = 3e-08
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASV-KIPVGKGCGFVQFANRENAEEALHKLNGTV 124
           T+FV  ++ NV DE+LR  F Q+G+I ++      +G   V + +   A  A   L GT 
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTE 62

Query: 125 IGKQS 129
           +G + 
Sbjct: 63  LGGRK 67

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

 Score = 48.3 bits (115), Expect = 4e-08
 Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PV---GKGCGFVQFANRENAEEAL--- 117
           +FVGGL  + T +DL++ FS++GE+    I   PV    +G GFV F +  + E+ L   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 118 -HKLNGTVI 125
            HKL+G VI
Sbjct: 61  EHKLDGRVI 69

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

 Score = 48.5 bits (116), Expect = 4e-08
 Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 6/62 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP----VGKGCG--FVQFANRENAEEALHK 119
           T++V  L  N T E L+  FS+YG +  V +P     G   G  F++F   E A++A   
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

Query: 120 LN 121
           LN
Sbjct: 61  LN 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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 48.5 bits (115), Expect = 4e-08
 Identities = 27/78 (34%), Positives = 45/78 (57%), Gaps = 6/78 (7%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 118
           T + V  L  N+T ++LR  FS  GE+ S K+   K      G GFV + N ++AE A++
Sbjct: 2   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61

Query: 119 KLNGTVIGKQSVRLSWGR 136
            LNG  +  +++++S+ R
Sbjct: 62  TLNGLRLQSKTIKVSYAR 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|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 48.1 bits (115), Expect = 4e-08
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 6/75 (8%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALH 118
           +T++V  L  ++T+ DL + FS+YG++  V I         KG  F+ F +RE+A + + 
Sbjct: 2   STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61

Query: 119 KLNGTVIGKQSVRLS 133
            LN   +  ++++ S
Sbjct: 62  ALNNKELFGRTLKCS 76

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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 48.1 bits (115), Expect = 4e-08
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI-----PVGKGCGFVQFANRENAEEALHK 119
           T +++  L  ++ ++DL      YG++ S +I        +G GF +  +RE  E+ + K
Sbjct: 1   TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISK 60

Query: 120 LNGTVIGKQSVRL 132
            NG  +  +   L
Sbjct: 61  FNGKYLKGEGEPL 73

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 51.5 bits (123), Expect = 4e-08
 Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 6/64 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKL 120
           ++V GL   +T  +L   FS +G+I + +I       + KG GF++F  R+ A+ A+  L
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151

Query: 121 NGTV 124
           NGT 
Sbjct: 152 NGTT 155

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|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 48.0 bits (115), Expect = 5e-08
 Identities = 20/55 (36%), Positives = 31/55 (56%)

Query: 70  GGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTV 124
           GGL   V+ E+L + F +YG +  + +P GK   FV +++ E+A  A   LNG  
Sbjct: 9   GGLGNGVSREELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDALNGKE 63

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

 Score = 48.0 bits (115), Expect = 5e-08
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 5/67 (7%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGKG--CGFVQFANRENAEEALHK 119
           + I V  L   VT++ LR+ F   GE+  VK+     GK    GFV F + E+A++A+  
Sbjct: 1   SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 120 LNGTVIG 126
            N T I 
Sbjct: 61  FNKTFID 67

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|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 = 6e-08
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 10/66 (15%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA---- 116
           IFVGGL  N T++D+++ FSQ+G++    +   K      G GFV F + +  ++     
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 117 LHKLNG 122
            H++N 
Sbjct: 62  FHEINN 67

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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 47.8 bits (113), Expect = 7e-08
 Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 6/80 (7%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA 116
           S T + V  L  N+T E+ R  F   GEI S K+   K      G GFV + + ++AE+A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 117 LHKLNGTVIGKQSVRLSWGR 136
           ++ LNG  +  +++++S+ R
Sbjct: 61  INTLNGLRLQTKTIKVSYAR 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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 47.6 bits (114), Expect = 7e-08
 Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 1/71 (1%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
           N  +F+  L    T E L   F+Q+     V++   +G  FV+F   E A  AL  L G 
Sbjct: 2   NKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPRRGIAFVEFETEEQATVALQALQGF 61

Query: 124 -VIGKQSVRLS 133
            +    ++++S
Sbjct: 62  KITPGHAMKIS 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|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 47.5 bits (114), Expect = 7e-08
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 64  NTTIFVGGLDPNVTDED-LRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALH 118
           NTT+ V  + P + +   L + FS++G I ++++        VQF+  E A++A  
Sbjct: 1   NTTLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPESALVQFSTSEEAKKAYR 56

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

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

 Score = 47.3 bits (113), Expect = 8e-08
 Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 10/70 (14%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEAL-- 117
            +FVG L   V  ++L++ FSQ+G++ S  +P      + KG GFV F++R+  E AL  
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 118 --HKLNGTVI 125
             H L G  +
Sbjct: 61  QKHILEGNKL 70

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|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 47.7 bits (113), Expect = 8e-08
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL--- 117
           +F+GGL  + T +DL+  FS++GE+    + +       +G GFV F   E+ ++ +   
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 118 -HKLNGTVI 125
            HKLNG VI
Sbjct: 61  EHKLNGKVI 69

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

 Score = 47.7 bits (113), Expect = 8e-08
 Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 6/65 (9%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL 117
           +  ++V GL   ++ +++ Q FSQYG I + +I       + +G GF++F  R  AEEA+
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60

Query: 118 HKLNG 122
             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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 47.6 bits (114), Expect = 8e-08
 Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 6/81 (7%)

Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANREN 112
           E   ++  IFVG L   VTDE L + FS+Y      K+         KG GFV F++  +
Sbjct: 1   EWPENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPND 60

Query: 113 AEEALHKLNGTVIGKQSVRLS 133
             +A+ ++NG  +G + ++L 
Sbjct: 61  YLKAMKEMNGKYVGNRPIKLR 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|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 47.3 bits (113), Expect = 8e-08
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIA------SVKIPVGKGCGFVQFANRENAEEALHK 119
            + VG L    TDE  R+  S +G +       S      KG GFV++A++ +A +A ++
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 120 LNGTVIGKQSVRLSW 134
           L+G  IG + +++ W
Sbjct: 61  LDGKQIGGRKLQVDW 75

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|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 47.3 bits (113), Expect = 9e-08
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 10/72 (13%)

Query: 64  NTTIFVGGL----DPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE---EA 116
           N T++VGG+         +E LR+ F ++G+I  +++   KG  FV++  R +AE   EA
Sbjct: 1   NRTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSKGIAFVRYKYRASAEFAKEA 60

Query: 117 LHK---LNGTVI 125
           +       G V+
Sbjct: 61  MADQSLDGGEVL 72

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 47.7 bits (113), Expect = 9e-08
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 5/75 (6%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-VGKGCG----FVQFANRENAEEALHKLN 121
           +F+G LD NV++ +LR+ F +YG I  V I    +G G    F++F N + A  A   ++
Sbjct: 11  LFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAMS 70

Query: 122 GTVIGKQSVRLSWGR 136
           G VIG+  +++ +G+
Sbjct: 71  GRVIGRNPIKIGYGK 85

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

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

 Score = 47.6 bits (113), Expect = 9e-08
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 6/66 (9%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALH 118
           T ++V  L   +T+++LR+ F  YG I    +       + +G  FV++  RE A+ A+ 
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 119 KLNGTV 124
            LNGT+
Sbjct: 61  SLNGTI 66

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 50.7 bits (121), Expect = 1e-07
 Identities = 28/88 (31%), Positives = 49/88 (55%), Gaps = 7/88 (7%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA 116
           S T + V  L   +T E++R  F+  GEI S K+   K      G GFV +   E+AE+A
Sbjct: 2   SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61

Query: 117 LHKLNGTVIGKQSVRLSWGRNPANKQFR 144
           ++ LNG  +  +++++S+ R P++   +
Sbjct: 62  VNSLNGLRLQNKTIKVSYAR-PSSDSIK 88

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

 Score = 47.2 bits (113), Expect = 1e-07
 Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 6/74 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG----CGF--VQFANRENAEEALHKL 120
           ++VG L    T+E + + FS+ G+I  + + + +     CGF  V++  RE+AE A+  L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 121 NGTVIGKQSVRLSW 134
           NGT +  + +R+ W
Sbjct: 61  NGTKLDDRIIRVDW 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|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 47.2 bits (113), Expect = 1e-07
 Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 12/82 (14%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG------CGFVQFANRENAEEALH 118
           +T++V    P+    D+R  F QYGEI S++ P  +       C +VQF + E+A  A+ 
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFC-YVQFTSPESAAAAVA 59

Query: 119 KLNGTVIG--KQSVRLSWGRNP 138
            LNG +    K  V++S   +P
Sbjct: 60  LLNGKLGEGYKLVVKIS---DP 78

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

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

 Score = 47.0 bits (112), Expect = 1e-07
 Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK---GCGFVQFANRENAEEAL--- 117
           +F+GGL    T E LR+ FS++GEI    +   P  K   G GFV F++  + ++ L   
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 118 -HKLNGTVI 125
            H+L+G  I
Sbjct: 61  PHELDGKKI 69

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

 Score = 47.3 bits (113), Expect = 1e-07
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 7/75 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIA-SVKI------PVGKGCGFVQFANRENAEEALHK 119
           +F+G LDP V ++ L   FS +G I  + KI         KG  F+ + + E ++ A+  
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 120 LNGTVIGKQSVRLSW 134
           +NG  +  + + +S+
Sbjct: 64  MNGQYLCNRPITVSY 78

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

 Score = 47.4 bits (112), Expect = 1e-07
 Identities = 27/82 (32%), Positives = 47/82 (57%), Gaps = 6/82 (7%)

Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAE 114
           + S T + V  L  N+T E+L+  F   GEI S K+   K      G GFV + + ++AE
Sbjct: 1   EDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAE 60

Query: 115 EALHKLNGTVIGKQSVRLSWGR 136
           +A++ LNG  +  +++++S+ R
Sbjct: 61  KAINTLNGLRLQTKTIKVSYAR 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|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 47.1 bits (112), Expect = 1e-07
 Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 5/64 (7%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI-----PVGKGCGFVQFANRENAEEALHKLN 121
           +FVG L+   T++++ + FS YG +  + +        +GC FV+++++E A+ A+  LN
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 122 GTVI 125
           G   
Sbjct: 62  GVYT 65

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|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 47.0 bits (112), Expect = 1e-07
 Identities = 16/54 (29%), Positives = 30/54 (55%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL 120
           +++G L  + ++E+LR+   ++G I  +KI   K   FV F +  NA + +  L
Sbjct: 6   VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVTTL 59

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|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 = 46.8 bits (112), Expect = 1e-07
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 120
           +FVG +  + T+E L + FS+ G + S ++         KG GF +F + E A  A+  L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 121 NGTVIGKQSVRLSW 134
           NG     +++R+ +
Sbjct: 61  NGYEFNGRALRVDF 74

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

 Score = 46.6 bits (111), Expect = 1e-07
 Identities = 17/56 (30%), Positives = 33/56 (58%), Gaps = 2/56 (3%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
           +++G L     + D+ + F  YG I  + +    G GFV+F +  +A++A+++LNG
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINLK--NGFGFVEFEDPRDADDAVYELNG 55

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|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 = 46.5 bits (111), Expect = 1e-07
 Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 6/67 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 120
           +F+  L    TD+DL Q F+ +G + S K+ V       K  GFV + N E+A+ A+  +
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 121 NGTVIGK 127
           NG  +G 
Sbjct: 61  NGFQVGG 67

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

 Score = 46.5 bits (110), Expect = 2e-07
 Identities = 23/66 (34%), Positives = 42/66 (63%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           +FVG L  ++T+++ ++ F++YGE   V I  GKG GF++  +R  AE A  +L+ T + 
Sbjct: 4   LFVGNLPADITEDEFKKLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTPMR 63

Query: 127 KQSVRL 132
            + +R+
Sbjct: 64  GRQLRV 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|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 46.6 bits (111), Expect = 2e-07
 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 6/64 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           +F+  L    T+EDL + FS+YG ++ V +P+       KG  FV +   E+A +A  +L
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 121 NGTV 124
           +GTV
Sbjct: 65  DGTV 68

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

 Score = 46.5 bits (111), Expect = 2e-07
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 7/75 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQ-YGEIASVKIPVG-----KGCGFVQFANRENAEEALHK 119
           ++FVG L P+V D  L + FS+ Y      K+ +      +G GFV+F++    + AL +
Sbjct: 3   SLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTE 62

Query: 120 LNGTV-IGKQSVRLS 133
           + G   +G + +R+S
Sbjct: 63  MQGASGLGGKPIRVS 77

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

 Score = 46.7 bits (111), Expect = 2e-07
 Identities = 22/69 (31%), Positives = 39/69 (56%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL--- 117
           +FVGGL+   +D  LR+ F++YG++    + V        G GF+ F++ + A+EA+   
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQ 64

Query: 118 -HKLNGTVI 125
            H ++G  I
Sbjct: 65  PHSIDGNQI 73

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

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 6/74 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           IFV G+     +ED+   F+++GEI ++ + +       KG   +++  ++ A+ A+  L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 121 NGTVIGKQSVRLSW 134
           NG  +  Q++ + W
Sbjct: 69  NGKELLGQTISVDW 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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 46.4 bits (110), Expect = 2e-07
 Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 5/62 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKL 120
           T+FVG LDP VT+E + + F Q G +  VKIP       K   FV F +  +   A++ L
Sbjct: 3   TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLL 62

Query: 121 NG 122
           NG
Sbjct: 63  NG 64

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|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 46.2 bits (109), Expect = 2e-07
 Identities = 28/75 (37%), Positives = 44/75 (58%), Gaps = 4/75 (5%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEI--ASVKIPVGK--GCGFVQFANRENAEEALHKLNG 122
           IFV  L  ++T + L++ FSQ G +  A +K+  GK  GCG V+F + E+AE+A   +NG
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKMENGKSKGCGTVRFDSPESAEKACRLMNG 61

Query: 123 TVIGKQSVRLSWGRN 137
             I  + + +   RN
Sbjct: 62  IKINGREIDVRLDRN 76

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 46.5 bits (110), Expect = 2e-07
 Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 6/68 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           IFVGGL+P  T+E +R+ F ++GEI ++++P+       +G  F+ F   +  ++ L K 
Sbjct: 7   IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLEKK 66

Query: 121 NGTVIGKQ 128
              V G +
Sbjct: 67  FHNVSGSK 74

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

>gnl|CDD|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 = 46.1 bits (110), Expect = 3e-07
 Identities = 17/53 (32%), Positives = 31/53 (58%), Gaps = 5/53 (9%)

Query: 76  VTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGT 123
            T ++LR+ FS +G++ SV++P       +G  FV+F  ++ A+ A+  L  T
Sbjct: 12  ATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKST 64

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|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 46.1 bits (109), Expect = 3e-07
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 7/71 (9%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALH 118
           +++FV  +  +   EDLR+ F +YG I  V +P+       +G  +VQF +  +AE+ALH
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 119 KLNGT-VIGKQ 128
            L+   + G+Q
Sbjct: 61  NLDRKWICGRQ 71

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|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 46.0 bits (110), Expect = 3e-07
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 7/78 (8%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG---CGFVQFANRENAEEALHKLN 121
            T+FV  L PN T+E+LRQ FS+      +K+   KG     FV+F +   A +AL+ L 
Sbjct: 3   NTLFVANLGPNTTEEELRQLFSRQPGFRRLKM-HNKGGGPVCFVEFEDVSFATQALNSLQ 61

Query: 122 GTVI---GKQSVRLSWGR 136
           G V+    +  +R+ + +
Sbjct: 62  GAVLSSSDRGGIRIEYAK 79

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

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

 Score = 46.2 bits (109), Expect = 3e-07
 Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 6/77 (7%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
           N  + V GL    T+ DLR+ FS+YG IA V I         +G  FV F N ++A+EA 
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68

Query: 118 HKLNGTVIGKQSVRLSW 134
            + NG  +  + +R+ +
Sbjct: 69  ERANGMELDGRRIRVDF 85

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 48.8 bits (116), Expect = 4e-07
 Identities = 30/95 (31%), Positives = 46/95 (48%), Gaps = 7/95 (7%)

Query: 54  QGPQ-SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQ 106
            G Q +  D +   IFV  L P+  +  L Q F  +G + +VKI         KG GFV 
Sbjct: 258 AGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVS 317

Query: 107 FANRENAEEALHKLNGTVIGKQSVRLSWGRNPANK 141
             N + A  A+  LNG  +G + +++S+  N A +
Sbjct: 318 MTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAYR 352

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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 46.1 bits (109), Expect = 4e-07
 Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 10/66 (15%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA---- 116
           +FVGGL  +V + DL + FSQ+G +   ++   K      G GFV F N ++A++A    
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61

Query: 117 LHKLNG 122
            H +NG
Sbjct: 62  FHPING 67

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

 Score = 45.3 bits (107), Expect = 4e-07
 Identities = 20/70 (28%), Positives = 42/70 (60%), Gaps = 2/70 (2%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           +F+G L+P   ++D+ + F  YG I  + +   +G GFV+F +  +A++A+++L+G  + 
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRIRDIDLK--RGFGFVEFDDPRDADDAVYELDGKELC 59

Query: 127 KQSVRLSWGR 136
            + V +   R
Sbjct: 60  NERVTIEHAR 69

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

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

 Score = 45.5 bits (108), Expect = 4e-07
 Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 9/75 (12%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 120
           +FVG L    T+++LR  F + G I  V++         KG  FV F   E A  A   L
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA---L 57

Query: 121 NGTVIGKQSVRLSWG 135
            G  +  +++R+ +G
Sbjct: 58  KGKHLNGRALRVEYG 72

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|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 = 45.3 bits (108), Expect = 5e-07
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 6/76 (7%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQ-YGEIASVKI---PVGK--GCGFVQFANRENAEEALH 118
           + + V  L  ++T+ +L++ FS+  GEI  VK+     GK     F+ +   E A++A  
Sbjct: 1   SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKD 60

Query: 119 KLNGTVIGKQSVRLSW 134
             N T I    + + +
Sbjct: 61  YFNNTYINTSKISVEF 76

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

 Score = 45.3 bits (107), Expect = 5e-07
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 9/68 (13%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI----PVG--KGCGFVQFANRENAEEAL--- 117
           +F+GGL+   TD+ LR+ F Q+GE+    +      G  +G GF+ F   ++  E +   
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 118 HKLNGTVI 125
           H L+G +I
Sbjct: 61  HILDGKII 68

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

 Score = 45.4 bits (108), Expect = 5e-07
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 118
           T + V  L  ++T E+LR  F   G I S KI   +      G GFV + +  +A++A++
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 119 KLNGTVIGKQSVRLSW 134
            LNG  I  + +++S+
Sbjct: 61  TLNGFEIRNKRLKVSY 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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 45.0 bits (106), Expect = 6e-07
 Identities = 18/57 (31%), Positives = 35/57 (61%), Gaps = 6/57 (10%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEAL 117
           +FVGGL P+ T+E +++ F  +GEI ++++P+       +G  FV + + E  ++ L
Sbjct: 2   VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLL 58

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

 Score = 45.3 bits (108), Expect = 6e-07
 Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 66  TIFVGGLDPNVTDED-LRQPFSQYG-----EIASVKIPVGKGCGFVQFANRENAEEALHK 119
            +FV  L     D   LR+ FSQ G     ++A       +G  FV++A  E+AEEA   
Sbjct: 4   CLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQA 63

Query: 120 LNGTVIGKQSVRLSWG 135
           LNG  +    +R+S+G
Sbjct: 64  LNGHSLQGSPIRVSFG 79

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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 45.3 bits (108), Expect = 7e-07
 Identities = 25/82 (30%), Positives = 34/82 (41%), Gaps = 24/82 (29%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGC----------------- 102
           T+FVG L      +DL++ F Q+G I SV+                              
Sbjct: 2   TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61

Query: 103 GFVQFANRENAEEALHKLNGTV 124
            +V F   E+AE+AL KLNGT 
Sbjct: 62  AYVVFKEEESAEKAL-KLNGTE 82

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

 Score = 45.0 bits (107), Expect = 7e-07
 Identities = 27/66 (40%), Positives = 37/66 (56%), Gaps = 7/66 (10%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC-----GFVQFANRENAEEALHKL 120
           TI+VG LDP  T + L + FSQ GE+  V++  G         FV+FA + +   AL KL
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRM-AGDETQPTRYAFVEFAEQTSVINAL-KL 63

Query: 121 NGTVIG 126
           NG + G
Sbjct: 64  NGAMFG 69

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|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 44.5 bits (106), Expect = 8e-07
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)

Query: 69  VGGLDPNVTDEDLRQPFSQYGEI--ASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           V GL    + +DL+    Q G++  A V     +G G V+F ++E+ E AL KL+GT   
Sbjct: 5   VSGLPEGASWQDLKDFGRQAGDVTYADVDRD-QEGEGVVEFTSQEDMERALRKLDGTEFR 63

Query: 127 KQSVRL 132
            + VR+
Sbjct: 64  GRRVRV 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|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 = 45.1 bits (107), Expect = 8e-07
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 9/68 (13%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRE-- 111
            D     +FVG +  N+ ++DLR  F Q+G+I  + +       + KGC F+ +  RE  
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESA 60

Query: 112 -NAEEALH 118
             A+ ALH
Sbjct: 61  LKAQSALH 68

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

 Score = 44.8 bits (106), Expect = 8e-07
 Identities = 26/69 (37%), Positives = 34/69 (49%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVG---KGCGFVQFANRENAEEAL--- 117
           +FVGGL    T E LR+ FSQYGE+     +K       +G GFV+F +       L   
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61

Query: 118 -HKLNGTVI 125
            H L+G  I
Sbjct: 62  PHTLDGRTI 70

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|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 44.6 bits (105), Expect = 1e-06
 Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 3/66 (4%)

Query: 64  NTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
           N+ +F+G L+   V   D+   FS+YG+I  V   V KG  FVQ+ N  NA  A+   +G
Sbjct: 1   NSRVFIGNLNTLVVKKSDVEAIFSKYGKI--VGCSVHKGFAFVQYVNERNARAAVAGEDG 58

Query: 123 TVIGKQ 128
            +I  Q
Sbjct: 59  RMIAGQ 64

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

 Score = 44.2 bits (105), Expect = 1e-06
 Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLN 121
           IFV  L  +VT +DL+  F + G +    +        KG G V F + E+A+ A+   N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 122 GTVI 125
           G  +
Sbjct: 61  GYDL 64

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|220013 pfam08777, RRM_3, RNA binding motif

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 71  GLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN--GTVIGKQ 128
           GL+   + ED+++ FSQ+GE+  V    G   G+V+F   E A++AL K       I + 
Sbjct: 8   GLNKPTSREDIKEAFSQHGEVKYVDFLEGDKEGYVRFKTPEAAKKALEKATEAKLKIKEA 67

Query: 129 SVRL 132
            V L
Sbjct: 68  EVTL 71

This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif. Length = 102

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

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 11/81 (13%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYG--EIASVKI------PVGKGCGFVQFANRENAEE 115
             T+ + GLD   T+ED+ Q  S      I  V++         +G  FV+F + E+A +
Sbjct: 2   TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQ 61

Query: 116 ALHKLNG---TVIGKQSVRLS 133
            +  LN     VI  + VR+S
Sbjct: 62  WMDALNNLDPFVIDGRVVRVS 82

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|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins

 Score = 44.5 bits (105), Expect = 1e-06
 Identities = 24/70 (34%), Positives = 36/70 (51%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
           T+F GG+  N+ + DLR  F ++GE+ S  +   K   FV+  NR +AE A   +     
Sbjct: 5   TLFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHAFVKMYNRRDAENAREAMEQYKS 64

Query: 126 GKQSVRLSWG 135
           G   +R  WG
Sbjct: 65  GDMQLRTRWG 74

This subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein encoded by gene NRD1 (for nuclear pre-mRNA down-regulation) from yeast S. cerevisiae. It is implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by polymerase II, and plays a critical role in pre-mRNA metabolism. Nrd1 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable. Seb1 is an RNA-binding protein encoded by gene seb1 (for seven binding) from fission yeast S. pombe. It is essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 is involved in processing of polymerase II transcripts. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain). Length = 79

>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 44.1 bits (105), Expect = 1e-06
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 67  IFVGGLDPNVTDED-LRQPFSQYGEIASVKIPVGK-GCGFVQFANRENAEEALHKLNGTV 124
           + V GLD +  + D L   F  YG +  +K    K G   VQ  + + AE A+  LNG V
Sbjct: 2   LMVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLNGVV 61

Query: 125 IGKQSVRLS 133
           +  Q + ++
Sbjct: 62  LFGQKLEVN 70

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RRMs. Length = 71

>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 44.0 bits (104), Expect = 2e-06
 Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 5/49 (10%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI-----PVGKGCGFVQFAN 109
           T+FVGG+D  + + ++R  F++YG +  VKI      V KG GFV F +
Sbjct: 7   TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYD 55

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

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 118
           T + +  L   +TDE+ R  F   G + + KI   K      G GFV + + E+A+ A+ 
Sbjct: 1   TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 119 KLNGTVIGKQSVRLSWGR 136
            LNG  +  + +++++ R
Sbjct: 61  TLNGLQLQNKRIKVAYAR 78

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

 Score = 43.7 bits (103), Expect = 2e-06
 Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 79  EDLRQPFSQYGEIASVKIPVGKG---CGF--VQFANRENAEEALHKLNGTVIGKQSVRLS 133
             L++ F +YG++    IP  +G   CGF  V    R+NAE AL   NG  I  + V + 
Sbjct: 16  VKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVD 75

Query: 134 W 134
           W
Sbjct: 76  W 76

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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 16/74 (21%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC------GFVQFANRENAEEAL 117
           +  +FVG L  ++T+++L++ F ++G +  V+I    G       GFV F + E  ++ L
Sbjct: 3   SHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKIL 62

Query: 118 ----------HKLN 121
                     H+LN
Sbjct: 63  ANKPIYFRGDHRLN 76

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

 Score = 43.5 bits (102), Expect = 2e-06
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA---- 116
           IFVGGL  N T ED++Q F Q+G++    +   K      G GFV F + +  E+     
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 117 LHKLNGTVI 125
            H++N  ++
Sbjct: 62  FHEINNKMV 70

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

 Score = 43.3 bits (102), Expect = 3e-06
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 7/75 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPF-SQYGEIASVKI------PVGKGCGFVQFANRENAEEALH 118
           +IFVG L P V + DL   F S++    S KI       V +G GFV+F++  + + AL 
Sbjct: 3   SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 119 KLNGTVIGKQSVRLS 133
           ++ G   G + +R+S
Sbjct: 63  EMQGVYCGGRPMRIS 77

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|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 43.1 bits (101), Expect = 3e-06
 Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           +FV  L   VT+E L + FS++G++  VK    K   FV F  R+ A  A+ ++NG  I 
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKL--KDYAFVHFEERDAAVRAMDEMNGKEIE 61

Query: 127 KQSVRL 132
            + + +
Sbjct: 62  GEEIEI 67

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 43.6 bits (103), Expect = 3e-06
 Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 9/84 (10%)

Query: 67  IFVGGLDPNVTDEDL----RQPFSQYGEIASVKI---PVGKGCGFVQFANRENAEEALHK 119
           +FV  L  + +D++L     + FS+YG +  VK+      +   FVQF N ++A+ AL K
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKNALAK 64

Query: 120 LNGTVIGKQSVRLSWGRNPANKQF 143
             GT++  + +R    R   N+  
Sbjct: 65  GQGTILDGRHIRCE--RAKVNRTL 86

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

 Score = 46.2 bits (109), Expect = 3e-06
 Identities = 37/128 (28%), Positives = 56/128 (43%), Gaps = 11/128 (8%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 117
           +T ++V  L   +TD+ L   F +YG+I    I   K      G  FV+F  RE A+EA+
Sbjct: 193 DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAI 252

Query: 118 HKLNGTVI--GKQ--SVRLSWGRNPANKQ-FRADYGNQWSGAYYGGQVYDGYGYAIPPPN 172
             LN  +   G Q  +VRL+     A    + +  G+   G    G +    G  + PPN
Sbjct: 253 SALNNVIPEGGSQPLTVRLAEEHGKAKAHHYMSQMGHGNMGNMGHGNMGMAGGSGMNPPN 312

Query: 173 DPSMYAAA 180
            P+     
Sbjct: 313 PPAFMGMN 320

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

 Score = 42.9 bits (101), Expect = 3e-06
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENAEEALHK 119
           T I V  L    T +D+R  FS YG++ SV++P       +G  FV+F+  + A  A++ 
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNA 60

Query: 120 LNGT-VIGKQSV 130
           L  T ++G++ V
Sbjct: 61  LKDTHLLGRRLV 72

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

 Score = 43.1 bits (102), Expect = 4e-06
 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 3/54 (5%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGKGCGFVQFANRENAEEAL 117
           I+VG +  + T  +LRQ F  +GEI  + +     G   GFV +    +A  A+
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRAI 58

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 43.2 bits (101), Expect = 4e-06
 Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA 116
           S T + V  L  N+T E+ +  F   GEI S K+   K      G GFV + +  +A++A
Sbjct: 2   SKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61

Query: 117 LHKLNGTVIGKQSVRLSWGR 136
           ++ LNG  +  +++++S+ R
Sbjct: 62  INTLNGLKLQTKTIKVSYAR 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|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 42.5 bits (101), Expect = 4e-06
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 7/74 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIA-SVKI---PVGK--GCGFVQFANRENAEEALHK 119
            + + GL  + T+ED+R  FS        + I     G+  G  +V+FA+ E+A  AL K
Sbjct: 1   VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRK 60

Query: 120 LNGTVIGKQSVRLS 133
            +   +G + + + 
Sbjct: 61  -HNNKMGGRYIEVF 73

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

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

 Score = 42.8 bits (101), Expect = 4e-06
 Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 6/64 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKL 120
           +FV  L  +  ++DL + FS++GE++ V +         KG  +V F + E+A +A  +L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 121 NGTV 124
           +G V
Sbjct: 65  DGKV 68

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|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 42.8 bits (100), Expect = 5e-06
 Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 4/81 (4%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG----FVQFANRENAEEALHKLN 121
           T++VG L  +VT+  + Q FSQ G   S K+           FV+F    +A  AL  +N
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60

Query: 122 GTVIGKQSVRLSWGRNPANKQ 142
           G  I  + V+++W   P++++
Sbjct: 61  GRKILGKEVKVNWATTPSSQK 81

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

 Score = 42.4 bits (100), Expect = 5e-06
 Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP--VGKGCGFVQFANRENAEEALHKLNG 122
           T++ G    +    D+++ F   G +  V +     +   F+ F N E A+ A+  LNG
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNG 59

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|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 = 42.5 bits (100), Expect = 6e-06
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           +FVG +    T+E L+  FS+ G + S ++         KG GF ++ ++E A  A+  L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 121 NGTVIGKQSVRL 132
           NG  +  + +R+
Sbjct: 61  NGYELNGRQLRV 72

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

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 42.6 bits (100), Expect = 6e-06
 Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 6/61 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALHKL 120
           +FVG +   +T++++R  F ++G +  V I   K      GC FV+++ R+ A+ A+  L
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 121 N 121
           +
Sbjct: 62  H 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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 42.3 bits (99), Expect = 7e-06
 Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 7/71 (9%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALH 118
           T++FV  +      EDLR+ F +YG I  V +P+       +G  ++QF +  +AE+AL+
Sbjct: 1   TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60

Query: 119 KLNGT-VIGKQ 128
            LN   V G+Q
Sbjct: 61  NLNRKWVCGRQ 71

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

 Score = 42.3 bits (100), Expect = 8e-06
 Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 9/63 (14%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEI--ASVKI-----PVGKGCGFVQFANRENAEEALH 118
            + V  L P V++E L Q FSQ+GE+  A V +       G+  G V+F+ +  A+ A+ 
Sbjct: 1   ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGE--GIVEFSRKPGAQAAIK 58

Query: 119 KLN 121
           + +
Sbjct: 59  RCS 61

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

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 41.9 bits (99), Expect = 8e-06
 Identities = 15/45 (33%), Positives = 27/45 (60%)

Query: 81  LRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
           L   F ++G +  V +  GK  G+ ++A+RE+AE A+  L+G  +
Sbjct: 16  LEDVFCRFGGLIDVYLVPGKNYGYAKYADRESAERAITTLHGKEV 60

This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 68

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 41.9 bits (98), Expect = 8e-06
 Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 6/59 (10%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHK 119
           IFVGGL P+  +E +R+ F  +GE+ S+++P+       +G  F+ F   E  ++ + K
Sbjct: 2   IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

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

 Score = 42.2 bits (100), Expect = 8e-06
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 6/71 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHKL 120
           I++GGL   +T+ D+   FSQYGEI  + +         KG  F+ + ++ +   A+  L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 121 NGTVIGKQSVR 131
           NG  +  +++R
Sbjct: 72  NGIKLLGRTIR 82

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

 Score = 41.8 bits (98), Expect = 9e-06
 Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 3/65 (4%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTV 124
             IFVG +    T ++LR  F ++G +  V+    K   FV     E A  A+  LNG  
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFGRV--VECDKVKDYAFVHMEREEEALAAIEALNGKE 58

Query: 125 I-GKQ 128
           + G++
Sbjct: 59  VKGRR 63

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

 Score = 41.8 bits (98), Expect = 9e-06
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 7/73 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLN 121
            + V  L  + +++ L++ F +     S++IP      KG  FV+F + E+A+EAL+  N
Sbjct: 3   VLVVNNLSYSASEDSLQEVFEK---ATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCN 59

Query: 122 GTVIGKQSVRLSW 134
            T I  +S+RL +
Sbjct: 60  NTEIEGRSIRLEF 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|240887 cd12441, RRM_Nup53_like, RNA recognition motif in nucleoporin Nup53 and similar proteins

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 4/61 (6%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
           T+F  G  P+  +  LR+ FS  G I  V+ P G     +++++R  AE AL   NGT+I
Sbjct: 5   TVF--GFPPSALNLVLRE-FSSCGTILEVRYPPGANWIHLKYSSRLEAERAL-SKNGTII 60

Query: 126 G 126
            
Sbjct: 61  N 61

This subfamily corresponds to the RRM domain of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). The family also includes Saccharomyces cerevisiae Nup53p, an ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Both, vertebrate Nup35 and yeast Nup53p, contain an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This family corresponds to the RRM domain which lacks the conserved residues that typically bind RNA in canonical RRM domains. Length = 73

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

 Score = 45.1 bits (106), Expect = 1e-05
 Identities = 20/80 (25%), Positives = 42/80 (52%), Gaps = 6/80 (7%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           I+V  + P++++ D++  F  +GEI   ++         KG GF+++ N ++  EA+  +
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM 266

Query: 121 NGTVIGKQSVRLSWGRNPAN 140
           N   +G Q +R+     P +
Sbjct: 267 NLFDLGGQYLRVGKCVTPPD 286

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

 Score = 41.4 bits (97), Expect = 1e-05
 Identities = 18/56 (32%), Positives = 40/56 (71%), Gaps = 2/56 (3%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
           +++G L  +V ++D+++ F  YG++  ++I +  G GFV+F +  +A++A+++LNG
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYGKL--LEIDLKNGYGFVEFEDSRDADDAVYELNG 55

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

 Score = 45.0 bits (106), Expect = 1e-05
 Identities = 27/140 (19%), Positives = 56/140 (40%), Gaps = 4/140 (2%)

Query: 52  PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRE 111
           P +    +  +    ++V  L    T+E + + FS++      ++   +   FV F +RE
Sbjct: 221 PEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDRE 280

Query: 112 NAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIPPP 171
           +A +A+ +LNG  +    + ++  +    K     Y     G    G+       ++   
Sbjct: 281 DAVKAMDELNGKELEGSEIEVTLAKPVDKKS----YVRYTRGTGGRGKERQAARQSLGQV 336

Query: 172 NDPSMYAAAAAAYGAYPVYG 191
            DP+  + A   Y  +P Y 
Sbjct: 337 YDPASRSLAYEDYYYHPPYA 356

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

 Score = 41.6 bits (98), Expect = 1e-05
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 3/59 (5%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASV-KIPVGKGCG--FVQFANRENAEEALHKLNG 122
           I +  + P+V  EDL    S YG + +  ++P         V + + E A++A++KLNG
Sbjct: 3   IQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVNVTYESPEQAQQAVNKLNG 61

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

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

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL--- 117
           +FVGGL  + + +DL+  F+++GE+    I +       +G GF+ F +  + E+ L   
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 118 -HKLNGTVI 125
            H+L+G +I
Sbjct: 62  EHRLDGRLI 70

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

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 64  NTTIFVGGLDPNVTDE-DLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
           N+ +F+G L+  V  + D+   FS+YG +      V KG  FVQ++N  +A  A+   NG
Sbjct: 1   NSRVFIGNLNTAVVKKSDVETIFSKYGRVVGCS--VHKGYAFVQYSNERHARGAVIGENG 58

Query: 123 TVIGKQSVRLSWGRNP 138
            V+  Q++ ++    P
Sbjct: 59  RVLAGQTLDINMAGEP 74

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

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 9/53 (16%)

Query: 79  EDLRQPFSQYGEIASVKIP---------VGKGCGFVQFANRENAEEALHKLNG 122
           ED+++   +YG++ SV IP          G G  FV+FA+ E+A++A   L G
Sbjct: 26  EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAG 78

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 5/55 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI-----PVGKGCGFVQFANRENAEEA 116
           ++VG L  NV +E + + F +YG + SVKI       G    FV F + ++A++A
Sbjct: 2   LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKA 56

This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 75

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 41.2 bits (97), Expect = 1e-05
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 11/71 (15%)

Query: 66  TIFVGGLDPNVTDED----LRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEE 115
           TIFV G D ++ ++D    L + FS  GEI  V IP        KG  +++F + +  E+
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 116 ALHKLNGTVIG 126
           AL  L+G+ +G
Sbjct: 61  ALE-LDGSDLG 70

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

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PV---GKGCGFVQFANRENAEEAL--- 117
           +F+GGL  + + +DL +  S++GE+    I   PV    +G GFV F +  + ++ L   
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 118 -HKLNGTVI 125
            HKL+G +I
Sbjct: 62  EHKLDGKLI 70

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

 Score = 41.5 bits (98), Expect = 1e-05
 Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 6/59 (10%)

Query: 75  NVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKLNGTVIGK 127
           +VT++DLR+ F+ +GEI  + +         KG  +V+FA   +A  A+ ++NG  +G 
Sbjct: 13  SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGG 71

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

 Score = 41.4 bits (97), Expect = 2e-05
 Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 8/70 (11%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKL 120
           T+FV  L  N+T ++L++ F    +I   ++P G     KG  +++F     AE+AL + 
Sbjct: 5   TLFVKNLPYNITVDELKEVFEDAVDI---RLPSGKDGSSKGIAYIEFKTEAEAEKALEEK 61

Query: 121 NGTVIGKQSV 130
            G  +  +S+
Sbjct: 62  QGAEVDGRSI 71

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

 Score = 41.6 bits (97), Expect = 2e-05
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 6/81 (7%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           IFV  L P+  +  L Q F  +G + +VK+         KG GFV   N + A  A+  L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 121 NGTVIGKQSVRLSWGRNPANK 141
           NG  +G + +++S+  N  +K
Sbjct: 66  NGYRLGDRVLQVSFKTNKTHK 86

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

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           +FV  L   VT+E L + F Q+G++  VK    K   F+ F  R+ A +A+ ++NG  + 
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKELE 61

Query: 127 KQSVRLSWGR 136
            +++ + + +
Sbjct: 62  GENIEIVFAK 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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 6/70 (8%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIP-VGKGC--GFVQFANRENAEEALH 118
           TT+FVG +   V+D+ +R+   + G++ S   VK P  GK    GF +F + E A  AL 
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 119 KLNGTVIGKQ 128
            LNG  +G +
Sbjct: 61  LLNGLELGGK 70

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 = 41.2 bits (96), Expect = 2e-05
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 8/61 (13%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANR---ENAEEALH 118
           +F+G +     + D+R  FS +G+I   +I  G     +GC FV F  R   + A +A+H
Sbjct: 4   LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63

Query: 119 K 119
           +
Sbjct: 64  Q 64

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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 41.0 bits (96), Expect = 2e-05
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI-----PVGKGCGFVQFANRENAEEALHKLN 121
           +FVG L     + D+R  F+ +G I    +        +GC FV FA+R+ A  A+  ++
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 63

Query: 122 GTVI 125
            +  
Sbjct: 64  HSQT 67

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

 Score = 41.0 bits (97), Expect = 2e-05
 Identities = 22/55 (40%), Positives = 27/55 (49%), Gaps = 6/55 (10%)

Query: 75  NVTDEDLRQPFSQYGEIASVKIPV---GKG-CGFVQFANRENAEEALHKLNGTVI 125
            VT + L Q FS YG +   KI +     G    VQF + E+AE A   LNG  I
Sbjct: 12  PVTVDVLHQVFSPYGAV--EKILIFEKNTGVQALVQFDSVESAENAKKALNGRNI 64

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

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

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 3/70 (4%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGKGCGFVQFANRENAEEALHKLNG 122
            I+VG L  ++ + D+   F +YG I ++ +     G    FV+F +  +AE+A+   +G
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60

Query: 123 TVIGKQSVRL 132
                  +R+
Sbjct: 61  YDFDGYRLRV 70

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

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

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 24/70 (34%), Positives = 30/70 (42%), Gaps = 10/70 (14%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL-- 117
            +FVG L  + T EDL   F   G   SV++         KGC FV+F   E   +AL  
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKL 61

Query: 118 --HKLNGTVI 125
               L G  I
Sbjct: 62  HHTLLKGRKI 71

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|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 40.9 bits (96), Expect = 3e-05
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 15/82 (18%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG---------FVQFANRENAEEA 116
           T++V  +D  VT+E L   FS  G++   ++     CG         F++F + E A  A
Sbjct: 4   TVYVSDIDQQVTEEQLAALFSNCGQVVDCRV-----CGDPNSVLRFAFIEFTDEEGARAA 58

Query: 117 LHKLNGTVIGKQSVRLSWGRNP 138
           L  L+GT++G   VR+   +  
Sbjct: 59  L-SLSGTMLGFYPVRVLPSKTA 79

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

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

 Score = 40.8 bits (95), Expect = 3e-05
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA---- 116
           IFVGGL  N   ED++Q F Q+G++    +   K      G GFV F N +  E+     
Sbjct: 6   IFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIH 65

Query: 117 LHKLNGTVI 125
            H++N  ++
Sbjct: 66  FHEINNKMV 74

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

 Score = 40.6 bits (96), Expect = 3e-05
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 11/67 (16%)

Query: 66  TIFVGGLDPNVTDEDLRQP----FSQYGEIASVKIPVGK-----GCGFVQFANRENAEEA 116
           T+++  L+  +  ++L++     FSQ+G +  + I   K     G  FV F + E+A  A
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPV--LDIVASKTLKMRGQAFVVFKDVESATNA 58

Query: 117 LHKLNGT 123
           L  L G 
Sbjct: 59  LRALQGF 65

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|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis thaliana zinc finger CCCH domain-containing protein 46 (AtC3H46) and similar proteins

 Score = 40.1 bits (94), Expect = 3e-05
 Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 73  DPNVTDEDLRQPFSQYGEIASVKIPVG--KGCGFVQFANRENAEEALHKLNGTVIGKQSV 130
           D   T+ED+ + F Q+G +  V+IP    +  GFV F N E  +  L K N   I    V
Sbjct: 8   DSRFTEEDVSEYFGQFGPVLDVRIPYQQKRMFGFVTFENAETVKRILSKGNPHFICGSRV 67

Query: 131 R 131
           R
Sbjct: 68  R 68

This subfamily corresponds to the RRM domain in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity. . Length = 70

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

 Score = 40.7 bits (96), Expect = 3e-05
 Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 6/66 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI----PVGK--GCGFVQFANRENAEEALHK 119
           T+FV  L+ + T+  LR+ F +YG I  +++      GK  G  F++F +  + + A   
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKY 62

Query: 120 LNGTVI 125
            +G  I
Sbjct: 63  ADGKKI 68

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|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 40.3 bits (95), Expect = 3e-05
 Identities = 20/69 (28%), Positives = 40/69 (57%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
              +++ GLD +VT++ L + FS+YG +  V I   +G   V F   E A+ A++++ G 
Sbjct: 7   TNCVWLDGLDESVTEQYLTRHFSRYGPVVHVVIDRQRGQALVFFDKVEAAQAAVNEMKGR 66

Query: 124 VIGKQSVRL 132
            +G + +++
Sbjct: 67  KLGGRKLQV 75

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 40.0 bits (94), Expect = 4e-05
 Identities = 18/59 (30%), Positives = 33/59 (55%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
           +++G L  +V + DLRQ F ++    S  +    G  FV   ++  A++A+ KLNG ++
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGGYAFVDCPDQSWADKAIEKLNGKIL 59

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|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 40.1 bits (94), Expect = 4e-05
 Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 3/67 (4%)

Query: 67  IFVGGL-DPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
           +F+G L    V+ EDL + FS YGE+A + +      GFVQF + E+   A++   G +I
Sbjct: 2   LFIGNLPTKRVSKEDLFRIFSTYGELAQIVLK--NAYGFVQFDSPESCANAINCEQGKMI 59

Query: 126 GKQSVRL 132
             + + L
Sbjct: 60  RGRKLHL 66

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

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

 Score = 40.1 bits (94), Expect = 4e-05
 Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 2/58 (3%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG--CGFVQFANRENAEEALHKLNG 122
           I+VG L P++  +D+   F +YG I  + +   +G    FV+F +  +AE+A++  +G
Sbjct: 2   IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDG 59

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

>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 39.8 bits (93), Expect = 4e-05
 Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 3/57 (5%)

Query: 66  TIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
           T+FV   DP N    DL + F  YG++ +V+I   +   FVQ+  +E+A +AL   N
Sbjct: 1   TLFVINFDPINTRTRDLERHFEPYGKLVNVRIR--RNFAFVQYETQEDATKALESTN 55

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

>gnl|CDD|240964 cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA-binding protein MRN1 and similar proteins

 Score = 40.1 bits (94), Expect = 4e-05
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 13/80 (16%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQ--YGEIASVKIPVGKGCGFVQFANRENA-----EEA 116
           + T+++G L PN T ++L    S    G I +V+I   K C F+ F +   A     +  
Sbjct: 1   SRTVYLGNLPPNTTVKEL---LSHVRSGPIENVRILPEKNCAFISFLDPSAATAFHSDAI 57

Query: 117 LHKLNGTVIGKQSVRLSWGR 136
           L +L+   I    +++ WG+
Sbjct: 58  LKRLS---IKGVELKIGWGK 74

This subgroup corresponds to the RRM1 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa,which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 39.9 bits (94), Expect = 4e-05
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 7/71 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 119
           T+FV  L   V + DL + FS+ G++  V+I         KG  +V+F + E+   AL  
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-G 59

Query: 120 LNGTVIGKQSV 130
           L G  +  Q +
Sbjct: 60  LTGQRLLGQPI 70

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

 Score = 40.0 bits (93), Expect = 4e-05
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGK---GCGFVQFANRENAEEAL--- 117
           +F+GGL    TDE LR  F Q+G +     ++ P  K   G GFV +++ E  + A+   
Sbjct: 5   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNAR 64

Query: 118 -HKLNGTVI 125
            HK++G V+
Sbjct: 65  PHKVDGRVV 73

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

 Score = 40.0 bits (93), Expect = 5e-05
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC------GFVQFANRENAEEALHKL 120
           +F+  L    TD DL Q F  +G + S K+ + K        GFV + N ++A+ A+  +
Sbjct: 7   LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 121 NGTVIGKQSVRL 132
           NG  IG + +++
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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 40.0 bits (93), Expect = 5e-05
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 6/62 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 120
           +++ GL   +T +D+   FS++G I + ++ V       +G  F++F  R  AEEA+   
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 121 NG 122
           NG
Sbjct: 63  NG 64

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

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 11/65 (16%)

Query: 69  VGGLDPNVTDEDLRQPFSQYGEIASVKI---------PVGKGCGFVQFANRENAEEALHK 119
           V  + P  T+E +R  F   G+I  +++          + K C FV++ + E+   ALH 
Sbjct: 4   VTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSKVC-FVKYEDPEDVGVALH- 61

Query: 120 LNGTV 124
           L  TV
Sbjct: 62  LTNTV 66

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

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

 Score = 39.7 bits (93), Expect = 6e-05
 Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 8/74 (10%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHK 119
           T+++G L  ++T++D+R+ F    EI SV++         KG G V FA+ E+ + AL K
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-K 58

Query: 120 LNGTVIGKQSVRLS 133
           L+GTV+  + +R++
Sbjct: 59  LDGTVLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
           T + V  L P+VT++D+ + FS  G +   ++ V  G   V +  +++A  A+ K N  
Sbjct: 1   TRLVVSNLHPSVTEDDIVELFSAIGALKRARL-VRPGVAEVVYVRKDDALTAIDKYNNR 58

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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 39.6 bits (92), Expect = 6e-05
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEI--ASVKIPVGK--GCGFVQFANRENAEEALHKLNG 122
           IFV  L  + T + L+  F++ G +  A +K+  GK  GCG V+F + E AE A   +NG
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVRFESPEVAERACRMMNG 61

Query: 123 TVIGKQSVRLSWGRN 137
             +  + + +   RN
Sbjct: 62  YKLNGREIDVRIDRN 76

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 16/47 (34%), Positives = 27/47 (57%)

Query: 71  GLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
            + P VT ED++  F+Q+GE+  V    G   G+++F   E A++A 
Sbjct: 8   SIGPGVTREDIKAVFAQFGEVKYVDFTEGADTGYIRFKTPEAAQKAR 54

This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

>gnl|CDD|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 = 39.4 bits (92), Expect = 8e-05
 Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 11/65 (16%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANRENAEEA-- 116
           +FVG +  + +++DLR+ F QYG +  + +        P  KGC FV F  R+ A EA  
Sbjct: 4   MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 63

Query: 117 -LHKL 120
            LH +
Sbjct: 64  ALHNM 68

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

 Score = 39.0 bits (91), Expect = 8e-05
 Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 2/56 (3%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
           IFVG +D + + E+LR  F  YG +  +   V +   FV       A+ A+ +LNG
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAV--LSCAVMRQFAFVHLRGEAAADRAIEELNG 56

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

 Score = 39.3 bits (92), Expect = 8e-05
 Identities = 21/71 (29%), Positives = 29/71 (40%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTV 124
           TTI V       T E+LR  F  +G++  V +P       V+FAN + A  A   L    
Sbjct: 1   TTILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAGTIAIVEFANPQQARLAFKALAYRR 60

Query: 125 IGKQSVRLSWG 135
                + L  G
Sbjct: 61  FKDSILYLEKG 71

This subgroup corresponds to the RRM3 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 72

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

 Score = 39.3 bits (91), Expect = 9e-05
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 4/74 (5%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG----FVQFANRENAEEALHKLN 121
           T++VG L  +VT+  + Q FSQ G   S K+ +         FV+F    +A  +L  +N
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60

Query: 122 GTVIGKQSVRLSWG 135
           G  I  + V+++W 
Sbjct: 61  GRKIMGKEVKVNWA 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|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 39.0 bits (91), Expect = 9e-05
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYG-----EIASVKIPVGKGCGFVQFANRENAEEALHKL 120
           ++FVG L+PN   ++L+   S++       +  V+I   K  G+V F + E+ E+AL +L
Sbjct: 2   SLFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKAL-EL 60

Query: 121 NGTVIGKQSVRL 132
            G  +    ++L
Sbjct: 61  TGKKLLGNEIKL 72

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

>gnl|CDD|241002 cd12558, RRM3_RBM15B, RNA recognition motif 3 in putative RNA-binding protein 15B (RBM15B) from vertebrate

 Score = 39.2 bits (91), Expect = 9e-05
 Identities = 19/69 (27%), Positives = 36/69 (52%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
            T ++VGGL PN +   L + F ++G I ++    G    ++Q+ + + A+ A  ++ G 
Sbjct: 2   TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDYVKGDSFAYIQYESLDAAQAACAQMRGF 61

Query: 124 VIGKQSVRL 132
            +G    RL
Sbjct: 62  PLGGPDRRL 70

This subgroup corresponds to the RRM3 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 76

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

 Score = 39.1 bits (92), Expect = 9e-05
 Identities = 16/57 (28%), Positives = 28/57 (49%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
           T I V  L    T+E+LR+ F ++G +  + +P  +    V+F    +A +A   L 
Sbjct: 1   TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKAFKSLA 57

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

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

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 6/60 (10%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 117
           + T+FV  L  + T+E L   FS++G +      + K      G GFV F ++      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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 39.4 bits (91), Expect = 1e-04
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEA 116
           S T +++ GL PN TD+DL +    YG+I S K  +       KG GFV F +   A++A
Sbjct: 6   SKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKA 65

Query: 117 LHKLNGTVIGKQSVR 131
           +  L  + +  Q  +
Sbjct: 66  VSALKASGVQAQMAK 80

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|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 10/66 (15%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAE----EA 116
           IFVGG+  +  +  LR  F QYG+I  ++I   +G G      FV F + ++ +    + 
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 62

Query: 117 LHKLNG 122
            H +NG
Sbjct: 63  YHTVNG 68

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

 Score = 39.0 bits (91), Expect = 1e-04
 Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 6/66 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 119
            I++G L     +++L++ FSQ+G + +V++         K  GF+QF N E A  A   
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 120 LNGTVI 125
           +N  ++
Sbjct: 61  MNNYLL 66

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|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 19/58 (32%), Positives = 31/58 (53%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
              +   G+    + EDL++ F ++GE+A V    G+  G+V+F     A+EAL KL 
Sbjct: 1   GCVLHFSGVGEQTSREDLKEAFEEFGEVAWVDFARGQTEGYVRFKEENAAKEALEKLK 58

This subgroup corresponds to the RRM2 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 76

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

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 6/81 (7%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           IFV  L P+  +  L Q F  +G + +VK+         KG GFV   N + A  A+  L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 121 NGTVIGKQSVRLSWGRNPANK 141
           NG  +G + +++S+  N  +K
Sbjct: 66  NGYRLGDRVLQVSFKTNKTHK 86

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           IFV  L P   +  L Q F  +G + +VK+         KG GFV   N + A  A+  L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 121 NGTVIGKQSVRLSWGRNPANK 141
           NG  +G + +++S+  +  +K
Sbjct: 64  NGYRLGDRVLQVSFKTSKQHK 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|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 69  VGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNG 122
           V GL    T+ DLR+ FS+YG +A V +         +G  FV F   ++++EA+   NG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 123 TVIGKQSVRLSW 134
             +  + +R+ +
Sbjct: 64  MELDGRRIRVDY 75

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|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 38.4 bits (90), Expect = 1e-04
 Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 3/67 (4%)

Query: 74  PNVTDEDLRQPFSQ-YGEIASVKI-PVGKGCGFVQFANRENAEEALHKL-NGTVIGKQSV 130
           P+VT+EDL++ F+Q  G + + K  P  +    +Q  + E A EAL  L N  +     +
Sbjct: 9   PSVTEEDLKELFTQTGGTVKAFKFFPKDRKMALIQMGSVEEAIEALIALHNYQLSESSHL 68

Query: 131 RLSWGRN 137
           R+S+ ++
Sbjct: 69  RVSFSKS 75

This subfamily corresponds to the RRM4 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 = 76

>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding Raly-like protein (RALYL)

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 64  NTTIFVGGLDPNVTDE-DLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
           N+ +F+G L+  +  + D+   F++YG+I  V   V KG  FVQ+ +  +A  A+   N 
Sbjct: 1   NSRVFIGNLNTAIVKKADIEAIFAKYGKI--VGCSVHKGYAFVQYISERHARAAVAGENA 58

Query: 123 TVIGKQSVRLS 133
            +I  Q + ++
Sbjct: 59  RIIAGQPLDIN 69

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

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 7/76 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENAEEALHKL 120
           T+FV GL  + T+E L++ F   G IA+  +        KG GFV F++ E+A+ A   +
Sbjct: 2   TLFVKGLSEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 121 NGTVIGKQSVRLSWGR 136
               I    V L + +
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|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 = 38.4 bits (90), Expect = 2e-04
 Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 8/72 (11%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG--------KGCGFVQFANRENAEEALH 118
           ++VG L    TDEDL    ++ G +    I           KG  +V+FA+   A     
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 119 KLNGTVIGKQSV 130
           KL G     +  
Sbjct: 61  KLEGREFNGKKC 72

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

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 9/63 (14%)

Query: 69  VGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL---HK 119
           V GL    T++DL+  FS +GE+  V++         KG GFV+FA+ E+  + L   H 
Sbjct: 4   VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRHM 63

Query: 120 LNG 122
           ++G
Sbjct: 64  IDG 66

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|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative RNA exonuclease NEF-sp

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 6/62 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GK--GCGFVQFANRENAEEALHKL 120
           I+V G   ++T+E L++ F Q  ++ ++ +P     GK     F++F   ++A  AL  +
Sbjct: 1   IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60

Query: 121 NG 122
            G
Sbjct: 61  TG 62

This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

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

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           ++V    P+ ++  +R+ FS YG +  VK+       FV+F + E+A  A   ++G V+ 
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI--SNFAFVEFESLESAIRAKDSVHGKVLN 59

Query: 127 KQSV 130
              +
Sbjct: 60  NNPL 63

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

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 1/47 (2%)

Query: 77  TDEDLRQPFSQYGEIASVKIPVGK-GCGFVQFANRENAEEALHKLNG 122
           ++++LR+ FS+YG+++ V +   K G   V+FA+++ AE A+    G
Sbjct: 17  SEDELRKIFSKYGDVSDVVVSSKKKGSAIVEFASKKAAEAAVENECG 63

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 21/78 (26%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGE---------IASVKI--------PVG----KGCG 103
           T + +  L  +V ++ L++ F +            I  VKI        P G    KG G
Sbjct: 1   TRLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYG 60

Query: 104 FVQFANRENAEEALHKLN 121
           FV+F N E+A +AL  LN
Sbjct: 61  FVEFTNHEHALKALRALN 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|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 10/71 (14%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASV-KIPVG---------KGCGFVQFANRENA 113
           +  ++V  L   VT+EDL   F ++ + +S  K             KG  FV F + E A
Sbjct: 1   SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIA 60

Query: 114 EEALHKLNGTV 124
            +AL+ +NG V
Sbjct: 61  TKALNLVNGYV 71

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

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 3/71 (4%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC---GFVQFANRENAEEALHKLNGT 123
           I+VG L  +V ++DL   F +YG I  +++   +G     FV+F +  +AE+A+   NG 
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNGY 61

Query: 124 VIGKQSVRLSW 134
             G+  +R+ +
Sbjct: 62  DFGQCRLRVEF 72

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

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

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 3/70 (4%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASV--KIPV-GKGCGFVQFANRENAEEALHKLNG 122
           T++VG L  ++ + ++   F +YG I  +  K+P    G  F++F +  +AE+A+   +G
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 123 TVIGKQSVRL 132
                Q +R+
Sbjct: 61  YDFDGQRLRV 70

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

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

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 29/78 (37%), Positives = 39/78 (50%), Gaps = 15/78 (19%)

Query: 65  TTIFVGGLDPNVTDED-------LRQPFSQYGEIASVKI--PVG-----KGCGFVQFANR 110
             + V GL P V +E        LR+ FS++G    V I  PV      KG  FV+FA  
Sbjct: 2   NVVVVDGL-PVVGEEKLEKLKKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATP 60

Query: 111 ENAEEALHKLNGTVIGKQ 128
           E A+EA+  LNG  + K+
Sbjct: 61  EEAKEAVKALNGYKLDKK 78

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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 38.3 bits (88), Expect = 2e-04
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEA 116
           S T +++ GL P  TD+DL +    YG+I S K  +       KG GFV F +   A++A
Sbjct: 3   SKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKA 62

Query: 117 LHKLNGTVIGKQSVR 131
           +  L    +  Q  +
Sbjct: 63  VASLKANGVQAQMAK 77

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|240889 cd12443, RRM_MCM3A_like, RNA recognition motif in 80 kDa MCM3-associated protein (Map80) and similar proteins

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 65  TTIFVGGLDPNVTDED-LRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
           TTI    +   + D+D L + F ++G++A V     K    V F +  +A  A  K  G 
Sbjct: 1   TTIQCKNIPDELNDKDWLERHFGKFGKVARVYCNPRKKSAVVHFFDHASAALA--KKKGK 58

Query: 124 VIGKQSVRLSWGR 136
           ++  + +++ WG 
Sbjct: 59  LLQHKPIQIFWGS 71

This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 73

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 13/79 (16%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------------GCGFVQFANRENA 113
            +++  L  + ++EDL +    +  + SV IP               G  + +F++ E A
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 114 EEALHKLNGTVIGKQSVRL 132
           E+ +  LNG V   + + +
Sbjct: 60  EKVVKDLNGKVFKNRKLFV 78

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

 Score = 37.9 bits (89), Expect = 2e-04
 Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 5/68 (7%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVG--KGCGFVQFANRENAEEALHK 119
             +FVG +  ++ +++L   F + G I  +++     G  +G  FV + N+E A+ A+ +
Sbjct: 2   CEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQ 61

Query: 120 LNGTVIGK 127
           L+   I  
Sbjct: 62  LHNYEIRP 69

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

 Score = 37.8 bits (88), Expect = 3e-04
 Identities = 22/72 (30%), Positives = 44/72 (61%), Gaps = 6/72 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVG---KGCGFVQFANRENAEEALHKL 120
           ++VG +   + ++ +RQ FS +G I S+ +   PV    KG  FV++   E A+ AL ++
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 121 NGTVIGKQSVRL 132
           NG ++G +++++
Sbjct: 63  NGVMLGGRNIKV 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|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 5/63 (7%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEI--ASV---KIPVGKGCGFVQFANRENAEEALHK 119
           T + V  LD  V+D+D+++ F+++G +  A+V   +     G   V F  R +A +A+ +
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60

Query: 120 LNG 122
            NG
Sbjct: 61  YNG 63

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|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 = 38.0 bits (89), Expect = 3e-04
 Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 6/66 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIAS---VK-IPVG--KGCGFVQFANRENAEEALHKL 120
           IF+GGL   ++++ +++    +G++ +   VK    G  KG  F ++ +    ++A+  L
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 121 NGTVIG 126
           NG  +G
Sbjct: 63  NGMQLG 68

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

 Score = 37.4 bits (86), Expect = 3e-04
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEAL 117
            T +++ GL P  TD+DL +    YG+I S K  +       KG GFV F +   A++A+
Sbjct: 1   KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

Query: 118 HKLNGTVIGKQSVR 131
             L  + +  Q  +
Sbjct: 61  TALKASGVQAQMAK 74

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

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 9/58 (15%)

Query: 69  VGGLDPNVTDEDLRQPFSQYGEIASVKI-------PVGKGCGFVQFANRENAEEALHK 119
           V  L P V++E L Q FSQ+G +    +       P GK  GFV+FA +  A +AL +
Sbjct: 4   VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGK--GFVEFAAKPAARKALER 59

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

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

 Score = 37.6 bits (87), Expect = 4e-04
 Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKL 120
           T+FVG L+  V +E L + F Q G +  V I        K  GFV F + E+   A+  L
Sbjct: 3   TLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALL 62

Query: 121 NG 122
           NG
Sbjct: 63  NG 64

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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 37.7 bits (87), Expect = 4e-04
 Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 6/81 (7%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           IF+  L  +  +  L Q F  +G + +VK+         KG GFV   N E A  A+  L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 121 NGTVIGKQSVRLSWGRNPANK 141
           NG  +G + +++S+  + ++K
Sbjct: 64  NGYRLGDKILQVSFKTSKSHK 84

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

 Score = 37.3 bits (86), Expect = 4e-04
 Identities = 15/59 (25%), Positives = 32/59 (54%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
           ++V  L    +++ +++ F Q+      ++   +   FV F +RE+A  A++ LNGT +
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTEL 62

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

 Score = 37.3 bits (86), Expect = 4e-04
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
           T + VG +  + T+++LR  F +YG +  ++  + K   FV     E+A EA+  L+ T
Sbjct: 1   TKLHVGNISSSCTNQELRAKFEEYGPV--IECDIVKDYAFVHMERAEDAVEAIRGLDNT 57

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

 Score = 37.3 bits (86), Expect = 4e-04
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGK---GCGFVQFANRENAEEAL--- 117
           +F+GGL    T E LR+ F Q+GE+     ++ P+ K   G GFV F ++   ++ L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 118 -HKLNGTVI 125
            H+L+   I
Sbjct: 63  RHELDSKTI 71

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|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast asparagine-rich protein (ARP) and similar proteins

 Score = 37.5 bits (87), Expect = 5e-04
 Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 15/75 (20%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYG-------------EIASVKIPVGKGCGFVQFANRENA 113
           +++  L P+ T  +L   F+QYG             E A V        GF  F + E A
Sbjct: 3   LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSK-DSISGFAVFQSHEEA 61

Query: 114 EEALHKLNGTVIGKQ 128
            EAL  LNG  +G++
Sbjct: 62  MEAL-ALNGRCLGER 75

This subfamily corresponds to the RRM of ARP, also termed NRP1, encoded by Saccharomyces cerevisiae YDL167C. Although its exact biological function remains unclear, ARP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), two Ran-binding protein zinc fingers (zf-RanBP), and an asparagine-rich region. It may possess RNA-binding and zinc ion binding activities. Additional research had indicated that ARP may function as a factor involved in the stress response. . Length = 88

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

 Score = 37.4 bits (86), Expect = 5e-04
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASV------KIPVGKGCGFVQFANRENAEEAL--- 117
           +F+GGL    TD+ LR+ F ++G +         +    +G GFV ++  E  + A+   
Sbjct: 5   LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSAR 64

Query: 118 -HKLNGTVI 125
            HK++G V+
Sbjct: 65  PHKVDGRVV 73

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 36.8 bits (86), Expect = 6e-04
 Identities = 15/57 (26%), Positives = 34/57 (59%), Gaps = 5/57 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEAL 117
           T++V G   + T +D+++ F ++G++ ++++        KG  FV+F   E+A++ L
Sbjct: 1   TVYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFL 57

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 36.7 bits (85), Expect = 6e-04
 Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           +F G  + +    ++ + F +YG +  V +    G  FV   +  +AE+A+  L+    G
Sbjct: 3   VFCGNFEYDARQSEIERLFGKYGRVDRVDMK--SGFAFVYMEDERDAEDAIRGLDNFEFG 60

Query: 127 KQSVRLS 133
           +Q  RL 
Sbjct: 61  RQRRRLR 67

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

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

 Score = 39.5 bits (92), Expect = 6e-04
 Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 9/61 (14%)

Query: 79  EDLRQPFSQYGEIASVKIP-------VGKGCG--FVQFANRENAEEALHKLNGTVIGKQS 129
           ED++  FS+YG + ++ IP          G G  F+++A+  +AE+A+  +NG     + 
Sbjct: 434 EDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRV 493

Query: 130 V 130
           V
Sbjct: 494 V 494

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

 Score = 36.8 bits (86), Expect = 6e-04
 Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGKGCGFVQFANRENAEEALHK 119
            N  ++V  L   ++ E+L   F +YG I  ++I      +G  FV + +  +A+ A   
Sbjct: 1   VNRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDH 60

Query: 120 LNG 122
           L+G
Sbjct: 61  LSG 63

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|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 = 36.8 bits (85), Expect = 6e-04
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC------GFVQFANRENAEEALHKL 120
           +F+  L     D +L Q F  +G + S K+ V +        GFV F N  +A+ A+  +
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 121 NGTVIGKQSVRL 132
           NG  IG + +++
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|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 36.7 bits (86), Expect = 8e-04
 Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 13/80 (16%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIAS--------VKIPV-----GKGCGFVQFANR 110
           NT ++V GL  ++T E+  + FS+ G I          +K+        KG     +   
Sbjct: 1   NTNVYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLKGDALCCYLKE 60

Query: 111 ENAEEALHKLNGTVIGKQSV 130
           E+ E A+  L+GT IG+   
Sbjct: 61  ESVELAIQLLDGTEIGRGYK 80

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

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 36.4 bits (85), Expect = 8e-04
 Identities = 14/51 (27%), Positives = 28/51 (54%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
           + +  L P+VT+ DL    S +G++ +V +  GK    V+  + E+A+  +
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMDSVESAKSMV 52

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

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

 Score = 36.5 bits (84), Expect = 9e-04
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           +++G L     + D+ + F  YG+I  V +    G GFV+F +  +A++A+++LNG  + 
Sbjct: 2   VYIGRLSYQARERDVERFFKGYGKILEVDLK--NGYGFVEFDDLRDADDAVYELNGKDLC 59

Query: 127 KQSVRLSWGRNP 138
            + V +   R P
Sbjct: 60  GERVIVEHARGP 71

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

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

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 21/64 (32%), Positives = 36/64 (56%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
           SS   ++V  L  + T+E + + F+     A  ++   +   FV F+NRE+A +A++ LN
Sbjct: 6   SSVKILYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVDAMNALN 65

Query: 122 GTVI 125
           G VI
Sbjct: 66  GKVI 69

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 6/63 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHK 119
            +++G L     + +LR+ FSQ+G +  +++         KG  FV+F + E A+     
Sbjct: 1   VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAET 60

Query: 120 LNG 122
           +N 
Sbjct: 61  MNN 63

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

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC------GFVQFANRENAEEALHKL 120
           +F+  L     D+DL Q F  +G + S K+ + K        GFV + N  +A+ A+  +
Sbjct: 10  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 121 NGTVIGKQSVRLSWGR 136
           NG  IG + +++   R
Sbjct: 70  NGFQIGMKRLKVQLKR 85

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|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2)

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 19/58 (32%), Positives = 31/58 (53%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTV 124
           +++G L P VT EDLRQ F       + ++ +  G  FV + ++  A  A+  L+G V
Sbjct: 4   LYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLKSGYAFVDYPDQNWAIRAIETLSGKV 61

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

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEALHKLN 121
           IFV  LD  V  + L++ F   G++    I        +G G VQF +   A +A+   N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 122 G 122
           G
Sbjct: 61  G 61

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|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEALHKL 120
           T++V G        DL   F +YG +    IP       +   FV++ +  +AE+A  ++
Sbjct: 1   TLYVTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAEDAYEEM 60

Query: 121 NG--TVIGKQSVRLSWGR 136
           +G        ++ + W +
Sbjct: 61  HGRRFPDTGDTLHVQWAK 78

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but 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. Some family members also contain another RRM domain. Length = 78

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

 Score = 36.0 bits (83), Expect = 0.001
 Identities = 19/82 (23%), Positives = 36/82 (43%), Gaps = 11/82 (13%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------GK----GCGFVQFANRENAE 114
           T+FV  L+ + T++ L   F         ++         G+    G GFV F  +E A+
Sbjct: 2   TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQ 61

Query: 115 EALHKLNGTVIGKQSVRLSWGR 136
            AL  ++G V+   ++ + +  
Sbjct: 62  AALKAMDGFVLDGHTLVVKFSH 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|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 7/72 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG----CGFVQFANRENAEEALHKLN 121
           T+ V  L P ++++D       +G  +SV++   +G      F  F N + A +AL +L+
Sbjct: 1   TLLVRHLPPELSEDDKEDLLKHFG-ASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLH 59

Query: 122 GTVIGKQSVRLS 133
              I  +  RL 
Sbjct: 60  QLKILGK--RLV 69

This subfamily corresponds to the RRM1 of 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 repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), 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. . Length = 73

>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 17/56 (30%), Positives = 25/56 (44%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL 120
           T I V  L       +LR+ FS++G +  V +P       V+F     A+ A  KL
Sbjct: 1   TVILVKNLPAGTLTAELRELFSKFGSLGRVLLPPAGITAIVEFLEPSEAKLAFRKL 56

This subgroup corresponds to the RRM4 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 = 72

>gnl|CDD|240881 cd12435, RRM_GW182_like, RNA recognition motif in the GW182 family proteins

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 14/63 (22%), Positives = 32/63 (50%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
           ++ + +  L P +    LR    Q+G + +  + +  G   ++++++E A +A   LN  
Sbjct: 1   SSWLVLRNLTPQIDGSTLRTLCMQHGPLLTFHLNLRHGNALIRYSSKEEAAKAQSALNNC 60

Query: 124 VIG 126
           V+G
Sbjct: 61  VLG 63

This subfamily corresponds to the RRM of the GW182 family which includes three paralogs of TNRC6 (GW182-related) proteins comprising GW182/TNGW1, TNRC6B (containing three isoforms) and TNRC6C in mammal, a single Drosophila ortholog (dGW182, also called Gawky) and two Caenorhabditis elegans orthologs AIN-1 and AIN-2, which contain multiple miRNA-binding sites and have important functions in miRNA-mediated translational repression, as well as mRNA degradation in Metazoa. The GW182 family proteins directly interact with Argonaute (Ago) proteins, and thus function as downstream effectors in the miRNA pathway, responsible for inhibition of translation and acceleration of mRNA decay. Members in this family are characterized by an abnormally high content of glycine/tryptophan (G/W) repeats, one or more glutamine (Q)-rich motifs, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The only exception is the worm protein that does not contain a recognizable RRM domain. The GW182 family proteins are recruited to miRNA targets through an interaction between their N-terminal domain and an Argonaute protein. Then they promote translational repression and/or degradation of miRNA targets through their C-terminal silencing domain. . Length = 71

>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX) proteins

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 15/30 (50%), Positives = 22/30 (73%)

Query: 66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVK 95
          T+FVGGL  N T+E +R+ F Q GEI +++
Sbjct: 8  TVFVGGLPENATEEIIREVFEQCGEIIAIR 37

This subgroup corresponds to the conserved RNA recognition motif (RRM) in ECTO-NOX proteins (also termed ENOX), comprising a family of plant and animal NAD(P)H oxidases exhibiting both, oxidative and protein disulfide isomerase-like, activities. They are growth-related and drive cell enlargement, and may play roles in aging and neurodegenerative diseases. ENOX proteins function as terminal oxidases of plasma membrane electron transport (PMET) through catalyzing electron transport from plasma membrane quinones to extracellular oxygen, forming water as a product. They are also hydroquinone oxidases that oxidize externally supplied NADH, hence NOX. ENOX proteins harbor a di-copper center that lack flavin. ENOX proteins display protein disulfide interchange activity that is also possessed by protein disulfide isomerase. In contrast to the classic protein disulfide isomerases, ENOX proteins lack the double CXXC motif. This family includes two ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed candidate growth-related and time keeping constitutive hydroquinone [NADH] oxidase (cCNOX), or cell proliferation-inducing gene 38 protein, or Constitutive Ecto-NOX (cNOX), is the constitutively expressed cell surface NADH (ubiquinone) oxidase that is ubiquitous and refractory to drugs. ENOX2, also termed APK1 antigen, or cytosolic ovarian carcinoma antigen 1, or tumor-associated hydroquinone oxidase (tNOX), is a cancer-specific variant of ENOX1 and plays a key role in cell proliferation and tumor progression. In contrast to ENOX1, ENOX2 is drug-responsive and harbors a drug binding site to which the cancer-specific S-peptide tagged pan-ENOX2 recombinant (scFv) is directed. Moreover, ENOX2 is specifically inhibited by a variety of quinone site inhibitors that have anticancer activity and is unique to the surface of cancer cells. ENOX proteins contain many functional motifs. Length = 84

>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein 44 (RBM44) and similar proteins

 Score = 35.7 bits (82), Expect = 0.001
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 13/72 (18%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANREN-------AEEALHK 119
           + VGGL P+V++ DLR  F +Y +++ + +     C    +            A  A+ K
Sbjct: 2   VHVGGLSPSVSEGDLRSHFQKY-QVSVISL-----CKLSNYRYASLHFDRASDALLAVKK 55

Query: 120 LNGTVIGKQSVR 131
           +NG V+   S++
Sbjct: 56  MNGGVLSGLSIK 67

This subgroup corresponds to the RRM of RBM44, a novel germ cell intercellular bridge protein that is localized in the cytoplasm and intercellular bridges from pachytene to secondary spermatocyte stages. RBM44 interacts with itself and testis-expressed gene 14 (TEX14). Unlike TEX14, RBM44 does not function in the formation of stable intercellular bridges. It carries an RNA recognition motif (RRM) that could potentially bind a multitude of RNA sequences in the cytoplasm and help to shuttle them through the intercellular bridge, facilitating their dispersion into the interconnected neighboring cells. Length = 74

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

 Score = 38.1 bits (88), Expect = 0.002
 Identities = 23/101 (22%), Positives = 46/101 (45%), Gaps = 7/101 (6%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCG 103
              G    ++ ++S T + V  L  ++TD +L   F   G I + +I          G  
Sbjct: 93  LGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYA 152

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFR 144
           FV F +  +++ A+  LNG  +  + +++S+ R P  +  +
Sbjct: 153 FVDFGSEADSQRAIKNLNGITVRNKRLKVSYAR-PGGESIK 192

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

 Score = 38.3 bits (89), Expect = 0.002
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 9/82 (10%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKL 120
           I++G L   + ++ +++    +G++ +  +       + KG  F ++ +    + A+  L
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 121 NGTVIGKQSV---RLSWGRNPA 139
           NG   G   +   R   G N A
Sbjct: 358 NGKDTGDNKLHVQRACVGANQA 379

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 7/69 (10%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---P-VGK--GCGFVQFANRENAEEALHK 119
            +    L+ N+ +  L+    +YGE+  VKI   P   K  G   V F + ++A+  + K
Sbjct: 4   EVTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEK 63

Query: 120 LNGT-VIGK 127
           LN T V+GK
Sbjct: 64  LNQTSVMGK 72

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|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 7/62 (11%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEALHKL 120
           +FVG L     +E L + F + G I  V+I       VGKG  +VQF +    E+AL  L
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL-LL 60

Query: 121 NG 122
           N 
Sbjct: 61  NE 62

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVI 125
           ++VG L       +L + FS YG + +V I     G  FV+F +  +AE+A+  L+G VI
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 61

Query: 126 GKQSVRL 132
               VR+
Sbjct: 62  CGSRVRV 68

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

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK---GCGFVQFANRENAEEAL--- 117
           +F+GGL    + + LR  FS++GEI    +   P  K   G GFV FA+  + ++ L   
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQP 61

Query: 118 -HKLNGTVI 125
            H+L+   I
Sbjct: 62  HHELDSKTI 70

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|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 7/64 (10%)

Query: 66  TIFVGGLDPNVTDEDLR---QPFSQYGEIASVKIPVGKGC----GFVQFANRENAEEALH 118
           T+FV GL  +V + +L    +PF  Y     V      G     GFV F++ + A  A+ 
Sbjct: 2   TLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAMD 61

Query: 119 KLNG 122
            L G
Sbjct: 62  ALQG 65

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 10/66 (15%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL--- 117
           +FVGG+  +  +  LR  F +YG+I +++I   +      G GFV F + +  ++ +   
Sbjct: 3   LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQK 62

Query: 118 -HKLNG 122
            H +NG
Sbjct: 63  YHTING 68

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|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 14/79 (17%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGF--VQFANR--------EN 112
           I + GL P  T + +R  F  +GEI   ++ +    G+  G   V F           E 
Sbjct: 1   ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60

Query: 113 AEEALHKLNGTVIGKQSVR 131
           A+ A+  LNG  IG + VR
Sbjct: 61  AKAAVDGLNGRRIGGKRVR 79

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

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

 Score = 35.1 bits (80), Expect = 0.003
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGK---GCGFVQFANRENAEEAL--- 117
           +F+GGL    T+E LR  + Q+G++     ++ P  K   G GFV F+     + A+   
Sbjct: 5   LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAAR 64

Query: 118 -HKLNGTVI 125
            H ++G V+
Sbjct: 65  PHTIDGRVV 73

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|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 24/80 (30%), Positives = 30/80 (37%), Gaps = 17/80 (21%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYG--EIASVKIPVGKGCGF----------VQFANR 110
           S  T++ G L   VTDEDLR+ F  Y   EI   +    K              V     
Sbjct: 1   SKDTVYCGKLPKKVTDEDLREFFKDYNPQEIWIFRTRKSKRNPLQLHRHFTAALVTLDTE 60

Query: 111 ENAEEAL-----HKLNGTVI 125
           E  +E +      KLNG  I
Sbjct: 61  ETLDEIIESLKSKKLNGKKI 80

This subfamily corresponds to the RRM2 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 = 93

>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 35.0 bits (80), Expect = 0.004
 Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 7/84 (8%)

Query: 64  NTTIFVGGLDPNVTDEDLRQP----FSQYG---EIASVKIPVGKGCGFVQFANRENAEEA 116
           N TI++  L+  +  E+L++     FSQ+G   +I ++K    +G  FV F    +A  A
Sbjct: 1   NHTIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNA 60

Query: 117 LHKLNGTVIGKQSVRLSWGRNPAN 140
           L +L G     + +R+ + +  ++
Sbjct: 61  LRQLQGFPFYGKPMRIQYAKTDSD 84

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate RNA-binding protein with multiple splicing (RBP-MS)

 Score = 34.6 bits (79), Expect = 0.004
 Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 4/60 (6%)

Query: 66  TIFVGGLDPNVTDEDLR---QPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
           T+FV GL  ++   +L    +PF  Y E + +K+   +  GFV F +R  AE A + LNG
Sbjct: 3   TLFVSGLPLDIKPRELYLLFRPFKGY-EGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNG 61

This subfamily corresponds to the RRM of RBP-MS, also termed heart and RRM expressed sequence (hermes), an RNA-binding proteins found in various vertebrate species. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RBP-MS physically interacts with Smad2, Smad3 and Smad4 and plays a role in regulation of Smad-mediated transcriptional activity. In addition, RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. . Length = 76

>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 37.1 bits (86), Expect = 0.004
 Identities = 20/82 (24%), Positives = 29/82 (35%), Gaps = 4/82 (4%)

Query: 45  GYASNGAPG--QGPQSEGDSSNTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVGK- 100
            Y +             G    + + V GL    V  + L   F  YG +  VK    K 
Sbjct: 254 AYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKK 313

Query: 101 GCGFVQFANRENAEEALHKLNG 122
               ++ A+   A+ AL  LNG
Sbjct: 314 ETALIEMADPYQAQLALTHLNG 335

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067). Length = 481

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	198
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.86
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.81
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.78
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.77
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.71
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.71
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.7
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.7
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.7
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.69
KOG0122	270	consensus Translation initiation factor 3, subunit	99.69
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.69
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.69
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.67
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.66
PLN03120	260	nucleic acid binding protein; Provisional	99.64
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.63
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.61
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.59
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.58
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.57
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.56
PLN03213	759	repressor of silencing 3; Provisional	99.56
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.56
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.56
PLN03121	243	nucleic acid binding protein; Provisional	99.55
smart00362	72	RRM_2 RNA recognition motif.	99.55
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.55
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.53
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.53
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.52
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.51
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.51
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.5
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.49
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.49
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.48
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.47
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.46
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.45
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.44
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.44
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.43
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.4
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.39
smart00360	71	RRM RNA recognition motif.	99.39
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.38
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.36
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.34
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.34
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.33
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.33
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.31
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.28
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.28
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.26
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.22
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.21
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.2
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.18
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.17
smart00361	70	RRM_1 RNA recognition motif.	99.16
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.14
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.12
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.11
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.1
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.08
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.06
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.02
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.0
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.0
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.96
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.96
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.95
KOG0151	877	consensus Predicted splicing regulator, contains R	98.91
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.88
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.84
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.81
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.8
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.77
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.64
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.64
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.63
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.54
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.54
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.34
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.32
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.31
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.3
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.29
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.29
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.25
KOG0226	290	consensus RNA-binding proteins [General function p	98.15
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	98.15
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.07
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.06
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.05
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.02
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.01
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.96
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.92
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.91
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.83
KOG4210	285	consensus Nuclear localization sequence binding pr	97.74
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.66
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.66
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.47
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.47
KOG3152	278	consensus TBP-binding protein, activator of basal	97.41
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.3
KOG2314	698	consensus Translation initiation factor 3, subunit	97.3
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.26
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.24
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.23
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.16
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.15
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.12
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.94
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.84
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.8
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.62
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.56
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.56
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.55
KOG2135	526	consensus Proteins containing the RNA recognition	96.23
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.19
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	96.11
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.03
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.01
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.74
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.68
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.66
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	95.65
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.57
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.38
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	94.92
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.78
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.73
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	94.26
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	94.15
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.6
KOG2318	650	consensus Uncharacterized conserved protein [Funct	90.84
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	89.06
KOG4660	549	consensus Protein Mei2, essential for commitment t	88.18
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	88.01
KOG4210	285	consensus Nuclear localization sequence binding pr	87.48
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	86.22
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	84.88
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	80.98
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	80.08

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

Probab=99.86  E-value=4.3e-20  Score=136.29  Aligned_cols=83  Identities=25%  Similarity=0.549  Sum_probs=75.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .......++|||+||+++++|++|+++|++||.|.+++|+.+      ++||||+|.+.++|++|++.|++.+|+++.|+
T Consensus        28 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~  107 (144)
T PLN03134         28 GSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIR  107 (144)
T ss_pred             ccccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344556789999999999999999999999999999999753      79999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 029166          132 LSWGRNPAN  140 (198)
Q Consensus       132 v~~a~~~~~  140 (198)
                      |+|++++..
T Consensus       108 V~~a~~~~~  116 (144)
T PLN03134        108 VNPANDRPS  116 (144)
T ss_pred             EEeCCcCCC
Confidence            999986544

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

Probab=99.81  E-value=1.5e-19  Score=145.64  Aligned_cols=127  Identities=37%  Similarity=0.605  Sum_probs=106.6

Q ss_pred             ccchhhhc--chhhhhhhhhhhhccCCCCcc--------------ccchhhhhhhhcCCCCCCCCCCCCCCCCCCCCCCe
Q 029166            3 KRRHCCER--KGEREERTLLYKLCFHRNSSY--------------CQFNIVFLLVLIGGYASNGAPGQGPQSEGDSSNTT   66 (198)
Q Consensus         3 ~~~~~c~~--~~~~~~~~~~~~~c~~~~~~~--------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (198)
                      ++||||+|  +++|+|    ++.|+++|...              ...+.+.+.+.......-+    .-.+..+...++
T Consensus       159 n~p~Icsf~v~geckR----G~ec~yrhEkp~d~~L~~qni~dryyg~ndPva~kil~ra~~~~----~lepPeD~~I~t  230 (377)
T KOG0153|consen  159 NRPHICSFFVKGECKR----GAECPYRHEKPPDDPLSLQNIKDRYYGLNDPVALKILNRAGSAG----TLEPPEDTSIKT  230 (377)
T ss_pred             CCCccccceeeccccc----cccccccccCCCCcchhhcccccccccccChHHHHHHhhccccc----ccCCCcccceeE
Confidence            68999999  899999    99999999855              2344556656544433221    245667778899


Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHh-CCceeCCeEeEEEeccC
Q 029166           67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL-NGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        67 lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l-~~~~~~g~~l~v~~a~~  137 (198)
                      |||++|...++|.+|+++|.+||+|+.|.+...++||||+|.++++|+.|.+++ +...|+|.+|+|.|+++
T Consensus       231 LyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  231 LYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             EEecccccchhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            999999999999999999999999999999999999999999999999988755 66778999999999998

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

Probab=99.78  E-value=5.7e-18  Score=132.69  Aligned_cols=82  Identities=35%  Similarity=0.689  Sum_probs=77.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ....+.++||||||+..++|++|++.|+.||.|.+|+|.+++||+||.|++.|+|..||..+|+.+|+|..+++.|.+..
T Consensus       159 Qssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~  238 (321)
T KOG0148|consen  159 QSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEG  238 (321)
T ss_pred             cCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecccceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccC
Confidence            34667899999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             CC
Q 029166          139 AN  140 (198)
Q Consensus       139 ~~  140 (198)
                      ..
T Consensus       239 ~~  240 (321)
T KOG0148|consen  239 DD  240 (321)
T ss_pred             CC
Confidence            54

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.77  E-value=1.6e-17  Score=138.65  Aligned_cols=79  Identities=29%  Similarity=0.529  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCC--eEeEEE
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGK--QSVRLS  133 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g--~~l~v~  133 (198)
                      ...++|||+|||+.++|++|+++|++||+|++++|+++      |+||||+|.+.++|++||+.||+..+.+  +.|+|+
T Consensus       191 ~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~  270 (346)
T TIGR01659       191 IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVR  270 (346)
T ss_pred             cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEE
Confidence            34678999999999999999999999999999999875      4899999999999999999999999865  689999


Q ss_pred             eccCCCC
Q 029166          134 WGRNPAN  140 (198)
Q Consensus       134 ~a~~~~~  140 (198)
                      |++....
T Consensus       271 ~a~~~~~  277 (346)
T TIGR01659       271 LAEEHGK  277 (346)
T ss_pred             ECCcccc
Confidence            9986544

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).

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

Probab=99.71  E-value=8.2e-17  Score=118.88  Aligned_cols=78  Identities=31%  Similarity=0.572  Sum_probs=72.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCCC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPAN  140 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~~  140 (198)
                      ..++||||||+..+++.+|+.+|..||.|..|-|... .|||||||+++.+|+.|+..|+|..|.|..|+|++++....
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            4789999999999999999999999999999988764 59999999999999999999999999999999999986544

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

Probab=99.71  E-value=6.4e-17  Score=120.54  Aligned_cols=78  Identities=22%  Similarity=0.455  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC---CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~---kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ...++|||+|||.+|.|.+|+++|.+||.|.+|+|...   -.||||+|++..+|+.||..-++..++|..|+|++++.-
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            34789999999999999999999999999999998664   379999999999999999999999999999999999864


Q ss_pred             C
Q 029166          139 A  139 (198)
Q Consensus       139 ~  139 (198)
                      .
T Consensus        84 r   84 (241)
T KOG0105|consen   84 R   84 (241)
T ss_pred             C
Confidence            3

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

Probab=99.70  E-value=4.1e-17  Score=114.71  Aligned_cols=77  Identities=29%  Similarity=0.607  Sum_probs=71.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCC------cEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~k------g~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ...+++|||+||+..++|+.|.++|+++|+|+.|-+..+|      |||||+|.+.++|+.|++.+++..++.+.|+|.|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            3457899999999999999999999999999999886653      9999999999999999999999999999999999


Q ss_pred             ccC
Q 029166          135 GRN  137 (198)
Q Consensus       135 a~~  137 (198)
                      ...
T Consensus       113 D~G  115 (153)
T KOG0121|consen  113 DAG  115 (153)
T ss_pred             ccc
Confidence            764

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

Probab=99.70  E-value=1.2e-16  Score=132.73  Aligned_cols=84  Identities=27%  Similarity=0.521  Sum_probs=76.0

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ++.+.....+.|||+||+.++||+.|+++|++||.|++|+.++  .||||.|.++++|.+|++.+|+++|+|..|.|.+|
T Consensus       251 ~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~r--DYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLA  328 (506)
T KOG0117|consen  251 PDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPR--DYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLA  328 (506)
T ss_pred             CChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeeccc--ceeEEeecchHHHHHHHHHhcCceecCceEEEEec
Confidence            3444556678999999999999999999999999999998884  59999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 029166          136 RNPANK  141 (198)
Q Consensus       136 ~~~~~~  141 (198)
                      +++..+
T Consensus       329 KP~~k~  334 (506)
T KOG0117|consen  329 KPVDKK  334 (506)
T ss_pred             CChhhh
Confidence            987654

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.70  E-value=2e-16  Score=132.63  Aligned_cols=77  Identities=35%  Similarity=0.572  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ...+|||+|||+++++++|+++|++||.|.+++|+++      ||||||+|.+.++|.+|+..|||..|+|+.|+|.|+.
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence            3457999999999999999999999999999999864      7999999999999999999999999999999999998


Q ss_pred             CCC
Q 029166          137 NPA  139 (198)
Q Consensus       137 ~~~  139 (198)
                      ++.
T Consensus       348 ~~~  350 (352)
T TIGR01661       348 NKA  350 (352)
T ss_pred             CCC
Confidence            754

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.69  E-value=1.6e-16  Score=132.65  Aligned_cols=79  Identities=27%  Similarity=0.511  Sum_probs=73.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ......++|||+|||++++|++|+++|++||+|++|+|+++      ++||||+|.++++|++||+.|++..|.+++|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            45557889999999999999999999999999999999764      599999999999999999999999999999999


Q ss_pred             EeccC
Q 029166          133 SWGRN  137 (198)
Q Consensus       133 ~~a~~  137 (198)
                      .|+++
T Consensus       182 ~~a~p  186 (346)
T TIGR01659       182 SYARP  186 (346)
T ss_pred             ecccc
Confidence            99865

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).

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

Probab=99.69  E-value=1.2e-16  Score=123.57  Aligned_cols=79  Identities=28%  Similarity=0.545  Sum_probs=74.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ...+..+|-|.||+.+++|++|+++|.+||.|.++.|.++      ||||||+|.++++|.+||+.|||+-+++..|+|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            3446789999999999999999999999999999999874      7999999999999999999999999999999999


Q ss_pred             eccCC
Q 029166          134 WGRNP  138 (198)
Q Consensus       134 ~a~~~  138 (198)
                      |++++
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99985

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

Probab=99.69  E-value=1.1e-16  Score=128.40  Aligned_cols=81  Identities=26%  Similarity=0.471  Sum_probs=74.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ......++|+|.|||+...|-||+.+|++||+|.+|+|+.    +|||+||+|++.++|++|-++|||..|.||+|+|..
T Consensus        91 ~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen   91 SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             CCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            3344568999999999999999999999999999999998    489999999999999999999999999999999999


Q ss_pred             ccCCC
Q 029166          135 GRNPA  139 (198)
Q Consensus       135 a~~~~  139 (198)
                      |..+.
T Consensus       171 ATarV  175 (376)
T KOG0125|consen  171 ATARV  175 (376)
T ss_pred             cchhh
Confidence            97643

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

Probab=99.69  E-value=5.5e-16  Score=136.20  Aligned_cols=79  Identities=25%  Similarity=0.479  Sum_probs=72.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccC--CceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQY--GEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~--G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ....++|||+||+++++|++|+++|++|  |+|++|+++  ++||||+|++.++|++|++.||+.+|+|+.|+|+|++++
T Consensus       230 ~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~  307 (578)
T TIGR01648       230 MAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPV  307 (578)
T ss_pred             cccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCC
Confidence            3446789999999999999999999999  999999886  579999999999999999999999999999999999886


Q ss_pred             CCC
Q 029166          139 ANK  141 (198)
Q Consensus       139 ~~~  141 (198)
                      ...
T Consensus       308 ~~~  310 (578)
T TIGR01648       308 DKK  310 (578)
T ss_pred             Ccc
Confidence            543

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.

>PF00076 RRM_1: RNA recognition motif

Probab=99.67  E-value=2.5e-16  Score=101.48  Aligned_cols=65  Identities=48%  Similarity=0.847  Sum_probs=61.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        67 lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      |||+|||+++++++|+++|++||.|..+++..+     +++|||+|.+.++|++|++.|++..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999998873     69999999999999999999999999999885

(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 ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.66  E-value=6.2e-16  Score=129.60  Aligned_cols=77  Identities=34%  Similarity=0.597  Sum_probs=71.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      +.++|||+|||..++|++|+++|++||+|.+|+|+++      +|||||+|.+.++|++||+.||+..|.|+.|+|+|++
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            3678999999999999999999999999999999864      5899999999999999999999999999999999997


Q ss_pred             CCC
Q 029166          137 NPA  139 (198)
Q Consensus       137 ~~~  139 (198)
                      +..
T Consensus        82 ~~~   84 (352)
T TIGR01661        82 PSS   84 (352)
T ss_pred             ccc
Confidence            654

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

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.64  E-value=1.8e-15  Score=119.93  Aligned_cols=73  Identities=29%  Similarity=0.417  Sum_probs=69.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC---CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~---kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      .++|||+||++.++|++|+++|+.||+|.+|+|+.+   ++||||+|.++++|+.||. |++..|.|+.|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            579999999999999999999999999999999875   5999999999999999996 999999999999999874

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

Probab=99.63  E-value=6.1e-15  Score=131.01  Aligned_cols=79  Identities=34%  Similarity=0.639  Sum_probs=72.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .....+|||+||++.+++++|+++|++||.|++++++.+     +|||||+|.+.++|++|++.||+..++|+.|.|.+|
T Consensus       282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             ccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            335678999999999999999999999999999999764     699999999999999999999999999999999999


Q ss_pred             cCCC
Q 029166          136 RNPA  139 (198)
Q Consensus       136 ~~~~  139 (198)
                      ..+.
T Consensus       362 ~~k~  365 (562)
T TIGR01628       362 QRKE  365 (562)
T ss_pred             cCcH
Confidence            8654

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

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

Probab=99.61  E-value=3.5e-15  Score=113.05  Aligned_cols=81  Identities=30%  Similarity=0.568  Sum_probs=74.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      +++.....+|-|-||...++.++|+.+|++||.|-+|.|..+      +|||||.|.+..+|+.|++.|+|.+|+|+.|.
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            444455678999999999999999999999999999999885      69999999999999999999999999999999


Q ss_pred             EEeccCC
Q 029166          132 LSWGRNP  138 (198)
Q Consensus       132 v~~a~~~  138 (198)
                      |.+|+-.
T Consensus        87 Vq~aryg   93 (256)
T KOG4207|consen   87 VQMARYG   93 (256)
T ss_pred             ehhhhcC
Confidence            9999743

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

Probab=99.59  E-value=7.1e-15  Score=113.36  Aligned_cols=77  Identities=35%  Similarity=0.548  Sum_probs=68.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      .+..-++||||+|+|++..++|+++|++||+|++..|+.|      |||+||+|.|.++|++|++. ...+|+||+-.|.
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcn   86 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCN   86 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccc
Confidence            4455789999999999999999999999999999988764      79999999999999999985 5578999999999


Q ss_pred             eccC
Q 029166          134 WGRN  137 (198)
Q Consensus       134 ~a~~  137 (198)
                      +|.-
T Consensus        87 lA~l   90 (247)
T KOG0149|consen   87 LASL   90 (247)
T ss_pred             hhhh
Confidence            8753

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.58  E-value=1.3e-14  Score=93.80  Aligned_cols=65  Identities=37%  Similarity=0.727  Sum_probs=59.7

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        67 lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      |||+|||+++++++|+++|+.||.|..+++..+     +++|||+|.+.++|++|++.+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999999999999886     59999999999999999999999999999875

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 ....

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

Probab=99.57  E-value=1.6e-15  Score=125.62  Aligned_cols=83  Identities=30%  Similarity=0.566  Sum_probs=74.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCce-eCC--eEeEEE
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEALHKLNGTV-IGK--QSVRLS  133 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~-~~g--~~l~v~  133 (198)
                      .++++||||-|+..++|.+++++|++||.|++|.|++     +||||||.|.+++.|..||+.||+.. +.|  ..|.|+
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            3478999999999999999999999999999999988     48999999999999999999999875 454  489999


Q ss_pred             eccCCCCCCCC
Q 029166          134 WGRNPANKQFR  144 (198)
Q Consensus       134 ~a~~~~~~~~~  144 (198)
                      ||++++.+..+
T Consensus       202 FADtqkdk~~~  212 (510)
T KOG0144|consen  202 FADTQKDKDGK  212 (510)
T ss_pred             ecccCCCchHH
Confidence            99988776543

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

Probab=99.56  E-value=2.3e-14  Score=125.11  Aligned_cols=76  Identities=20%  Similarity=0.336  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHh--CCceeCCeEeEEEeccCC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL--NGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l--~~~~~~g~~l~v~~a~~~  138 (198)
                      ++++|||+|||+.++|++|+++|++||.|.+|.|+++|+||||+|.+.++|++|++.+  ++..|+|+.|.|.|+..+
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~   78 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQ   78 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCc
Confidence            3678999999999999999999999999999999999999999999999999999864  788999999999998643

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).

>PLN03213 repressor of silencing 3; Provisional

Probab=99.56  E-value=1.5e-14  Score=121.87  Aligned_cols=76  Identities=22%  Similarity=0.420  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC--CcEEEEEeCCH--HHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG--KGCGFVQFANR--ENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~--kg~afV~f~~~--~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      ....+||||||++.+++++|+.+|..||.|.+|.|++.  ||||||+|.+.  .++.+||..||+.+|.|+.|+|..|++
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            34579999999999999999999999999999999974  79999999987  689999999999999999999999876

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

Probab=99.56  E-value=4.2e-14  Score=112.40  Aligned_cols=84  Identities=21%  Similarity=0.462  Sum_probs=76.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ..+-+||||+.|+.+++|.+|+..|++||.|+.|+|+.+      +|||||+|+++.+...|.+..++..|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            356789999999999999999999999999999999874      79999999999999999999999999999999999


Q ss_pred             ccCCCCCCCC
Q 029166          135 GRNPANKQFR  144 (198)
Q Consensus       135 a~~~~~~~~~  144 (198)
                      -+.+..+.+.
T Consensus       178 ERgRTvkgW~  187 (335)
T KOG0113|consen  178 ERGRTVKGWL  187 (335)
T ss_pred             cccccccccc
Confidence            8877666543

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

Probab=99.56  E-value=3.4e-14  Score=125.37  Aligned_cols=78  Identities=26%  Similarity=0.546  Sum_probs=72.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ..++|||+||++++++++|+++|+.||.|++++|.+      +||||||+|.+.++|.+||+.||+..|+|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            457999999999999999999999999999999976      37999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      ++..
T Consensus       283 ~pP~  286 (612)
T TIGR01645       283 TPPD  286 (612)
T ss_pred             CCcc
Confidence            6543

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.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.55  E-value=3.8e-14  Score=110.79  Aligned_cols=75  Identities=28%  Similarity=0.344  Sum_probs=68.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC---CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~---kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      ....+|||+||++.++|++|+++|+.||+|.+|+|+++   ++||||+|.++++|+.|+. |+|..|.++.|.|.....
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            34689999999999999999999999999999999986   4899999999999999995 999999999999987653

>smart00362 RRM_2 RNA recognition motif

Probab=99.55  E-value=5.7e-14  Score=89.81  Aligned_cols=68  Identities=50%  Similarity=0.894  Sum_probs=64.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCC----cEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK----GCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~k----g~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      +|||+|||..+++++|+++|.+||.|..+.+..++    ++|||+|.+.+.|++|++.+++..+.++.|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999998865    999999999999999999999999999998874

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

Probab=99.55  E-value=3.3e-14  Score=125.08  Aligned_cols=81  Identities=22%  Similarity=0.384  Sum_probs=70.3

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeC-CeE
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEALHKLNGTVIG-KQS  129 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~-g~~  129 (198)
                      +........++|||+|||++++|++|+++|++||.|.+++|++     +|+||||+|.+.++|++||+.||+.+|. ++.
T Consensus        50 ~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~  129 (578)
T TIGR01648        50 WSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRL  129 (578)
T ss_pred             ccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcc
Confidence            3333344578999999999999999999999999999999975     4799999999999999999999999885 777


Q ss_pred             eEEEecc
Q 029166          130 VRLSWGR  136 (198)
Q Consensus       130 l~v~~a~  136 (198)
                      |.|.++.
T Consensus       130 l~V~~S~  136 (578)
T TIGR01648       130 LGVCISV  136 (578)
T ss_pred             ccccccc
Confidence            7777654

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=99.53  E-value=6.3e-14  Score=122.35  Aligned_cols=79  Identities=24%  Similarity=0.385  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           61 DSSNTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        61 ~~~~~~lfV~~l~~-~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ....++|||+||++ .+++++|+++|++||.|.+|+|+++ ++||||+|.+.++|+.|+..||+..|.|+.|+|++++.+
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            34678999999998 6999999999999999999999876 699999999999999999999999999999999998764


Q ss_pred             C
Q 029166          139 A  139 (198)
Q Consensus       139 ~  139 (198)
                      .
T Consensus       352 ~  352 (481)
T TIGR01649       352 N  352 (481)
T ss_pred             c
Confidence            3

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).

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

Probab=99.53  E-value=2.1e-14  Score=113.84  Aligned_cols=73  Identities=27%  Similarity=0.585  Sum_probs=69.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      .+|||||||.++++.+|+.+|++||+|++++|+  |.|+||..++...|+.||++||+..|+|..|+|+-+++++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv--KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV--KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee--cccceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            479999999999999999999999999999998  5699999999999999999999999999999999998873

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

Probab=99.52  E-value=5.6e-14  Score=123.97  Aligned_cols=75  Identities=24%  Similarity=0.558  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ...++|||+||++.+++++|+++|++||.|.+|+|+.      ++|||||+|.+.++|++|++.||+..|+|+.|+|.+.
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            3568999999999999999999999999999999975      4799999999999999999999999999999999875


Q ss_pred             c
Q 029166          136 R  136 (198)
Q Consensus       136 ~  136 (198)
                      .
T Consensus       185 ~  185 (612)
T TIGR01645       185 S  185 (612)
T ss_pred             c
Confidence            4

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.

>PF13893 RRM_5: RNA recognition motif

Probab=99.51  E-value=1.8e-13  Score=84.72  Aligned_cols=55  Identities=36%  Similarity=0.667  Sum_probs=51.9

Q ss_pred             HHHHhccCCceEEEEEeCCC-cEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           81 LRQPFSQYGEIASVKIPVGK-GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        81 l~~~F~~~G~i~~v~i~~~k-g~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      |.++|++||+|.++.+..++ ++|||+|.+.++|+.|++.||+..+.|+.|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999999987 99999999999999999999999999999999986

(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 ....

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

Probab=99.51  E-value=1.9e-14  Score=110.10  Aligned_cols=82  Identities=29%  Similarity=0.622  Sum_probs=75.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ....++||||+|..+++|..|...|-.||.|++|+++.+      |+|+||+|...|+|.+||..||+.+|-|+.|+|.+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            345689999999999999999999999999999999874      79999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 029166          135 GRNPANKQ  142 (198)
Q Consensus       135 a~~~~~~~  142 (198)
                      |+|.+-+.
T Consensus        87 AkP~kike   94 (298)
T KOG0111|consen   87 AKPEKIKE   94 (298)
T ss_pred             cCCccccC
Confidence            99876543

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

Probab=99.50  E-value=1.4e-13  Score=119.40  Aligned_cols=75  Identities=33%  Similarity=0.686  Sum_probs=70.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.      +++||||+|.+.++|.+|++.|++..|.|+.|+|.|+.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            368999999999999999999999999999999984      46999999999999999999999999999999999986


Q ss_pred             C
Q 029166          137 N  137 (198)
Q Consensus       137 ~  137 (198)
                      .
T Consensus       265 ~  265 (457)
T TIGR01622       265 D  265 (457)
T ss_pred             C
Confidence            4

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=99.49  E-value=2.5e-13  Score=92.35  Aligned_cols=76  Identities=21%  Similarity=0.422  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC---CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~---kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      ...+.|||.|||..+|.++..++|.+||.|..|+|...   +|-|||.|++..+|.+|++.|.|..+.++.|.|-+-.+
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            34678999999999999999999999999999999764   79999999999999999999999999999999887544

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

Probab=99.49  E-value=1.5e-13  Score=122.09  Aligned_cols=72  Identities=35%  Similarity=0.716  Sum_probs=68.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      +|||+|||.+++|++|+++|++||.|.+|+|.++      +|||||+|.+.++|++|++.|++..|.|+.|+|.|+..
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            6999999999999999999999999999999764      58999999999999999999999999999999999864

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

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

Probab=99.48  E-value=3.4e-13  Score=118.39  Aligned_cols=76  Identities=17%  Similarity=0.430  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ..++|||+|||..+++++|+++|+.||.|..+.|++      ++|||||+|.+.++|+.||+.|++..|.|+.|.|.++.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            457999999999999999999999999999999876      37999999999999999999999999999999999997


Q ss_pred             CC
Q 029166          137 NP  138 (198)
Q Consensus       137 ~~  138 (198)
                      ..
T Consensus       374 ~~  375 (509)
T TIGR01642       374 VG  375 (509)
T ss_pred             cC
Confidence            54

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

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

Probab=99.47  E-value=3.6e-13  Score=112.19  Aligned_cols=88  Identities=25%  Similarity=0.462  Sum_probs=76.7

Q ss_pred             CCCCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCC
Q 029166           49 NGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNG  122 (198)
Q Consensus        49 ~~~~~~~~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~  122 (198)
                      -+++++.+........+-||||.||.++.|++|..+|++.|+|-+++|+.+      ||||||+|.+.+.|+.||+.||+
T Consensus        68 ~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn  147 (506)
T KOG0117|consen   68 YGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNN  147 (506)
T ss_pred             cCCCCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhC
Confidence            334444465566678899999999999999999999999999999999885      79999999999999999999999


Q ss_pred             ceeC-CeEeEEEecc
Q 029166          123 TVIG-KQSVRLSWGR  136 (198)
Q Consensus       123 ~~~~-g~~l~v~~a~  136 (198)
                      ++|. |+.|.|+.+.
T Consensus       148 ~Eir~GK~igvc~Sv  162 (506)
T KOG0117|consen  148 YEIRPGKLLGVCVSV  162 (506)
T ss_pred             ccccCCCEeEEEEee
Confidence            9985 8888888653

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

Probab=99.46  E-value=1.6e-13  Score=97.58  Aligned_cols=83  Identities=29%  Similarity=0.563  Sum_probs=75.6

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQS  129 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~  129 (198)
                      +.+..+.....|||.++.+..+|++|.+.|..||+|+.|++..+      ||||+|+|++.+.|++|+..+|+..|-+..
T Consensus        64 pgPqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~  143 (170)
T KOG0130|consen   64 PGPQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQN  143 (170)
T ss_pred             CCCccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCc
Confidence            34566667889999999999999999999999999999999765      699999999999999999999999999999


Q ss_pred             eEEEeccCC
Q 029166          130 VRLSWGRNP  138 (198)
Q Consensus       130 l~v~~a~~~  138 (198)
                      |.|.|+--+
T Consensus       144 v~VDw~Fv~  152 (170)
T KOG0130|consen  144 VSVDWCFVK  152 (170)
T ss_pred             eeEEEEEec
Confidence            999998643

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

Probab=99.45  E-value=6.8e-13  Score=115.05  Aligned_cols=78  Identities=24%  Similarity=0.397  Sum_probs=70.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ...+.++|||+|||..+++++|+++|++||.|.+|+|+++      +|||||+|.+.++|++||. |++..+.|+.|.|.
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~  163 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQ  163 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEe
Confidence            3455789999999999999999999999999999999864      6999999999999999997 89999999999999


Q ss_pred             eccCC
Q 029166          134 WGRNP  138 (198)
Q Consensus       134 ~a~~~  138 (198)
                      ++...
T Consensus       164 ~~~~~  168 (457)
T TIGR01622       164 SSQAE  168 (457)
T ss_pred             ecchh
Confidence            87543

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.

>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=99.44  E-value=1.2e-12  Score=84.00  Aligned_cols=69  Identities=48%  Similarity=0.877  Sum_probs=64.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      +|+|+|||..+++++|+++|..+|.|..+.+..+     +++|||+|.+.++|..|++.+++..++++.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999998875     58999999999999999999999999999999875

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).

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

Probab=99.44  E-value=5.3e-13  Score=104.55  Aligned_cols=81  Identities=35%  Similarity=0.619  Sum_probs=75.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCC------cEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~k------g~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      .+...+.|.|.-||.++|+++|+.+|...|+|+++++++||      ||+||.|-++++|++|+..|||..+..+.|+|.
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            44556789999999999999999999999999999999975      999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 029166          134 WGRNPAN  140 (198)
Q Consensus       134 ~a~~~~~  140 (198)
                      +|++...
T Consensus       117 yARPSs~  123 (360)
T KOG0145|consen  117 YARPSSD  123 (360)
T ss_pred             eccCChh
Confidence            9998554

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

Probab=99.43  E-value=4.5e-13  Score=111.27  Aligned_cols=82  Identities=27%  Similarity=0.607  Sum_probs=71.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCce-eC--CeEe
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTV-IG--KQSV  130 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~-~~--g~~l  130 (198)
                      .+.+.-+|||+.||..++|.||+++|++||.|.+|.|++|      +|||||.|.++++|.+|+..||... |-  ...|
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            3456679999999999999999999999999999999996      5999999999999999999998765 43  5588


Q ss_pred             EEEeccCCCCC
Q 029166          131 RLSWGRNPANK  141 (198)
Q Consensus       131 ~v~~a~~~~~~  141 (198)
                      .|++|+...++
T Consensus       110 qvk~Ad~E~er  120 (510)
T KOG0144|consen  110 QVKYADGERER  120 (510)
T ss_pred             eecccchhhhc
Confidence            99998765443

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

Probab=99.40  E-value=1.3e-12  Score=102.89  Aligned_cols=77  Identities=36%  Similarity=0.827  Sum_probs=72.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      ..-|||+-|...|+.++|++.|.+||+|.+.+|++|      |||+||.|-.+++|+.||..|||.-|++|.|+..||..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            458999999999999999999999999999999884      89999999999999999999999999999999999976


Q ss_pred             CCC
Q 029166          138 PAN  140 (198)
Q Consensus       138 ~~~  140 (198)
                      +..
T Consensus       142 Kp~  144 (321)
T KOG0148|consen  142 KPS  144 (321)
T ss_pred             Ccc
Confidence            554

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

Probab=99.39  E-value=8.3e-13  Score=116.28  Aligned_cols=78  Identities=33%  Similarity=0.741  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCCCC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANK  141 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~~~  141 (198)
                      ++|||||+|+.+++|.+|..+|+.||+|.+|.++..++||||.+..+++|++|+.+|+.+.+.++.|+|.||..+.-+
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~k  498 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPK  498 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcc
Confidence            489999999999999999999999999999999999999999999999999999999999999999999999865544

>smart00360 RRM RNA recognition motif

Probab=99.39  E-value=2e-12  Score=82.12  Aligned_cols=65  Identities=43%  Similarity=0.787  Sum_probs=60.0

Q ss_pred             EcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           69 VGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        69 V~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      |+|||..+++++|+++|++||.|..+.+..+      +++|||+|.+.++|..|++.+++..++++.|+|+
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            5799999999999999999999999988775      4799999999999999999999999999998874

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

Probab=99.38  E-value=2.6e-12  Score=102.23  Aligned_cols=73  Identities=37%  Similarity=0.695  Sum_probs=69.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ..+|||+|||..+++++|+++|.+||.|..+.+..+      +|||||+|.+.++|..|++.+++..|.|+.|.|.++.
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            689999999999999999999999999999988765      5999999999999999999999999999999999965

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

Probab=99.36  E-value=1.1e-12  Score=97.64  Aligned_cols=75  Identities=31%  Similarity=0.545  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ....+|||+||+..++++.|.++|-+.|.|.+++++++      +|||||+|.++|+|+-|++.||...|-|++|+|..+
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            34679999999999999999999999999999999885      599999999999999999999999999999999998


Q ss_pred             c
Q 029166          136 R  136 (198)
Q Consensus       136 ~  136 (198)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            7

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

Probab=99.34  E-value=2.3e-12  Score=109.75  Aligned_cols=77  Identities=31%  Similarity=0.582  Sum_probs=72.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      +.|||||+|++++|++|..+|+..|.|.+++++.|      |||+|++|.+.++|+.|++.||+.++.|++|+|.|+...
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            88999999999999999999999999999999875      699999999999999999999999999999999999876


Q ss_pred             CCC
Q 029166          139 ANK  141 (198)
Q Consensus       139 ~~~  141 (198)
                      ..+
T Consensus        99 ~~~  101 (435)
T KOG0108|consen   99 KNA  101 (435)
T ss_pred             chh
Confidence            553

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

Probab=99.34  E-value=3.7e-12  Score=108.62  Aligned_cols=77  Identities=29%  Similarity=0.549  Sum_probs=71.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      ...+|.|+|||+.+.+.+|+.+|+.||.|.+|.|++.     .|||||.|....+|+.|++.+|+..|+|+.|-|.||-+
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            3679999999999999999999999999999999874     49999999999999999999999999999999999976


Q ss_pred             CC
Q 029166          138 PA  139 (198)
Q Consensus       138 ~~  139 (198)
                      +.
T Consensus       196 Kd  197 (678)
T KOG0127|consen  196 KD  197 (678)
T ss_pred             cc
Confidence            43

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

Probab=99.33  E-value=2.1e-13  Score=101.55  Aligned_cols=77  Identities=29%  Similarity=0.490  Sum_probs=70.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      .-.++.-|||||||+..||.+|.-+|++||+|+.|.++++      +||||+.|++..+..-|+..|||..|.|+.|+|.
T Consensus        31 ~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVD  110 (219)
T KOG0126|consen   31 EYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVD  110 (219)
T ss_pred             hcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEee
Confidence            3445678999999999999999999999999999999985      6999999999999999999999999999999998


Q ss_pred             ecc
Q 029166          134 WGR  136 (198)
Q Consensus       134 ~a~  136 (198)
                      -..
T Consensus       111 Hv~  113 (219)
T KOG0126|consen  111 HVS  113 (219)
T ss_pred             ecc
Confidence            653

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

Probab=99.33  E-value=8e-12  Score=109.72  Aligned_cols=77  Identities=21%  Similarity=0.411  Sum_probs=67.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccC------------CceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeC
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQY------------GEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG  126 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~------------G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~  126 (198)
                      ......++|||+|||+.+++++|+++|.++            +.|..+.+..+++||||+|.+.++|..||. |++..|.
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~~~  248 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMA-LDSIIYS  248 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhc-CCCeEee
Confidence            345567899999999999999999999874            457777888889999999999999999995 9999999


Q ss_pred             CeEeEEEecc
Q 029166          127 KQSVRLSWGR  136 (198)
Q Consensus       127 g~~l~v~~a~  136 (198)
                      |+.|+|....
T Consensus       249 g~~l~v~r~~  258 (509)
T TIGR01642       249 NVFLKIRRPH  258 (509)
T ss_pred             CceeEecCcc
Confidence            9999997543

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

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

Probab=99.31  E-value=4.7e-12  Score=103.05  Aligned_cols=85  Identities=27%  Similarity=0.577  Sum_probs=77.5

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCC------cEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALHKLNGTVIGKQS  129 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~k------g~afV~f~~~~~a~~a~~~l~~~~~~g~~  129 (198)
                      +..+..++...|||-.|++.++.++|+-+|+.||.|.++.|++++      .||||+|++.+++++|.-+|+...|++++
T Consensus       231 pdAd~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrR  310 (479)
T KOG0415|consen  231 PDADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRR  310 (479)
T ss_pred             cccccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccce
Confidence            455667778899999999999999999999999999999999964      79999999999999999999999999999


Q ss_pred             eEEEeccCCCC
Q 029166          130 VRLSWGRNPAN  140 (198)
Q Consensus       130 l~v~~a~~~~~  140 (198)
                      |+|.|+.+-..
T Consensus       311 IHVDFSQSVsk  321 (479)
T KOG0415|consen  311 IHVDFSQSVSK  321 (479)
T ss_pred             EEeehhhhhhh
Confidence            99999876544

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

Probab=99.28  E-value=2.6e-11  Score=101.15  Aligned_cols=75  Identities=23%  Similarity=0.451  Sum_probs=68.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhc-cCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFS-QYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~-~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ..+.+||.|||++..+.+|+++|. +.|+|+.|++..+     |+||.|||+++|.+++|++.||.+++.|+.|.|+...
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            456699999999999999999995 6899999999874     7999999999999999999999999999999999765


Q ss_pred             C
Q 029166          137 N  137 (198)
Q Consensus       137 ~  137 (198)
                      .
T Consensus       123 d  123 (608)
T KOG4212|consen  123 D  123 (608)
T ss_pred             c
Confidence            4

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

Probab=99.28  E-value=3.1e-11  Score=94.75  Aligned_cols=79  Identities=33%  Similarity=0.555  Sum_probs=73.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      .......|||-||.++++|..|-++|..||.|..|+|++|      |||+||++.+-++|..||..|||+.++++.|.|.
T Consensus       274 ~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVs  353 (360)
T KOG0145|consen  274 GPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVS  353 (360)
T ss_pred             CCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEE
Confidence            3344789999999999999999999999999999999985      7999999999999999999999999999999999


Q ss_pred             eccCC
Q 029166          134 WGRNP  138 (198)
Q Consensus       134 ~a~~~  138 (198)
                      |...+
T Consensus       354 FKtnk  358 (360)
T KOG0145|consen  354 FKTNK  358 (360)
T ss_pred             EecCC
Confidence            97654

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

Probab=99.26  E-value=8.1e-12  Score=99.27  Aligned_cols=78  Identities=27%  Similarity=0.516  Sum_probs=72.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCCC
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPAN  140 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~~  140 (198)
                      +...++|+|+||.+.++.++|+..|++||.|.+++|+  |+|+||.|+-.++|..|++.|++.+++|++|+|.++.++-.
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv--kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlr  152 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV--KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR  152 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeee--cceeEEEEeeccchHHHHhcccccccccceeeeeeeccccc
Confidence            4567899999999999999999999999999999998  57999999999999999999999999999999999876543

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

Probab=99.22  E-value=7.8e-11  Score=99.94  Aligned_cols=78  Identities=29%  Similarity=0.440  Sum_probs=67.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----C--cEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----K--GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----k--g~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ...+|||.|||.++++++|+++|.+||.|+...|...    +  .||||+|.+.++++.||.. +-..|++++|.|+..+
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            4456999999999999999999999999999877552    2  8999999999999999985 5778999999999987


Q ss_pred             CCCCC
Q 029166          137 NPANK  141 (198)
Q Consensus       137 ~~~~~  141 (198)
                      ....+
T Consensus       366 ~~~~g  370 (419)
T KOG0116|consen  366 PGFRG  370 (419)
T ss_pred             ccccc
Confidence            65443

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.21  E-value=1.7e-11  Score=96.48  Aligned_cols=82  Identities=29%  Similarity=0.469  Sum_probs=75.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ...++.|.|||-.||.+..+.+|..+|-.||.|.+.++..|      |.|+||.|+++.+|+.||..|||..|+-++|+|
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKV  359 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV  359 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhh
Confidence            34567899999999999999999999999999999888664      799999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 029166          133 SWGRNPAN  140 (198)
Q Consensus       133 ~~a~~~~~  140 (198)
                      .+.+++..
T Consensus       360 QLKRPkda  367 (371)
T KOG0146|consen  360 QLKRPKDA  367 (371)
T ss_pred             hhcCcccc
Confidence            99988754

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

Probab=99.20  E-value=1.4e-11  Score=100.76  Aligned_cols=72  Identities=25%  Similarity=0.585  Sum_probs=67.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .++||||.|.+++.|+.|+..|..||.|++|.+..      .|+||||+|+-+|.|+-|++.||+..++|+.|+|..-
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            68899999999999999999999999999998865      3899999999999999999999999999999999743

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

Probab=99.18  E-value=9.3e-11  Score=90.33  Aligned_cols=78  Identities=26%  Similarity=0.521  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----HhccCCceEEEEEeC---CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQ----PFSQYGEIASVKIPV---GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~----~F~~~G~i~~v~i~~---~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      +..||||.||++.+..++|++    +|++||.|.+|...+   -||-|||.|.+.+.|-.|++.|+|..+-|+.++|.+|
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA   87 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYA   87 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecc
Confidence            345999999999999999988    999999999998765   4799999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      +....
T Consensus        88 ~s~sd   92 (221)
T KOG4206|consen   88 KSDSD   92 (221)
T ss_pred             cCccc
Confidence            87655

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.17  E-value=2.8e-11  Score=95.36  Aligned_cols=80  Identities=25%  Similarity=0.572  Sum_probs=72.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeC---CeEeEEEe
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEALHKLNGTVIG---KQSVRLSW  134 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~---g~~l~v~~  134 (198)
                      ++++||||-|...-.|+|++++|..||.|.++.+.+     +|||+||.|.+.-+|+.||..||+....   ...|.|++
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            678999999999999999999999999999999987     5899999999999999999999998652   56899999


Q ss_pred             ccCCCCCC
Q 029166          135 GRNPANKQ  142 (198)
Q Consensus       135 a~~~~~~~  142 (198)
                      ++..+++.
T Consensus        98 ADTdkER~  105 (371)
T KOG0146|consen   98 ADTDKERT  105 (371)
T ss_pred             ccchHHHH
Confidence            98776654

>smart00361 RRM_1 RNA recognition motif

Probab=99.16  E-value=1.7e-10  Score=74.74  Aligned_cols=56  Identities=30%  Similarity=0.612  Sum_probs=49.2

Q ss_pred             HHHHHHHhc----cCCceEEEE-EeC--------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           78 DEDLRQPFS----QYGEIASVK-IPV--------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        78 e~~l~~~F~----~~G~i~~v~-i~~--------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      +++|+++|+    +||.|.+|. |..        ++||+||+|.+.++|.+|++.||+..++|+.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578999998    999999885 322        37999999999999999999999999999999863

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

Probab=99.14  E-value=1.1e-10  Score=99.66  Aligned_cols=77  Identities=27%  Similarity=0.390  Sum_probs=71.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      ..||||++||+.++.++|.++|+.+|.|..+.++.      .|||+||+|.-.++++.|+..++...++|+.|+|+.|+.
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            48999999999999999999999999999998876      379999999999999999999999999999999999976


Q ss_pred             CCC
Q 029166          138 PAN  140 (198)
Q Consensus       138 ~~~  140 (198)
                      +..
T Consensus        85 R~r   87 (678)
T KOG0127|consen   85 RAR   87 (678)
T ss_pred             ccc
Confidence            543

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

Probab=99.12  E-value=9.8e-11  Score=100.05  Aligned_cols=73  Identities=34%  Similarity=0.638  Sum_probs=67.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      +|||+||..+++|++|+.+|+.||.|..|.++++      |||+||+|.+.++|.+|++.||+.+|-|+.|+|.....+
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            3999999999999999999999999999998874      799999999999999999999999999999999876543

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

Probab=99.11  E-value=3.2e-10  Score=95.59  Aligned_cols=73  Identities=32%  Similarity=0.611  Sum_probs=68.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCCC
Q 029166           67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPAN  140 (198)
Q Consensus        67 lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~~  140 (198)
                      |||.||++.++..+|.++|+.||+|++|++..+    +|| ||+|+++++|++|++.+||..+.++.|.|.....+..
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            999999999999999999999999999999874    799 9999999999999999999999999999988765444

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

Probab=99.10  E-value=2.3e-10  Score=85.40  Aligned_cols=84  Identities=30%  Similarity=0.532  Sum_probs=71.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEE-EEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASV-KIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v-~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .....+.+|||+||.++++|..|.+.|+.||.+... ++++      .++|+||.|++.+.+.+|++.+|+..+..++|.
T Consensus        91 ~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~it  170 (203)
T KOG0131|consen   91 KNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPIT  170 (203)
T ss_pred             ccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceE
Confidence            334445899999999999999999999999987653 4444      368999999999999999999999999999999


Q ss_pred             EEeccCCCCCC
Q 029166          132 LSWGRNPANKQ  142 (198)
Q Consensus       132 v~~a~~~~~~~  142 (198)
                      |+++..+..++
T Consensus       171 v~ya~k~~~kg  181 (203)
T KOG0131|consen  171 VSYAFKKDTKG  181 (203)
T ss_pred             EEEEEecCCCc
Confidence            99998765443

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

Probab=99.08  E-value=4.3e-10  Score=98.67  Aligned_cols=72  Identities=39%  Similarity=0.594  Sum_probs=67.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC---------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~---------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ++|||.||++.++.++|+.+|.+.|.|.++.|.+.         .|||||+|.+.++|+.|++.|+|+.|+|+.|.|+++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            44999999999999999999999999999988763         399999999999999999999999999999999999


Q ss_pred             c
Q 029166          136 R  136 (198)
Q Consensus       136 ~  136 (198)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            8

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

Probab=99.06  E-value=7.6e-10  Score=95.19  Aligned_cols=79  Identities=22%  Similarity=0.462  Sum_probs=72.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ....+.|||.+|+..+...+|+.+|++||+|+-.+|+.+      +.|+||++.+.++|.++|+.||.++|+|+.|.|+.
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            344679999999999999999999999999999888764      68999999999999999999999999999999999


Q ss_pred             ccCCC
Q 029166          135 GRNPA  139 (198)
Q Consensus       135 a~~~~  139 (198)
                      +++..
T Consensus       482 aKNEp  486 (940)
T KOG4661|consen  482 AKNEP  486 (940)
T ss_pred             cccCc
Confidence            88643

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.02  E-value=2.9e-09  Score=87.37  Aligned_cols=79  Identities=29%  Similarity=0.502  Sum_probs=70.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ...+|||++||..+++++|+++|.+||.|..+.++.+      ++|+||+|.+++++++++. .+-+.|.++.+.|+.|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            4669999999999999999999999999999888764      6999999999999999987 58889999999999998


Q ss_pred             CCCCCC
Q 029166          137 NPANKQ  142 (198)
Q Consensus       137 ~~~~~~  142 (198)
                      ++....
T Consensus       175 pk~~~~  180 (311)
T KOG4205|consen  175 PKEVMQ  180 (311)
T ss_pred             chhhcc
Confidence            866544

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.00  E-value=4.5e-10  Score=92.07  Aligned_cols=77  Identities=30%  Similarity=0.522  Sum_probs=68.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      +.++|||++|+|+++++.|+++|.+||+|.++.++++      ++|+||+|++.+.+.+++. ..-+.|+++.|.++.|.
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            6889999999999999999999999999999999884      6999999999999888876 45678999999999887


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      ++..
T Consensus        84 ~r~~   87 (311)
T KOG4205|consen   84 SRED   87 (311)
T ss_pred             Cccc
Confidence            6554

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

Probab=99.00  E-value=5.6e-10  Score=86.59  Aligned_cols=72  Identities=25%  Similarity=0.588  Sum_probs=67.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      .++||++||+.+.+.+|+++|..||.|.++.+.  .+|+||+|.+..+|+.|+..||+.+|.+..+.|+|++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            469999999999999999999999999998874  589999999999999999999999999999999999864

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

Probab=98.96  E-value=9e-10  Score=96.66  Aligned_cols=79  Identities=27%  Similarity=0.554  Sum_probs=72.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ....++|+|.|||+..+-.+++.+|..||.|++|+|++.      +|||||+|-++.+|.+|++.|..+.+-|++|.++|
T Consensus       610 kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEw  689 (725)
T KOG0110|consen  610 KKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEW  689 (725)
T ss_pred             ccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheeh
Confidence            334679999999999999999999999999999999874      79999999999999999999999999999999999


Q ss_pred             ccCCC
Q 029166          135 GRNPA  139 (198)
Q Consensus       135 a~~~~  139 (198)
                      |+...
T Consensus       690 A~~d~  694 (725)
T KOG0110|consen  690 AKSDN  694 (725)
T ss_pred             hccch
Confidence            98643

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

Probab=98.96  E-value=2.5e-09  Score=89.48  Aligned_cols=78  Identities=23%  Similarity=0.341  Sum_probs=68.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .......++|||.|||.++|++.|++-|..||.|+.++|+.. +..+.|.|.++++|+.|+..|++..|+|+.|+|.+.
T Consensus       530 ~gaarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  530 VGAARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccccccccEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            344556788999999999999999999999999999988542 445599999999999999999999999999999863

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

Probab=98.95  E-value=1.2e-08  Score=78.73  Aligned_cols=82  Identities=18%  Similarity=0.359  Sum_probs=66.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-C------CcEEEEEeCCHHHHHHHHHHhCCceeC---CeE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-G------KGCGFVQFANRENAEEALHKLNGTVIG---KQS  129 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-~------kg~afV~f~~~~~a~~a~~~l~~~~~~---g~~  129 (198)
                      .....+||||.+||.++-..+|..+|..|-.-+...|.. +      +-+|||+|.+...|++|+..|||..++   +..
T Consensus        30 ~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~st  109 (284)
T KOG1457|consen   30 EPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGST  109 (284)
T ss_pred             cccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCce
Confidence            344578999999999999999999999884333333321 2      379999999999999999999999997   789


Q ss_pred             eEEEeccCCCCC
Q 029166          130 VRLSWGRNPANK  141 (198)
Q Consensus       130 l~v~~a~~~~~~  141 (198)
                      |+|++|+.....
T Consensus       110 LhiElAKSNtK~  121 (284)
T KOG1457|consen  110 LHIELAKSNTKR  121 (284)
T ss_pred             eEeeehhcCccc
Confidence            999999865543

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.91  E-value=5.3e-09  Score=91.92  Aligned_cols=80  Identities=40%  Similarity=0.824  Sum_probs=73.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC---------CCcEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV---------GKGCGFVQFANRENAEEALHKLNGTVIGKQ  128 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~---------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~  128 (198)
                      .+.++..+.|||+||++.++|+.|...|..||.|..|+|+.         .+.|+||.|-++.+|++|++.|++..+.+.
T Consensus       168 DdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~  247 (877)
T KOG0151|consen  168 DDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEY  247 (877)
T ss_pred             CCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeee
Confidence            34467788999999999999999999999999999999976         258999999999999999999999999999


Q ss_pred             EeEEEeccC
Q 029166          129 SVRLSWGRN  137 (198)
Q Consensus       129 ~l~v~~a~~  137 (198)
                      .+++-|++.
T Consensus       248 e~K~gWgk~  256 (877)
T KOG0151|consen  248 EMKLGWGKA  256 (877)
T ss_pred             eeeeccccc
Confidence            999999975

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

Probab=98.88  E-value=8.1e-09  Score=78.66  Aligned_cols=80  Identities=16%  Similarity=0.304  Sum_probs=70.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccC-CceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQY-GEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~-G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      +......-++|..+|.-+.+.+|..+|.+| |.|+.+++.+      +||||||+|++++.|+-|-+.||++.+.++.|.
T Consensus        44 p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~  123 (214)
T KOG4208|consen   44 PEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLE  123 (214)
T ss_pred             CccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheee
Confidence            334455678999999999999999999998 7888888865      479999999999999999999999999999999


Q ss_pred             EEeccCC
Q 029166          132 LSWGRNP  138 (198)
Q Consensus       132 v~~a~~~  138 (198)
                      |.+-.+.
T Consensus       124 c~vmppe  130 (214)
T KOG4208|consen  124 CHVMPPE  130 (214)
T ss_pred             eEEeCch
Confidence            9987664

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

Probab=98.84  E-value=7.1e-09  Score=85.09  Aligned_cols=77  Identities=26%  Similarity=0.544  Sum_probs=70.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      .-.+|||..+.++.+|+||+..|+.||+|+.|.+.+      .|||+||+|.+..+...||..||-..++|..|+|-.+.
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            347999999999999999999999999999999976      37999999999999999999999999999999998775


Q ss_pred             CCC
Q 029166          137 NPA  139 (198)
Q Consensus       137 ~~~  139 (198)
                      .+.
T Consensus       289 TPP  291 (544)
T KOG0124|consen  289 TPP  291 (544)
T ss_pred             CCC
Confidence            443

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

Probab=98.81  E-value=4.7e-09  Score=90.08  Aligned_cols=74  Identities=32%  Similarity=0.488  Sum_probs=67.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-GKGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      ...+....+|+|-|||..+++++|+++|+.||+|+.|+..+ .++.+||+|-|..+|+.|++.|++.++.|++|+
T Consensus        69 ~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   69 SEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            33455678999999999999999999999999999987755 469999999999999999999999999999988

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

Probab=98.80  E-value=1.9e-08  Score=84.87  Aligned_cols=71  Identities=30%  Similarity=0.589  Sum_probs=65.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC---CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~---kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ..||||   +++||..|.++|+.+|+|.+|++.++   -|||||.|.++++|++|++.+|-..+.|+.|+|.|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            368999   89999999999999999999998775   599999999999999999999999999999999998643

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

Probab=98.77  E-value=3.5e-08  Score=78.18  Aligned_cols=81  Identities=27%  Similarity=0.504  Sum_probs=71.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .+....+|+|.||+..+++++|+++|..||.++.+-|..+     .|.|-|.|...++|+.|++.+++..++|+.|++..
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3444578999999999999999999999999888888764     49999999999999999999999999999999998


Q ss_pred             ccCCCC
Q 029166          135 GRNPAN  140 (198)
Q Consensus       135 a~~~~~  140 (198)
                      ..+...
T Consensus       159 i~~~~~  164 (243)
T KOG0533|consen  159 ISSPSQ  164 (243)
T ss_pred             ecCccc
Confidence            765443

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

Probab=98.64  E-value=1.2e-08  Score=78.52  Aligned_cols=74  Identities=24%  Similarity=0.333  Sum_probs=67.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCC----cEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK----GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~k----g~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ..++|||+|+...++|+.|.++|-+-|.|.+|.|...+    .||||+|.++.++.-|++.+||..+.+..|+|.+..
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            46789999999999999999999999999999997642    599999999999999999999999999988888754

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

Probab=98.64  E-value=1.4e-07  Score=74.68  Aligned_cols=80  Identities=28%  Similarity=0.476  Sum_probs=72.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      ...+.+...+||+|+...++-++++.+|+.||.|..+.|..+      |+|+||+|.+.+.++.++. |++..|.++.++
T Consensus        95 ~~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~  173 (231)
T KOG4209|consen   95 RQKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIE  173 (231)
T ss_pred             hhhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccce
Confidence            356677889999999999998889999999999988877663      6899999999999999999 999999999999


Q ss_pred             EEeccCC
Q 029166          132 LSWGRNP  138 (198)
Q Consensus       132 v~~a~~~  138 (198)
                      |.+.+..
T Consensus       174 vt~~r~~  180 (231)
T KOG4209|consen  174 VTLKRTN  180 (231)
T ss_pred             eeeeeee
Confidence            9998765

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

Probab=98.63  E-value=1.3e-06  Score=72.16  Aligned_cols=79  Identities=22%  Similarity=0.299  Sum_probs=65.0

Q ss_pred             CCCCeEEEcCCC--CCCCHHHHHHHhccCCceEEEEEeCCCcE-EEEEeCCHHHHHHHHHHhCCcee--CCeEeEEEecc
Q 029166           62 SSNTTIFVGGLD--PNVTDEDLRQPFSQYGEIASVKIPVGKGC-GFVQFANRENAEEALHKLNGTVI--GKQSVRLSWGR  136 (198)
Q Consensus        62 ~~~~~lfV~~l~--~~~~e~~l~~~F~~~G~i~~v~i~~~kg~-afV~f~~~~~a~~a~~~l~~~~~--~g~~l~v~~a~  136 (198)
                      ...+.|.+.=|.  +.||.+.|..+....|+|.+|.|.+..+. |.|||++.+.|++|.+.|||..|  +-..|+|++|+
T Consensus       118 ~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAk  197 (494)
T KOG1456|consen  118 TPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAK  197 (494)
T ss_pred             CCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccceeEEEEecC
Confidence            344555555444  46999999999999999999999887665 99999999999999999999987  35589999999


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      +.+-
T Consensus       198 P~rl  201 (494)
T KOG1456|consen  198 PTRL  201 (494)
T ss_pred             ccee
Confidence            8543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.54  E-value=5.2e-07  Score=75.19  Aligned_cols=78  Identities=24%  Similarity=0.433  Sum_probs=70.9

Q ss_pred             CCeEEEcCCCCC-CCHHHHHHHhccCCceEEEEEeCCC-cEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCCCC
Q 029166           64 NTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGK-GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANK  141 (198)
Q Consensus        64 ~~~lfV~~l~~~-~~e~~l~~~F~~~G~i~~v~i~~~k-g~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~~~  141 (198)
                      ...|.|.||.+. +|.+.|..+|+-||.|.+|+|..+| .-|.|.|.|...|+-|++.|+|+.|.|++|+|.+++-+.-.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vq  376 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQ  376 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcccc
Confidence            578899999876 9999999999999999999998864 67999999999999999999999999999999999865543

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

Probab=98.54  E-value=3.8e-07  Score=74.48  Aligned_cols=80  Identities=24%  Similarity=0.378  Sum_probs=68.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEE--------EEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeC
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS--------VKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIG  126 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~--------v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~  126 (198)
                      .....+.|||.|||..+|.+++.++|++||-|.+        |+|-++     ||=|.|+|-..++++-|+..|++..+.
T Consensus       130 ~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  130 EPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             ccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            3455678999999999999999999999997743        344332     688999999999999999999999999


Q ss_pred             CeEeEEEeccCCC
Q 029166          127 KQSVRLSWGRNPA  139 (198)
Q Consensus       127 g~~l~v~~a~~~~  139 (198)
                      |+.|+|+.|+-+.
T Consensus       210 g~~~rVerAkfq~  222 (382)
T KOG1548|consen  210 GKKLRVERAKFQM  222 (382)
T ss_pred             CcEEEEehhhhhh
Confidence            9999999987543

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.34  E-value=2.2e-06  Score=73.00  Aligned_cols=74  Identities=24%  Similarity=0.425  Sum_probs=62.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      .+..-|-+.+|||++|+++|.++|+.++ |..+.+.+.    .|-|||+|.+++++++|++ .+...+..+-|+|-.+..
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGG   85 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCC
Confidence            3455677889999999999999999984 677777653    5999999999999999998 588889999999987743

>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=98.32  E-value=1.6e-06  Score=60.50  Aligned_cols=70  Identities=34%  Similarity=0.548  Sum_probs=45.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCc-----eeCCeEeEEEe
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT-----VIGKQSVRLSW  134 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~-----~~~g~~l~v~~  134 (198)
                      +.|.|.++...++.++|++.|++||.|..|.+.+.-.-|+|.|.+.+.|+.|++.+...     .|.+..++++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            46888899999999999999999999999999887789999999999999999877433     45565555553

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

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

Probab=98.31  E-value=7.5e-07  Score=69.29  Aligned_cols=74  Identities=26%  Similarity=0.455  Sum_probs=65.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ...+.+.++|.+++..+.+.+|.++|.++|.+....+  .++++||+|...++|..|++.|++..+.++.|++...
T Consensus        95 p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen   95 PSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             cccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            3556788999999999999999999999999955444  5789999999999999999999999999999999544

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

Probab=98.30  E-value=5.4e-06  Score=56.76  Aligned_cols=74  Identities=24%  Similarity=0.371  Sum_probs=61.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccC--CceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeC----CeEeEE
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQY--GEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIG----KQSVRL  132 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~--G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~----g~~l~v  132 (198)
                      +||-|+|||-..+.++|.+++...  |...-+-++.      +.|||||.|.+.+.|.+-.+.++|..+.    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            689999999999999999988653  5555555544      3699999999999999999999999885    667889


Q ss_pred             EeccCC
Q 029166          133 SWGRNP  138 (198)
Q Consensus       133 ~~a~~~  138 (198)
                      .+|+-+
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            998754

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

>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=98.29  E-value=3.6e-06  Score=55.51  Aligned_cols=69  Identities=26%  Similarity=0.430  Sum_probs=48.5

Q ss_pred             CeEEEcCCCCCCCHH----HHHHHhccCC-ceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           65 TTIFVGGLDPNVTDE----DLRQPFSQYG-EIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~----~l~~~F~~~G-~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      +.|+|.|||.+.+..    -|++++..+| +|.+|    ..+.|+|.|.+.+.|++|.+.|++-.+-|.+|.|.+...
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCC
Confidence            468999999998865    4566777775 77766    368999999999999999999999999999999999853

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

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

Probab=98.29  E-value=7.6e-07  Score=68.89  Aligned_cols=64  Identities=30%  Similarity=0.579  Sum_probs=54.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC--CcEEEEEeCCHHHHHHHHHHhCCceeC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG--KGCGFVQFANRENAEEALHKLNGTVIG  126 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~--kg~afV~f~~~~~a~~a~~~l~~~~~~  126 (198)
                      -..+|||.||..+++|++|+.+|+.|-....++|...  -..||++|++.+.|..|+..|.|..|.
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcceec
Confidence            3469999999999999999999999976666666443  368999999999999999999887663

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

Probab=98.25  E-value=5.8e-06  Score=64.06  Aligned_cols=78  Identities=21%  Similarity=0.407  Sum_probs=69.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCceeC-CeEeEEEecc
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVIG-KQSVRLSWGR  136 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~~~-g~~l~v~~a~  136 (198)
                      ....+...||+.|||.+++.+.|..+|.+|...++|+++.. ++.|||+|.+...|..|...+.+..|. ...+.|.+++
T Consensus       141 ~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  141 QMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             cCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            34566789999999999999999999999999999998874 689999999999999999999998887 7788888875

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

Probab=98.15  E-value=2.5e-06  Score=67.19  Aligned_cols=79  Identities=28%  Similarity=0.537  Sum_probs=66.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .+.+.+..+||-|-|.-+++.+.|-+.|.+|-.....++++      ++||+||.|.+..++..|+..|++..++.+.|+
T Consensus       184 ~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpik  263 (290)
T KOG0226|consen  184 AEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIK  263 (290)
T ss_pred             ccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhH
Confidence            34455678999999999999999999999986554455544      579999999999999999999999999999988


Q ss_pred             EEecc
Q 029166          132 LSWGR  136 (198)
Q Consensus       132 v~~a~  136 (198)
                      ++...
T Consensus       264 lRkS~  268 (290)
T KOG0226|consen  264 LRKSE  268 (290)
T ss_pred             hhhhh
Confidence            76554

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=98.15  E-value=5.9e-06  Score=50.30  Aligned_cols=52  Identities=29%  Similarity=0.640  Sum_probs=44.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHH
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL  117 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~  117 (198)
                      +.|-|.+.+.+..+ ++..+|..||+|.++.+.....+.+|.|.++.+|++||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            45778888887654 55668999999999999877899999999999999985

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

Probab=98.07  E-value=2.8e-05  Score=64.46  Aligned_cols=81  Identities=22%  Similarity=0.336  Sum_probs=72.1

Q ss_pred             CCCCCCCeEEEcCCCCC-CCHHHHHHHhccCCceEEEEEeCCC-cEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           59 EGDSSNTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGK-GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~-~~e~~l~~~F~~~G~i~~v~i~~~k-g~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ....+.+.+-|-+|... ++-+.|..+|..||.|.+|+.++.| +-|.|++.|....++|+..||+..+-|.+|.|++++
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~Sk  361 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSK  361 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeecc
Confidence            34456788999999876 7889999999999999999999875 899999999999999999999999999999999987


Q ss_pred             CCC
Q 029166          137 NPA  139 (198)
Q Consensus       137 ~~~  139 (198)
                      ...
T Consensus       362 Q~~  364 (494)
T KOG1456|consen  362 QNF  364 (494)
T ss_pred             ccc
Confidence            543

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

Probab=98.06  E-value=4.7e-06  Score=72.21  Aligned_cols=82  Identities=22%  Similarity=0.471  Sum_probs=72.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      .......++||++||..++++.++++...||.++...++.      +++|||.+|.+......|+..|||..++++.|.|
T Consensus       284 ~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvv  363 (500)
T KOG0120|consen  284 DVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVV  363 (500)
T ss_pred             CcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEe
Confidence            3444567899999999999999999999999998887765      4899999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 029166          133 SWGRNPAN  140 (198)
Q Consensus       133 ~~a~~~~~  140 (198)
                      ..|.....
T Consensus       364 q~A~~g~~  371 (500)
T KOG0120|consen  364 QRAIVGAS  371 (500)
T ss_pred             ehhhccch
Confidence            99876443

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

Probab=98.05  E-value=0.00016  Score=54.77  Aligned_cols=69  Identities=22%  Similarity=0.413  Sum_probs=61.7

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeC
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG  126 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~  126 (198)
                      .++...+..+|.|.+||++-++++|+++..+-|.|+...+.++ +.+.|+|...|+.+-|+.+|+...+.
T Consensus       108 gppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  108 GPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             CCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-cceeeeeeehhhHHHHHHhhcccccc
Confidence            3555667789999999999999999999999999999999877 79999999999999999999887664

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.02  E-value=2.3e-05  Score=66.92  Aligned_cols=73  Identities=26%  Similarity=0.431  Sum_probs=58.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEE-EEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS-VKIPV-----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~-v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .....|-+++||+.|++++|.++|+-.-.|.. |.++.     ..+-|||.|++.+.|++|+.. |...|+.+-|+|..+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            35678899999999999999999997644333 33333     248899999999999999985 777889998888765

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

Probab=98.01  E-value=1.1e-05  Score=66.45  Aligned_cols=81  Identities=27%  Similarity=0.332  Sum_probs=69.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEE--------EeC------CCcEEEEEeCCHHHHHHHHHHhCCce
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVK--------IPV------GKGCGFVQFANRENAEEALHKLNGTV  124 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~--------i~~------~kg~afV~f~~~~~a~~a~~~l~~~~  124 (198)
                      .......+|||-+|+..+++++|.++|.++|.|..-+        |-+      .|+-|.|+|.|...|+.|++.+++..
T Consensus        61 ~~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkd  140 (351)
T KOG1995|consen   61 ADKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKD  140 (351)
T ss_pred             ccccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccc
Confidence            3456677999999999999999999999999875422        212      37999999999999999999999999


Q ss_pred             eCCeEeEEEeccCCC
Q 029166          125 IGKQSVRLSWGRNPA  139 (198)
Q Consensus       125 ~~g~~l~v~~a~~~~  139 (198)
                      +.+..|+|.+|..+.
T Consensus       141 f~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  141 FCGNTIKVSLAERRT  155 (351)
T ss_pred             ccCCCchhhhhhhcc
Confidence            999999999997655

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.96  E-value=1.1e-05  Score=67.87  Aligned_cols=65  Identities=29%  Similarity=0.406  Sum_probs=56.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-------------------CcEEEEEeCCHHHHHHHHHH
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-------------------KGCGFVQFANRENAEEALHK  119 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-------------------kg~afV~f~~~~~a~~a~~~  119 (198)
                      ..+...++|.+-|||.+-.-+.|.++|+.+|.|+.|+|...                   +-||+|+|+..+.|.+|.+.
T Consensus       226 ~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  226 EEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             ccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            34457899999999999777999999999999999999652                   57899999999999999997


Q ss_pred             hCCc
Q 029166          120 LNGT  123 (198)
Q Consensus       120 l~~~  123 (198)
                      |+..
T Consensus       306 ~~~e  309 (484)
T KOG1855|consen  306 LNPE  309 (484)
T ss_pred             hchh
Confidence            7543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.92  E-value=3e-05  Score=63.55  Aligned_cols=73  Identities=22%  Similarity=0.588  Sum_probs=60.4

Q ss_pred             CCeEEEcCCCCCCCHHH----H--HHHhccCCceEEEEEeCC-------Cc--EEEEEeCCHHHHHHHHHHhCCceeCCe
Q 029166           64 NTTIFVGGLDPNVTDED----L--RQPFSQYGEIASVKIPVG-------KG--CGFVQFANRENAEEALHKLNGTVIGKQ  128 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~----l--~~~F~~~G~i~~v~i~~~-------kg--~afV~f~~~~~a~~a~~~l~~~~~~g~  128 (198)
                      ..-+||-+|++.+..++    |  .++|.+||+|..|.|.+.       .+  -.||+|.+.|+|.++|...+|..++|+
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            35689999998865544    3  578999999999988662       12  249999999999999999999999999


Q ss_pred             EeEEEecc
Q 029166          129 SVRLSWGR  136 (198)
Q Consensus       129 ~l~v~~a~  136 (198)
                      .|+..+..
T Consensus       194 ~lkatYGT  201 (480)
T COG5175         194 VLKATYGT  201 (480)
T ss_pred             eEeeecCc
Confidence            99998754

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.91  E-value=6.5e-05  Score=51.76  Aligned_cols=72  Identities=28%  Similarity=0.377  Sum_probs=54.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEE-------------EeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCe-
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVK-------------IPVGKGCGFVQFANRENAEEALHKLNGTVIGKQ-  128 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~-------------i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~-  128 (198)
                      ..+.|.|-+.|+. ....|.++|++||.|.+..             +.....+--|+|+++.+|.+||. -||..++|. 
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            4566889999998 4567888999999998875             44567899999999999999998 599999876 


Q ss_pred             EeEEEecc
Q 029166          129 SVRLSWGR  136 (198)
Q Consensus       129 ~l~v~~a~  136 (198)
                      .+-|.+.+
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence            45577764

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.

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

Probab=97.83  E-value=8.7e-06  Score=70.25  Aligned_cols=82  Identities=24%  Similarity=0.352  Sum_probs=71.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      ...+.+.+++|+--|...+++.+|.++|+.+|+|.+|.++.+      +|.+||+|.|.+++..||. |.|..+.|..|.
T Consensus       173 ~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~  251 (549)
T KOG0147|consen  173 SPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVI  251 (549)
T ss_pred             CchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeE
Confidence            445556789999999999999999999999999999999874      6999999999999999996 999999999999


Q ss_pred             EEeccCCCC
Q 029166          132 LSWGRNPAN  140 (198)
Q Consensus       132 v~~a~~~~~  140 (198)
                      |.......+
T Consensus       252 vq~sEaekn  260 (549)
T KOG0147|consen  252 VQLSEAEKN  260 (549)
T ss_pred             ecccHHHHH
Confidence            988654443

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.74  E-value=3.8e-05  Score=62.81  Aligned_cols=76  Identities=36%  Similarity=0.595  Sum_probs=66.3

Q ss_pred             CCeEE-EcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           64 NTTIF-VGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        64 ~~~lf-V~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ..++| |++|+..+++++|+.+|..+|.|..+++...      ++|++|+|.+...+..++.. ....+.++.+.+....
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDE  262 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCC
Confidence            44555 9999999999999999999999999998763      69999999999999999886 7888999999999888


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      +...
T Consensus       263 ~~~~  266 (285)
T KOG4210|consen  263 PRPK  266 (285)
T ss_pred             CCcc
Confidence            6543

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.66  E-value=0.00019  Score=59.23  Aligned_cols=68  Identities=24%  Similarity=0.302  Sum_probs=55.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCC--ceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYG--EIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G--~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ..+|||||-|.+|+++|.+.+...|  .+.++++..      +||||+|...+..+.++.++.|...+|+|..-.|
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            4789999999999999988887665  444444433      5899999999999999999999999998875444

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.66  E-value=0.0002  Score=60.18  Aligned_cols=77  Identities=23%  Similarity=0.428  Sum_probs=65.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEE-EE-eCCCcEEEEEeCCHHHHHHHHHHhCCceeCCe-EeEEEeccC
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASV-KI-PVGKGCGFVQFANRENAEEALHKLNGTVIGKQ-SVRLSWGRN  137 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v-~i-~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~-~l~v~~a~~  137 (198)
                      -++..+|...|+|.+++|++|+.+|.+-|...+. +. .+++.++.+.+.+.|+|..|+-.++.+.++.. .|+|.|++.
T Consensus       411 ~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  411 FPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             CCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            3556799999999999999999999988765444 33 44788999999999999999999999999755 899999875

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

Probab=97.47  E-value=0.00041  Score=60.40  Aligned_cols=58  Identities=31%  Similarity=0.570  Sum_probs=49.7

Q ss_pred             HHHHHhccCCceEEEEEeCC---------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           80 DLRQPFSQYGEIASVKIPVG---------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        80 ~l~~~F~~~G~i~~v~i~~~---------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      +++.-+++||.|..|++.++         -|..||+|.+.+++++|.+.|+|..+.++.|...+-..
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            34445678999999999875         38899999999999999999999999999998887643

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.47  E-value=0.00046  Score=59.49  Aligned_cols=58  Identities=28%  Similarity=0.550  Sum_probs=47.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC---------CCc---EEEEEeCCHHHHHHHHHH
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV---------GKG---CGFVQFANRENAEEALHK  119 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~---------~kg---~afV~f~~~~~a~~a~~~  119 (198)
                      ..-.++||||+||+.++|+.|...|..||.+. |++..         .+|   |+|+.|+++.++...+..
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~a  325 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSA  325 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHH
Confidence            34468999999999999999999999999853 44442         256   999999999888877654

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.41  E-value=7.8e-05  Score=58.92  Aligned_cols=67  Identities=28%  Similarity=0.493  Sum_probs=58.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----------------C--cEEEEEeCCHHHHHHHHHHhCCce
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----------------K--GCGFVQFANRENAEEALHKLNGTV  124 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----------------k--g~afV~f~~~~~a~~a~~~l~~~~  124 (198)
                      ..-.||+++||+.++...|+++|+.||+|-+|.+-+.                .  .-+.|+|.+...|..+.+.||+..
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            4568999999999999999999999999999988651                1  226799999999999999999999


Q ss_pred             eCCeE
Q 029166          125 IGKQS  129 (198)
Q Consensus       125 ~~g~~  129 (198)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            98874

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.30  E-value=0.00099  Score=55.68  Aligned_cols=76  Identities=21%  Similarity=0.291  Sum_probs=61.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCC-ceEE--EEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYG-EIAS--VKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G-~i~~--v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ......|.+++||++.+.++|.++|..|. .|..  |++..+     .|-|||+|.+.|.|..|..+-+.+....+.|+|
T Consensus       277 ~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEv  356 (508)
T KOG1365|consen  277 TRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEV  356 (508)
T ss_pred             CCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEE
Confidence            33456789999999999999999999985 3433  555442     589999999999999999888877777888888


Q ss_pred             Eecc
Q 029166          133 SWGR  136 (198)
Q Consensus       133 ~~a~  136 (198)
                      -.+.
T Consensus       357 fp~S  360 (508)
T KOG1365|consen  357 FPCS  360 (508)
T ss_pred             eecc
Confidence            7654

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

Probab=97.30  E-value=0.0013  Score=57.55  Aligned_cols=73  Identities=25%  Similarity=0.418  Sum_probs=58.8

Q ss_pred             CCCCeEEEcCCCCCCC------HHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeC-CeE
Q 029166           62 SSNTTIFVGGLDPNVT------DEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIG-KQS  129 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~------e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~-g~~  129 (198)
                      .-...|+|.|+|.--.      ...|..+|+++|+|....++.+     +||.|++|.+..+|+.|++.|||+.|+ .++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            4457889999986432      2345678999999999888753     799999999999999999999999987 556


Q ss_pred             eEEEe
Q 029166          130 VRLSW  134 (198)
Q Consensus       130 l~v~~  134 (198)
                      +.|..
T Consensus       136 f~v~~  140 (698)
T KOG2314|consen  136 FFVRL  140 (698)
T ss_pred             EEeeh
Confidence            66664

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.26  E-value=0.00029  Score=61.69  Aligned_cols=81  Identities=12%  Similarity=0.174  Sum_probs=67.8

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhcc-CCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCcee---CCeEeEE
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQ-YGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI---GKQSVRL  132 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~-~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~---~g~~l~v  132 (198)
                      .+.....+..|+|.||-.-.|.-.|+.++.+ .|.|.+.-|-+-|..|||.|.+.++|.+.+..||+..|   +.+.|.+
T Consensus       437 SPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~a  516 (718)
T KOG2416|consen  437 SPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIA  516 (718)
T ss_pred             CCCCCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEe
Confidence            3445666789999999999999999999985 66777764434478999999999999999999999987   6889999


Q ss_pred             EeccC
Q 029166          133 SWGRN  137 (198)
Q Consensus       133 ~~a~~  137 (198)
                      .|+..
T Consensus       517 df~~~  521 (718)
T KOG2416|consen  517 DFVRA  521 (718)
T ss_pred             eecch
Confidence            99864

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.24  E-value=0.00069  Score=61.93  Aligned_cols=81  Identities=22%  Similarity=0.475  Sum_probs=72.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeC--CeEeEEEeccC
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG--KQSVRLSWGRN  137 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~--g~~l~v~~a~~  137 (198)
                      .....+.+||++|..++....|...|..||.|..|.+-....|++|.|++.+.++.|++.|-+..|+  .+.|.|.+|.+
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~  530 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASP  530 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccC
Confidence            5556789999999999999999999999999999999877789999999999999999999999997  56799999986


Q ss_pred             CCC
Q 029166          138 PAN  140 (198)
Q Consensus       138 ~~~  140 (198)
                      ...
T Consensus       531 ~~~  533 (975)
T KOG0112|consen  531 PGA  533 (975)
T ss_pred             CCC
Confidence            543

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

Probab=97.23  E-value=0.0015  Score=53.92  Aligned_cols=80  Identities=18%  Similarity=0.317  Sum_probs=63.2

Q ss_pred             CCCCCCCCeEEEcCCCC----CCC-------HHHHHHHhccCCceEEEEEe--CCCcEEEEEeCCHHHHHHHHHHhCCce
Q 029166           58 SEGDSSNTTIFVGGLDP----NVT-------DEDLRQPFSQYGEIASVKIP--VGKGCGFVQFANRENAEEALHKLNGTV  124 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~----~~~-------e~~l~~~F~~~G~i~~v~i~--~~kg~afV~f~~~~~a~~a~~~l~~~~  124 (198)
                      .......++|.+.|+=.    ..+       +++|.+-..+||.|.+|.|.  ...|.+-|.|.+.+.|..||+.|+|..
T Consensus       259 ~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  259 PSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             cccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCee
Confidence            34455678888888732    223       24555667889999999887  457999999999999999999999999


Q ss_pred             eCCeEeEEEeccC
Q 029166          125 IGKQSVRLSWGRN  137 (198)
Q Consensus       125 ~~g~~l~v~~a~~  137 (198)
                      ++|+.|..++-..
T Consensus       339 fdgRql~A~i~DG  351 (382)
T KOG1548|consen  339 FDGRQLTASIWDG  351 (382)
T ss_pred             ecceEEEEEEeCC
Confidence            9999998876543

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.16  E-value=0.00029  Score=59.49  Aligned_cols=77  Identities=22%  Similarity=0.378  Sum_probs=61.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCc-eeCCeEeEEEeccCCCCC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT-VIGKQSVRLSWGRNPANK  141 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~-~~~g~~l~v~~a~~~~~~  141 (198)
                      .++|++||.+..+.++|+.+|...-.-..-.++...+|+||.+.+...|.+|++.+++. ++.|+++.|+..-++..+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqr   79 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQR   79 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHH
Confidence            46999999999999999999975411111223334699999999999999999999886 588999999988765443

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

Probab=97.15  E-value=0.0024  Score=46.76  Aligned_cols=55  Identities=27%  Similarity=0.473  Sum_probs=45.6

Q ss_pred             HHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           80 DLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        80 ~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      +|.+.|..||++.-|++.-  +.-.|+|.+-++|-+|+. +++..+.|+.|+|++..+
T Consensus        52 ~ll~~~~~~GevvLvRfv~--~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVG--DTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEET--TCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE---
T ss_pred             HHHHHHHhCCceEEEEEeC--CeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCc
Confidence            6677888999998888774  578999999999999998 899999999999998654

; PDB: 1UFW_A 2DNR_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.12  E-value=0.0032  Score=39.36  Aligned_cols=56  Identities=23%  Similarity=0.361  Sum_probs=45.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccC---CceEEEEEeCCCcEEEEEeCCHHHHHHHHHHh
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQY---GEIASVKIPVGKGCGFVQFANRENAEEALHKL  120 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~---G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l  120 (198)
                      ...+|+|.|+. +++.++|+.+|..|   ....+|+++.+ .-|-|.|.+.+.|.+||..|
T Consensus         4 rpeavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdD-tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    4 RPEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDD-TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eeceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecC-CcEEEEECCHHHHHHHHHcC
Confidence            34679999984 57788999999988   24567888877 46788899999999999764

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.94  E-value=0.0026  Score=56.89  Aligned_cols=69  Identities=28%  Similarity=0.348  Sum_probs=58.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCce-EEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEI-ASVKIPV-----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i-~~v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .|-+.|+|++++-+||.++|..|-.+ -+|.+-+     ..|-|.|.|++.++|.+|...|++..|..+.|.+.+
T Consensus       869 V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            67889999999999999999999544 2333332     248999999999999999999999999999988764

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.84  E-value=0.0056  Score=53.02  Aligned_cols=62  Identities=31%  Similarity=0.477  Sum_probs=53.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhc-cCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHH
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFS-QYGEIASVKIPVG------KGCGFVQFANRENAEEALHK  119 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~-~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~  119 (198)
                      ...-.+.+|||||+||.-++.++|-.+|+ -||.|+.+-|-.|      +|-|=|+|.+-.+-.+||+.
T Consensus       364 sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  364 NQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            33445678999999999999999999998 6999999887664      69999999999999999873

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

Probab=96.80  E-value=0.00062  Score=53.95  Aligned_cols=56  Identities=27%  Similarity=0.440  Sum_probs=46.7

Q ss_pred             HHHHHhc-cCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           80 DLRQPFS-QYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        80 ~l~~~F~-~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      +|...|+ +||+|+++.|-.+     +|=++|.|...++|++|++.||+-.+.|++|..++.
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            3344444 8999999877553     578999999999999999999999999999988874

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.62  E-value=0.0063  Score=49.30  Aligned_cols=59  Identities=25%  Similarity=0.372  Sum_probs=48.9

Q ss_pred             HHHHHHHhccCCceEEEEEeCC------C-cEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           78 DEDLRQPFSQYGEIASVKIPVG------K-GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        78 e~~l~~~F~~~G~i~~v~i~~~------k-g~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      |+++++-.++||.|..|.|...      . ---||+|+..++|.+|+-.|||..++|+.+...|-.
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            3567778889999998876542      2 457999999999999999999999999998877753

>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=96.56  E-value=0.0091  Score=45.78  Aligned_cols=62  Identities=23%  Similarity=0.252  Sum_probs=49.3

Q ss_pred             CHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhC--CceeCCeEeEEEeccCC
Q 029166           77 TDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN--GTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        77 ~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~--~~~~~g~~l~v~~a~~~  138 (198)
                      ..+.|+++|..++.+..+...++-+-..|.|.+.+.|.+|...|+  +..+.|..|+|.++...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            457899999999999999999888899999999999999999999  89999999999999543

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.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.56  E-value=0.023  Score=37.58  Aligned_cols=56  Identities=23%  Similarity=0.379  Sum_probs=42.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN  121 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~  121 (198)
                      ..+.++|. +|.++-..||.++|+.||.|. |.++.+ .-|||...+++.|..++..+.
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-TEEEEEECCCHHHHHHHHHHT
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-CcEEEEeecHHHHHHHHHHhc
Confidence            35566666 999999999999999999874 555544 689999999999999988775

; 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.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=96.55  E-value=0.0033  Score=52.75  Aligned_cols=70  Identities=20%  Similarity=0.353  Sum_probs=57.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC---------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~---------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ..|-|.||.++++.++++.+|.-.|+|.++.|..+         ...|||-|.|...+..|-. |..+.+-++.|.|-..
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            37899999999999999999999999999998762         4789999999999888866 6666655555555443

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=96.23  E-value=0.0036  Score=53.67  Aligned_cols=79  Identities=23%  Similarity=0.381  Sum_probs=64.0

Q ss_pred             CCCCCCCCeEEEcCCCCCC-CHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           58 SEGDSSNTTIFVGGLDPNV-TDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~-~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      .....+.+.|-+.-.+... +.++|..+|.+||+|..|.+-.+---|.|+|.+..+|-.|.. .++..|+++.|+|.|-.
T Consensus       366 g~~~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whn  444 (526)
T KOG2135|consen  366 GHAVVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHN  444 (526)
T ss_pred             cchhcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCchhhheeeeeccccccchhc-cccceecCceeEEEEec
Confidence            3444555666666666664 568999999999999999997766789999999999966655 68999999999999987


Q ss_pred             C
Q 029166          137 N  137 (198)
Q Consensus       137 ~  137 (198)
                      +
T Consensus       445 p  445 (526)
T KOG2135|consen  445 P  445 (526)
T ss_pred             C
Confidence            6

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.19  E-value=0.0014  Score=60.04  Aligned_cols=80  Identities=25%  Similarity=0.505  Sum_probs=66.9

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      ..++...+.+||++||...+++.+|+..|..+|.|.+|.|-..     ..|+||.|.+.+.+-.|+..+.+..|..-.++
T Consensus       365 ~~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r  444 (975)
T KOG0112|consen  365 KLDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHR  444 (975)
T ss_pred             cccchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccc
Confidence            3455566789999999999999999999999999999988653     37999999999999999988888887655666


Q ss_pred             EEecc
Q 029166          132 LSWGR  136 (198)
Q Consensus       132 v~~a~  136 (198)
                      +.+..
T Consensus       445 ~glG~  449 (975)
T KOG0112|consen  445 IGLGQ  449 (975)
T ss_pred             ccccc
Confidence            66653

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=96.11  E-value=0.046  Score=44.60  Aligned_cols=74  Identities=23%  Similarity=0.342  Sum_probs=57.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeE-eEEEeccCCC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQS-VRLSWGRNPA  139 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~-l~v~~a~~~~  139 (198)
                      +.=|-|-++++.-. ..|..+|++||+|++......-.|-.|.|.++-+|++||. .++.+|++.. |-|+....+.
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtDks  271 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTDKS  271 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCCHH
Confidence            44455667777633 5677899999999888777666899999999999999998 4999998764 4566655443

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.03  E-value=0.0066  Score=54.45  Aligned_cols=74  Identities=12%  Similarity=0.101  Sum_probs=61.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEE-EEEeC---C--CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS-VKIPV---G--KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~-v~i~~---~--kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .....|||..||..+++.++.++|..--.|++ |.|.+   +  ++.|||+|..++++.+|+..-+.+.++.+.|+|.-.
T Consensus       432 ~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  432 GAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             CccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            34578999999999999999999998766666 66644   2  589999999988888888777788888999988753

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.01  E-value=0.03  Score=49.18  Aligned_cols=71  Identities=10%  Similarity=0.182  Sum_probs=55.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhcc--CCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhC--CceeCCeEeEEE
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQ--YGEIASVKIPVGKGCGFVQFANRENAEEALHKLN--GTVIGKQSVRLS  133 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~--~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~--~~~~~g~~l~v~  133 (198)
                      ...+.|.++.||..+.+++++.+|..  +-++.+|+...+.+ =||+|++..+|+.|.+.|.  -.+|.|+.|..+
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-WyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-WYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-eEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            34567788999999999999999964  77888888766543 3999999999999998773  346778766443

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=95.74  E-value=0.0082  Score=53.45  Aligned_cols=76  Identities=22%  Similarity=0.221  Sum_probs=65.3

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      +......+..++||+|+...+..+-++.+...+|-|..++...   |+|.+|.+......|+..++...+++..|.+..
T Consensus        32 p~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   32 PVFQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             ccccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            4455566678999999999999999999999999998876653   999999999999999999998899888776655

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.68  E-value=0.0037  Score=51.42  Aligned_cols=74  Identities=20%  Similarity=0.431  Sum_probs=58.2

Q ss_pred             CCeEEEcCCCCCCC-HHHHH--HHhccCCceEEEEEeCCC---------cEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           64 NTTIFVGGLDPNVT-DEDLR--QPFSQYGEIASVKIPVGK---------GCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        64 ~~~lfV~~l~~~~~-e~~l~--~~F~~~G~i~~v~i~~~k---------g~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      ..-+||-+|+.... |..|+  +.|.+||.|..|.+.++.         .-++|+|...++|..||...++..++++.|+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            45678889988754 44443  579999999999886632         2379999999999999999999999998877


Q ss_pred             EEeccC
Q 029166          132 LSWGRN  137 (198)
Q Consensus       132 v~~a~~  137 (198)
                      ..+...
T Consensus       157 a~~gtt  162 (327)
T KOG2068|consen  157 ASLGTT  162 (327)
T ss_pred             HhhCCC
Confidence            776544

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.66  E-value=0.079  Score=38.72  Aligned_cols=78  Identities=27%  Similarity=0.397  Sum_probs=58.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCC-HHHHH---HHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           58 SEGDSSNTTIFVGGLDPNVT-DEDLR---QPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~-e~~l~---~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ...+.+-.+|.|+=|..++. .+||+   ..++.||+|.+|.+. .+.-|.|.|.|..+|=+|+..++. ..-|..+.+.
T Consensus        80 ~~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCs  157 (166)
T PF15023_consen   80 NTKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCS  157 (166)
T ss_pred             cCCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEee
Confidence            34466678898987766643 34444   456789999998775 467899999999999999988765 5667788888


Q ss_pred             eccC
Q 029166          134 WGRN  137 (198)
Q Consensus       134 ~a~~  137 (198)
                      |-..
T Consensus       158 Wqqr  161 (166)
T PF15023_consen  158 WQQR  161 (166)
T ss_pred             cccc
Confidence            8654

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=95.65  E-value=0.0055  Score=55.94  Aligned_cols=75  Identities=15%  Similarity=0.213  Sum_probs=65.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ...|||.|+|+..|.++|+.++.++|.++++.++.     .+|.++|.|.++.++.+++...+...+..+.+.|..+.+.
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~  815 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPE  815 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCc
Confidence            46899999999999999999999999999987765     3699999999999999999888888787777777776553

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=95.57  E-value=0.032  Score=42.48  Aligned_cols=76  Identities=17%  Similarity=0.271  Sum_probs=50.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhcc-CCce---EEEE--EeC------CCcEEEEEeCCHHHHHHHHHHhCCceeC---
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQ-YGEI---ASVK--IPV------GKGCGFVQFANRENAEEALHKLNGTVIG---  126 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~-~G~i---~~v~--i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~---  126 (198)
                      ....+|.|++||+++||+++.+.++. ++..   ..+.  ...      .-.-|+|.|.+.+++..-...++|+.+.   
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34569999999999999999987776 5554   3333  111      1267999999999999999999998763   


Q ss_pred             C--eEeEEEeccC
Q 029166          127 K--QSVRLSWGRN  137 (198)
Q Consensus       127 g--~~l~v~~a~~  137 (198)
                      |  ..-.|++|--
T Consensus        85 g~~~~~~VE~Apy   97 (176)
T PF03467_consen   85 GNEYPAVVEFAPY   97 (176)
T ss_dssp             S-EEEEEEEE-SS
T ss_pred             CCCcceeEEEcch
Confidence            2  2456777754

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

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

Probab=95.38  E-value=0.025  Score=36.69  Aligned_cols=67  Identities=27%  Similarity=0.442  Sum_probs=40.0

Q ss_pred             eEEEc-CCCCCCCHHHHHHHhccCC-----ceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           66 TIFVG-GLDPNVTDEDLRQPFSQYG-----EIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        66 ~lfV~-~l~~~~~e~~l~~~F~~~G-----~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ++||. +--..++..+|..++..-+     .|-.|+|.  ..|+||+-.. +.|+.+++.|++..+.|+.|+|+.|
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~--~~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIF--DNFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE---SS-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEe--eeEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            45553 2234578888988887653     45666665  4699999975 5889999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=94.92  E-value=0.22  Score=42.05  Aligned_cols=65  Identities=29%  Similarity=0.363  Sum_probs=46.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccC----CceEEEE-EeC----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQY----GEIASVK-IPV----GKGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~----G~i~~v~-i~~----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      -.|..++||+++++.++.++|..-    |..+.|- +.+    ..|-|||.|..+++|+.||.+ |...|+.+.|
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYI  235 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYI  235 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHH
Confidence            356778999999999999999631    2333333 332    248999999999999999975 4444444443

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=94.78  E-value=0.018  Score=52.78  Aligned_cols=73  Identities=25%  Similarity=0.283  Sum_probs=62.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeC--CeEeEEEeccCC
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG--KQSVRLSWGRNP  138 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~--g~~l~v~~a~~~  138 (198)
                      +.++.|..-..+...|..+|++||.|.+....++-..|.|+|.+.+.|..|++.|+|.++.  |-..+|.+|+.-
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            3444555667788899999999999999999998899999999999999999999999864  778999999864

>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=94.73  E-value=0.44  Score=33.39  Aligned_cols=62  Identities=16%  Similarity=0.173  Sum_probs=46.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccC-CceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQY-GEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIG  126 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~-G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~  126 (198)
                      ..+.+...|..++.++|..+.+.+ ..|..++|+++    +--+.+.|.+.+.|..-...+||..++
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            334444555556667776666665 46788899885    456999999999999999999999876

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=94.26  E-value=0.051  Score=43.32  Aligned_cols=57  Identities=26%  Similarity=0.446  Sum_probs=49.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLN  121 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~  121 (198)
                      ..|+|.||+.-++.+.|+..|+.||.|....++.+     .+-++|+|...-.|.+|+....
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhc
Confidence            67999999999999999999999999987665543     3778999999999999998763

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=94.15  E-value=0.002  Score=58.70  Aligned_cols=63  Identities=33%  Similarity=0.515  Sum_probs=51.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEe--C----CCcEEEEEeCCHHHHHHHHHHhCCceeC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP--V----GKGCGFVQFANRENAEEALHKLNGTVIG  126 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~--~----~kg~afV~f~~~~~a~~a~~~l~~~~~~  126 (198)
                      ..++||.||+..+.+.+|...|..+|.+..+++.  .    -||.|+++|...+++.+|+.......++
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            4688999999999999999999999877766553  1    2699999999999999999865554443

>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=91.60  E-value=1.6  Score=27.59  Aligned_cols=55  Identities=18%  Similarity=0.322  Sum_probs=43.0

Q ss_pred             CCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           75 NVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        75 ~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      .++-++|+..+.+|+- .+|  ..++.-=||.|.+..+|+++....++..+...+|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~I--~~d~tGfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DRI--RDDRTGFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ceE--EecCCEEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4678899999999963 333  335545589999999999999999998887777654

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

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.84  E-value=1.3  Score=39.50  Aligned_cols=75  Identities=24%  Similarity=0.290  Sum_probs=61.2

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhccC----CceEEEEEeCC------------------------------------
Q 029166           61 DSSNTTIFVGGLDPN-VTDEDLRQPFSQY----GEIASVKIPVG------------------------------------   99 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~-~~e~~l~~~F~~~----G~i~~v~i~~~------------------------------------   99 (198)
                      ...+++|-|-|+.|. +...+|..+|+.|    |.|.+|.|-.+                                    
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            456789999999997 8889999999887    69999998431                                    


Q ss_pred             ----------------C-cEEEEEeCCHHHHHHHHHHhCCceeCCe--EeEEEec
Q 029166          100 ----------------K-GCGFVQFANRENAEEALHKLNGTVIGKQ--SVRLSWG  135 (198)
Q Consensus       100 ----------------k-g~afV~f~~~~~a~~a~~~l~~~~~~g~--~l~v~~a  135 (198)
                                      + -||.|+|.+.+.|....+.-+|.++...  .|.++|.
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFI  305 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFI  305 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeec
Confidence                            1 5799999999999999999999999744  5555553

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=89.06  E-value=0.36  Score=36.68  Aligned_cols=75  Identities=21%  Similarity=0.229  Sum_probs=58.7

Q ss_pred             CCeEEEcCCCCCCC-----HHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCe-EeEEEeccC
Q 029166           64 NTTIFVGGLDPNVT-----DEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQ-SVRLSWGRN  137 (198)
Q Consensus        64 ~~~lfV~~l~~~~~-----e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~-~l~v~~a~~  137 (198)
                      .+++.+.++...+-     ....+.+|.+|-+....+++++.++.-|.|.+++.|..|...++...+.|+ .++.-++.+
T Consensus        10 p~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lrsfrrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~yfaQ~   89 (193)
T KOG4019|consen   10 PTAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLRSFRRVRINFSNPEAAADARIKLHSTSFNGKNELKLYFAQP   89 (193)
T ss_pred             cceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHHhhceeEEeccChhHHHHHHHHhhhcccCCCceEEEEEccC
Confidence            34567777776532     234566777777777777888888899999999999999999999999988 888888875


Q ss_pred             C
Q 029166          138 P  138 (198)
Q Consensus       138 ~  138 (198)
                      .
T Consensus        90 ~   90 (193)
T KOG4019|consen   90 G   90 (193)
T ss_pred             C
Confidence            4

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

Probab=88.18  E-value=1.1  Score=39.65  Aligned_cols=41  Identities=15%  Similarity=0.302  Sum_probs=33.7

Q ss_pred             CcEEEEEeCCHHHHHHHHHHhCCceeC----CeEeEEEeccCCCC
Q 029166          100 KGCGFVQFANRENAEEALHKLNGTVIG----KQSVRLSWGRNPAN  140 (198)
Q Consensus       100 kg~afV~f~~~~~a~~a~~~l~~~~~~----g~~l~v~~a~~~~~  140 (198)
                      .|||||.|.+.+++..+.+..||+.+.    .+...+.||+-+..
T Consensus       431 vGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQGk  475 (549)
T KOG4660|consen  431 VGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQGK  475 (549)
T ss_pred             cceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhhch
Confidence            499999999999999999999998763    55667888875543

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=88.01  E-value=1.6  Score=37.79  Aligned_cols=63  Identities=16%  Similarity=0.325  Sum_probs=55.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccC-CceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQY-GEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIG  126 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~-G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~  126 (198)
                      .+.|+|-.+|-.++-.||-.|...+ -.|.+++|+++    +-...|.|.+.++|..-.+.+||..++
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            7889999999999999999988875 57889999885    455899999999999999999999875

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=87.48  E-value=0.45  Score=39.08  Aligned_cols=75  Identities=23%  Similarity=0.249  Sum_probs=58.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ...+++|++++.+.+.+.++..++...|.+....+..      +++++.+.|...+.+..++.......+.+..+...+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            3578999999999999998889999998766655533      4799999999999999999854444566666555544


Q ss_pred             c
Q 029166          136 R  136 (198)
Q Consensus       136 ~  136 (198)
                      .
T Consensus       166 ~  166 (285)
T KOG4210|consen  166 T  166 (285)
T ss_pred             c
Confidence            4

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=86.22  E-value=3.6  Score=33.67  Aligned_cols=48  Identities=23%  Similarity=0.304  Sum_probs=39.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCce-EEEEEeCCCcEEEEEeCCHH
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEI-ASVKIPVGKGCGFVQFANRE  111 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i-~~v~i~~~kg~afV~f~~~~  111 (198)
                      .+-|+++||+.++.-.+|+..+.+-+.+ .++.+.-.++-||+.|.+..
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswkg~~~k~flh~~~~~  378 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWKGHFGKCFLHFGNRK  378 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCceeEeeecCCcceeEecCCcc
Confidence            3459999999999999999999887754 56666666789999998753

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=84.88  E-value=9.6  Score=34.96  Aligned_cols=69  Identities=14%  Similarity=0.213  Sum_probs=50.6

Q ss_pred             CeEEEc-CCCCCCCHHHHHHHhccCCceE-----EEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           65 TTIFVG-GLDPNVTDEDLRQPFSQYGEIA-----SVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        65 ~~lfV~-~l~~~~~e~~l~~~F~~~G~i~-----~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      .++||. +-...++..+|..++..-+.|.     .|+|.  ..|.||+.. .+.|...++.|+...+.|+.|.|+.++
T Consensus       487 ~~~~~~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~--~~~s~v~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  561 (629)
T PRK11634        487 QLYRIEVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLF--ASHSTIELP-KGMPGEVLQHFTRTRILNKPMNMQLLG  561 (629)
T ss_pred             EEEEEecccccCCCHHHHHHHHHhhcCCChhhCCcEEEe--CCceEEEcC-hhhHHHHHHHhccccccCCceEEEECC
Confidence            446553 3344578888888887655443     34443  469999997 467888999999999999999999875

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=80.98  E-value=4.5  Score=33.17  Aligned_cols=79  Identities=16%  Similarity=0.315  Sum_probs=60.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCC-------------cEEEEEeCCHHHHHHH----HHHh
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-------------GCGFVQFANRENAEEA----LHKL  120 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~k-------------g~afV~f~~~~~a~~a----~~~l  120 (198)
                      .++.-.++.|.+.|+..+++--.+...|.+||.|++|.++.+.             ....+.|-+++.+..-    ++.|
T Consensus         9 GdD~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrL   88 (309)
T PF10567_consen    9 GDDEYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRL   88 (309)
T ss_pred             CCccceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHH
Confidence            4455567889999999999988899999999999999998754             6788999998876553    3334


Q ss_pred             CC--ceeCCeEeEEEecc
Q 029166          121 NG--TVIGKQSVRLSWGR  136 (198)
Q Consensus       121 ~~--~~~~g~~l~v~~a~  136 (198)
                      ..  ..+....|.+.|..
T Consensus        89 sEfK~~L~S~~L~lsFV~  106 (309)
T PF10567_consen   89 SEFKTKLKSESLTLSFVS  106 (309)
T ss_pred             HHHHHhcCCcceeEEEEE
Confidence            32  24667778877765

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=80.08  E-value=0.15  Score=43.63  Aligned_cols=77  Identities=19%  Similarity=0.361  Sum_probs=64.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-C--CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-G--KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-~--kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      ....+++-|.|+|+...++.|..++..||.+..+.... +  ....-|+|...+.++.||.+|++..+....++|.+--.
T Consensus        77 kqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPd  156 (584)
T KOG2193|consen   77 KQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPD  156 (584)
T ss_pred             HHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCch
Confidence            34567799999999999999999999999998886543 2  24455788999999999999999999999988887543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	198
2ytc_A	85	Solution Structure Of Rna Binding Domain In Pre-Mrn		7e-12
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		2e-10
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		1e-09
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		3e-09
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		6e-08
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		3e-07
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		4e-07
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		4e-07
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		4e-07
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		6e-07
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		6e-07
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		7e-07
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		8e-07
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		8e-07
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		9e-07
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		1e-06
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		1e-06
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		1e-06
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		2e-06
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-06
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-06
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		2e-06
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		3e-06
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		5e-06
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		5e-06
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		5e-06
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		5e-06
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		6e-06
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		6e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		6e-06
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		7e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		8e-06
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-05
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		1e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		2e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		2e-05
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		2e-05
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		2e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-05
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		2e-05
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		2e-05
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		2e-05
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		3e-05
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		3e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		3e-05
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		5e-05
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		5e-05
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		5e-05
1wf1_A	110	Solution Structure Of Rrm Domain In Rna-Binding Pro		5e-05
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		5e-05
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		5e-05
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		6e-05
2dnh_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		8e-05
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		8e-05
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		8e-05
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		9e-05
1x5p_A	97	Solution Structure Of Rrm Domain In Parp14 Length =		1e-04
2jx2_A	121	Solution Structure Of Nelf E Rrm Length = 121		1e-04
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-04
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		1e-04
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		2e-04
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		2e-04
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-04
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-04
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-04
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		2e-04
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		2e-04
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		2e-04
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		2e-04
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-04
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		3e-04
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		3e-04
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		3e-04
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		3e-04
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		3e-04
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		3e-04
2cqi_A	103	Solution Structure Of The Rna Binding Domain Of Nuc		3e-04
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		3e-04
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		3e-04
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		4e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		4e-04
2cpx_A	115	Solution Structure Of Rna Binding Domain In Hypothe		4e-04
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		4e-04
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		4e-04
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		4e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		4e-04
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		5e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		5e-04
3u1l_A	240	Structure Of The Mrna Splicing Complex Component Cw		5e-04
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		5e-04
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		5e-04
3tp2_A	229	Crystal Structure Of The Splicing Factor Cwc2 From		5e-04
1sxl_A	97	Resonance Assignments And Solution Structure Of The		6e-04
2div_A	99	Solution Structure Of The Rrm Domain Of Trna Seleno		6e-04
1why_A	97	Solution Structure Of The Rna Recognition Motif Fro		6e-04
2ghp_A	292	Crystal Structure Of The N-Terminal 3 Rna Binding D		7e-04
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		7e-04
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		7e-04
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		8e-04
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		8e-04

>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna- Splicing Factor Rbm22 Length = 85

Iteration: 1
 Score = 67.0 bits (162), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 53/90 (58%), Gaps = 7/90 (7%)
Query: 48  SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQF 107
           S+G+ G+      D + TT++VGGL   +T+ DLR  F Q+GEI ++ +   + C F+QF
Sbjct: 2   SSGSSGE------DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQF 55
Query: 108 ANRENAEEALHK-LNGTVIGKQSVRLSWGR 136
           A R+ AE A  K  N  ++  + + + WGR
Sbjct: 56  ATRQAAEVAAEKSFNKLIVNGRRLNVKWGR 85

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 45/73 (61%)
Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
           N T++ GG+   +TD+ +RQ FS +G+I  +++   KG  FV+F+  E+A  A+  +NGT
Sbjct: 25  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 84
Query: 124 VIGKQSVRLSWGR 136
            I    V+  WG+
Sbjct: 85  TIEGHVVKCYWGK 97

>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 = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/96 (32%), Positives = 53/96 (55%), Gaps = 7/96 (7%)
Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCG 103
           G+ G   Q +  S++  +FVG L P +T ED++  F+ +G I+  ++         KG G
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWG-RNP 138
           FV F N+ +AE A+ ++ G  +G + +R +W  R P
Sbjct: 61  FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP 96

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 31/96 (32%), Positives = 53/96 (55%), Gaps = 7/96 (7%)
Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCG 103
           G+ G   Q +  S++  +FVG L P +T ED++  F+ +G+I+  ++         KG G
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWG-RNP 138
           FV F N+ +AE A+  + G  +G + +R +W  R P
Sbjct: 61  FVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKP 96

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 53.9 bits (128), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 46/73 (63%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           +FVG L  ++T+ED ++ F +YGE + V I   +G GF++  +R  AE A  +L+GT++ 
Sbjct: 25  LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 84
Query: 127 KQSVRLSWGRNPA 139
            + +R+ +  + A
Sbjct: 85  SRPLRIRFATHGA 97

>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 = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 122
           IF+  LD ++ ++ L   FS +G I S K+       KG GFV F  +E AE A+ K+NG
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 160
Query: 123 TVIGKQSVRLSWGRNPANKQFRADYG 148
            ++  + V +  GR  + K+  A+ G
Sbjct: 161 MLLNDRKVFV--GRFKSRKEREAELG 184

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRE 111
           S     +  ++V GL   +T ++L Q FSQYG I + +I       V +G GF++F  R 
Sbjct: 82  SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 141
Query: 112 NAEEALHKLNG 122
            AEEA+  LNG
Sbjct: 142 EAEEAIKGLNG 152

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 33/98 (33%), Positives = 51/98 (52%), Gaps = 11/98 (11%)
Query: 55  GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANR 110
           GP   G+     IF+  LD ++ ++ L   FS +G I S K+       KG GFV F  +
Sbjct: 1   GPLGSGN-----IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQ 55
Query: 111 ENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
           E AE A+ K+NG ++  + V +  GR  + K+  A+ G
Sbjct: 56  EAAERAIEKMNGMLLNDRKVFV--GRFKSRKEREAELG 91

>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 = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 122
           IF+  LD ++ ++ L   FS +G I S K+       KG GFV F  +E AE A+ K+NG
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165
Query: 123 TVIGKQSVRLSWGRNPANKQFRADYG 148
            ++  + V +  GR  + K+  A+ G
Sbjct: 166 MLLNDRKVFV--GRFKSRKEREAELG 189

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 50.4 bits (119), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 122
           ++V  LD  + DE LR+ FS +G I S K+ +     KG GFV F++ E A +A+ ++NG
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 123 TVIGKQSVRLSWGRNPANKQ 142
            ++  + + ++  +    +Q
Sbjct: 78  RIVATKPLYVALAQRKEERQ 97

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 50.4 bits (119), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 48/82 (58%), Gaps = 7/82 (8%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 120
           +FVGGL  +  ++ L Q FS+YG+I+ V +         +G GFV F N ++A++A+  +
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 121 NGTVIGKQSVRLSW-GRNPANK 141
           NG  +  + +R+   G++  N+
Sbjct: 75  NGKSVDGRQIRVDQAGKSSDNR 96

>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 = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 6/78 (7%)
Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 118
           T + V  L  N+T ++LR  FS  GE+ S K+   K      G GFV +   ++AE A++
Sbjct: 5   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 119 KLNGTVIGKQSVRLSWGR 136
            LNG  +  +++++S+ R
Sbjct: 65  TLNGLRLQSKTIKVSYAR 82

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 50.1 bits (118), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 6/78 (7%)
Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 118
           T + V  L  N+T ++LR  FS  GE+ S K+   K      G GFV +   ++AE A++
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 119 KLNGTVIGKQSVRLSWGR 136
            LNG  +  +++++S+ R
Sbjct: 63  TLNGLRLQSKTIKVSYAR 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 = 50.1 bits (118), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 6/78 (7%)
Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 118
           T + V  L  N+T ++LR  FS  GE+ S K+   K      G GFV +   ++AE A++
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 119 KLNGTVIGKQSVRLSWGR 136
            LNG  +  +++++S+ R
Sbjct: 63  TLNGLRLQSKTIKVSYAR 80

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 50.1 bits (118), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 47/83 (56%)
Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
           +  + +FVG L P++T+E++R+ F +YG+   V I   KG GF++   R  AE A  +L+
Sbjct: 20  TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 79
Query: 122 GTVIGKQSVRLSWGRNPANKQFR 144
              +  + +R+ +  + A+   R
Sbjct: 80  NMPLRGKQLRVRFACHSASLTVR 102

>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 = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALH 118
           T + V  L  N T ++LR  FS  GE+ S K+   K      G GFV +   ++AE A++
Sbjct: 20  TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 119 KLNGTVIGKQSVRLSWGR 136
            LNG  +  +++++S+ R
Sbjct: 80  TLNGLRLQSKTIKVSYAR 97

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 46/84 (54%), Gaps = 6/84 (7%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNG 122
           IF+  LD ++ ++ L   FS +G I S K+       KG GFV F  +E AE A+ K+NG
Sbjct: 14  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 123 TVIGKQSVRLSWGRNPANKQFRAD 146
            ++  + V +  GR  + K+  A+
Sbjct: 74  MLLNDRKVFV--GRFKSRKEREAE 95

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 46/79 (58%)
Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
           +  + +FVG L P++T+E++R+ F +YG+   V I   KG GF++   R  AE A  +L+
Sbjct: 13  TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 72
Query: 122 GTVIGKQSVRLSWGRNPAN 140
              +  + +R+ +  + A+
Sbjct: 73  NMPLRGKQLRVRFACHSAS 91

>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 = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 50/98 (51%), Gaps = 16/98 (16%)
Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK----GCGF--VQFANRENAEEALHK 119
           T++VG L    T+E + + FS+ G+I  + + + K     CGF  V++ +R +AE A+  
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 120 LNGTVIGKQSVRLSW----------GRNPANKQFRADY 147
           +NGT +  + +R  W          GR  +  Q R +Y
Sbjct: 101 INGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEY 138

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 49/88 (55%), Gaps = 7/88 (7%)
Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA 116
           S T + V  L  N+T ++ +  F   G+I S K+   K      G GFV +++  +A++A
Sbjct: 3   SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 117 LHKLNGTVIGKQSVRLSWGRNPANKQFR 144
           ++ LNG  +  +++++S+ R P++   R
Sbjct: 63  INTLNGLKLQTKTIKVSYAR-PSSASIR 89

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 46/84 (54%), Gaps = 8/84 (9%)
Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEAL 117
           +  ++V GL   ++ +++ Q FSQYG I + +I       V +G GF++F  R  AEEA+
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 118 HKLNGT--VIGKQSVRLSWGRNPA 139
             LNG   +   + + + +  NP+
Sbjct: 61  KGLNGQKPLGAAEPITVKFANNPS 84

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK---GCGF--VQFANRENAEEALHKL 120
           T++VG L    T+E + + FS+ G+I  + + + K    CGF  V++ +R +AE A+  +
Sbjct: 20  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 121 NGTVIGKQSVRLSW 134
           NGT +  + +R  W
Sbjct: 80  NGTRLDDRIIRTDW 93

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 7/73 (9%)
Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------GKGCGFVQFANRENAEEAL 117
           T + +G L  NVT + + + FS YG+I  + +PV        KG  +V+F N + AE+AL
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 118 HKLNGTVIGKQSV 130
             ++G  I  Q +
Sbjct: 65  KHMDGGQIDGQEI 77

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 47.8 bits (112), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 46/85 (54%), Gaps = 2/85 (2%)
Query: 57  QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEA 116
           + EG+ SNT +FV     +V + +L + F  +G +  VKI    G  FV+F   E+A +A
Sbjct: 24  RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKA 81
Query: 117 LHKLNGTVIGKQSVRLSWGRNPANK 141
           + +++G     Q + + + + PA +
Sbjct: 82  IEEVHGKSFANQPLEVVYSKLPAKR 106

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 5/75 (6%)
Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENAEEALHKL 120
            ++VG LD  +T++ L+Q F   G IA++KI + K        FV++    +A  AL  L
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 121 NGTVIGKQSVRLSWG 135
           NG  I    V+++W 
Sbjct: 62  NGKQIENNIVKINWA 76

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
           N  + V GL    T+ DLR+ FS+YG IA V I         +G  FV F N ++A+EA 
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 118 HKLNGTVIGKQSVRLS 133
            + NG  +  + +R+S
Sbjct: 75  ERANGMELDGRRIRVS 90

>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 = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 43/85 (50%), Gaps = 4/85 (4%)
Query: 53  GQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFA 108
           G    +E  S    + V  +     D DLRQ F Q+G+I  V+I       KG GFV F 
Sbjct: 18  GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFE 77
Query: 109 NRENAEEALHKLNGTVIGKQSVRLS 133
           N  +A+ A  KL+GTV+  + + ++
Sbjct: 78  NSADADRAREKLHGTVVEGRKIEVN 102

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 10/69 (14%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL--- 117
           +F+GGL  + T +DL+  FS++GE+    + +       +G GFV F   E+ ++ +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 118 -HKLNGTVI 125
            HKLNG VI
Sbjct: 62  EHKLNGKVI 70

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
           N  + V GL    T+ DLR+ FS+YG IA V I         +G  FV F N ++A+EA 
Sbjct: 12  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 118 HKLNGTVIGKQSVRLSW 134
            + NG  +  + +R+ +
Sbjct: 72  ERANGMELDGRRIRVDF 88

>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 = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 44/91 (48%), Gaps = 6/91 (6%)
Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCG 103
           G+ G          N  + V GL    T+ DLR+ FS+YG IA V I         +G  
Sbjct: 1   GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSW 134
           FV F N ++A+EA  + NG  +  + +R+ +
Sbjct: 61  FVYFENVDDAKEAKERANGMELDGRRIRVDF 91

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 47.0 bits (110), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 78  DEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS 133
           D DLRQ F Q+G+I  V+I       KG GFV F N  +A+ A  KL+GTV+  + + ++
Sbjct: 29  DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN 88

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 47.0 bits (110), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
           N  + V GL    T+ DLR+ FS+YG IA V I         +G  FV F N ++A+EA 
Sbjct: 46  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 118 HKLNGTVIGKQSVRLSW 134
            + NG  +  + +R+ +
Sbjct: 106 ERANGMELDGRRIRVDF 122

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 55  GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFAN 109
           GP   G     T+FVGG+D  + + ++R  F++YG +  VKI      V KG GFV F N
Sbjct: 1   GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 60
Query: 110 RENAEEALH 118
             + ++ + 
Sbjct: 61  DVDVQKIVE 69

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 6/70 (8%)
Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANREN 112
           +G +    ++VG L  N+T++ LR  F  +G I S+++ +       KG GF+ F++ E 
Sbjct: 21  KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80
Query: 113 AEEALHKLNG 122
           A++AL +LNG
Sbjct: 81  AKKALEQLNG 90

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 9/87 (10%)
Query: 56  PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFAN 109
           P  EG    T++ V  L    + + LR+ F +YG +  V IP        +G  FV+F +
Sbjct: 42  PDVEG---MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 98
Query: 110 RENAEEALHKLNGTVIGKQSVRLSWGR 136
           + +AE+A+  ++G V+  + +R+   R
Sbjct: 99  KRDAEDAMDAMDGAVLDGRELRVQMAR 125

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/83 (26%), Positives = 45/83 (54%), Gaps = 6/83 (7%)
Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENA 113
           G ++   ++VGGL   V D+ L   F  +G+I  ++IP+       +G  FV+F   E+A
Sbjct: 1   GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 114 EEALHKLNGTVIGKQSVRLSWGR 136
             A+  +N + +  +++R++  +
Sbjct: 61  AAAIDNMNESELFGRTIRVNLAK 83

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 49/88 (55%), Gaps = 7/88 (7%)
Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA 116
           S T + V  L  N+T ++ +  F   G+I S K+   K      G GFV +++  +A++A
Sbjct: 3   SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 117 LHKLNGTVIGKQSVRLSWGRNPANKQFR 144
           ++ LNG  +  +++++S+ R P++   R
Sbjct: 63  INTLNGLKLQTKTIKVSYAR-PSSASIR 89

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 31/90 (34%), Positives = 47/90 (52%), Gaps = 8/90 (8%)
Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAE 114
           D++ T IFVGGL  + TD  LR+ F  +G+I    +         +G GFV  A+R  AE
Sbjct: 14  DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 115 EALHKLNGTVIGKQS-VRLSW-GRNPANKQ 142
            A    N  + G+++ V L++ G  P + Q
Sbjct: 74  RACKDPNPIIDGRKANVNLAYLGAKPRSLQ 103

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALH 118
           T++ V  L    + + LR+ F +YG +  V IP        +G  FV+F ++ +AE+A+ 
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 119 KLNGTVIGKQSVRLSWGR 136
            ++G V+  + +R+   R
Sbjct: 131 AMDGAVLDGRELRVQMAR 148

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 49/94 (52%), Gaps = 13/94 (13%)
Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENA 113
           G S ++ ++VG L  N+T++ LR  F  +G+I ++ +         KG GF+ F++ E A
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 114 EEALHKLNG-------TVIGKQSVRLSWGRNPAN 140
             AL +LNG         +G  + RL  G  P++
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVTERLDGGSGPSS 94

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 6/95 (6%)
Query: 46  YASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF- 104
           Y S    G  P  +       +FV G+    T+ED+   F++YGEI ++ + + +  G+ 
Sbjct: 5   YDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 64
Query: 105 -----VQFANRENAEEALHKLNGTVIGKQSVRLSW 134
                V++   + A+ A+  LNG  +  Q + + W
Sbjct: 65  KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 46/85 (54%), Gaps = 2/85 (2%)
Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
           S G +    +FV  L   VT+E L + FSQ+G++  VK    K   F+ F  R+ A +A+
Sbjct: 5   SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAM 62
Query: 118 HKLNGTVIGKQSVRLSWGRNPANKQ 142
            ++NG  +  +++ + + + P  K+
Sbjct: 63  EEMNGKDLEGENIEIVFAKPPDQKR 87

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 6/95 (6%)
Query: 46  YASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------ 99
           Y S    G  P  +       +FV G+    T+ED+   F++YGEI ++ + +       
Sbjct: 4   YDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 63
Query: 100 KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW 134
           KG   V++   + A+ A+  LNG  +  Q + + W
Sbjct: 64  KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIAS------VKIPVGKGCGFVQFANRENAEEALHKL 120
           +FVG L+ NV DE LR  F  +    S      ++    +G GFV F ++++A+ A+  +
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 121 NGTVIGKQSVRLSWG 135
            G  +  + +R++W 
Sbjct: 64  QGQDLNGRPLRINWA 78

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENA 113
           EG     T+FVGG+D  + + ++R  F++YG +  VKI      V KG GFV F N  + 
Sbjct: 4   EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
Query: 114 EEAL 117
           ++ +
Sbjct: 64  QKIV 67

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 5/65 (7%)
Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENA 113
           EG     T+FVGG+D  + + ++R  F++YG +  VKI      V KG GFV F N  + 
Sbjct: 4   EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
Query: 114 EEALH 118
           ++ + 
Sbjct: 64  QKIVE 68

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           +FV G+    T+ED+   F++YGEI ++ + +       KG   V++   + A+ A+  L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 121 NGTVIGKQSVRLSW 134
           NG  +  Q + + W
Sbjct: 70  NGQDLMGQPISVDW 83

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           +FV G+    T+ED+   F++YGEI ++ + +       KG   V++   + A+ A+  L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 121 NGTVIGKQSVRLSW 134
           NG  +  Q + + W
Sbjct: 70  NGQDLMGQPISVDW 83

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           +FV G+    T+ED+   F++YGEI ++ + +       KG   V++   + A+ A+  L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 121 NGTVIGKQSVRLSW 134
           NG  +  Q + + W
Sbjct: 70  NGQDLMGQPISVDW 83

>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein Np_057951 Length = 110

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 62  SSNTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL 120
           S N+ +F+G L+   V   D+   FS+YG +A     V KG  FVQ++N  +A  A+   
Sbjct: 25  SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCS--VHKGYAFVQYSNERHARAAVLGE 82
Query: 121 NGTVIGKQSVRLSWGRNP 138
           NG V+  Q++ ++    P
Sbjct: 83  NGRVLAGQTLDINMAGEP 100

>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 = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           +FV G+    T+ED+   F++YGEI ++ + +       KG   V++   + A+ A+  L
Sbjct: 12  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 121 NGTVIGKQSVRLSW 134
           NG  +  Q + + W
Sbjct: 72  NGQDLMGQPISVDW 85

>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 = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 6/88 (6%)
Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAE 114
           D S  ++FVG +    T+E L+  FS+ G + S ++         KG GF ++ ++E A 
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 115 EALHKLNGTVIGKQSVRLSWGRNPANKQ 142
            A+  LNG     +++R+    +  NK+
Sbjct: 65  SAMRNLNGREFSGRALRVDNAASEKNKE 92

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/81 (25%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEE 115
           ++   ++VGGL   V D+ L   F  +G+I  ++IP+       +G  FV+F   E+A  
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 116 ALHKLNGTVIGKQSVRLSWGR 136
           A+  +N + +  +++R++  +
Sbjct: 65  AIDNMNESELFGRTIRVNLAK 85

>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5 Rna Binding Protein Length = 105

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 5/62 (8%)
Query: 67  IFVGGLDPNVTDED---LRQPFSQYGEIASVKIPVG--KGCGFVQFANRENAEEALHKLN 121
           +FVG L+   ++ED   L QPF    E   ++ P G  KGC FV+F++   A+ A+H L+
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 122 GT 123
           G+
Sbjct: 78  GS 79

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 6/79 (7%)
Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEA 116
           S   ++VGGL   V D+ L   F  +G+I  ++IP+       +G  FV+F   E+A  A
Sbjct: 1   SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 117 LHKLNGTVIGKQSVRLSWG 135
           +  +N + +  +++R++  
Sbjct: 61  IDNMNESELFGRTIRVNLA 79

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/81 (25%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEE 115
           ++   ++VGGL   V D+ L   F  +G+I  ++IP+       +G  FV+F   E+A  
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69
Query: 116 ALHKLNGTVIGKQSVRLSWGR 136
           A+  +N + +  +++R++  +
Sbjct: 70  AIDNMNESELFGRTIRVNLAK 90

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 43.1 bits (100), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEE 115
           ++   ++VGGL   V D+ L   F  +G+I  ++IP+       +G  FV+F   E+A  
Sbjct: 61  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 120
Query: 116 ALHKLNGTVIGKQSVRLSWG 135
           A+  +N + +  +++R++  
Sbjct: 121 AIDNMNESELFGRTIRVNLA 140

>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14 Length = 97

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 46/83 (55%), Gaps = 6/83 (7%)
Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI 125
           T++V G D  +T   LR  FS +G I  + +   + C FV +   E+A++A+ +LNGT +
Sbjct: 17  TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV 74
Query: 126 GKQSVRLSWGRNPANKQFRADYG 148
             +SV+L    N A KQ   D G
Sbjct: 75  --ESVQLKV--NIARKQPMLDSG 93

>pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm Length = 121

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 56  PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEE 115
           P+        T++V G D  +T   LR  FS +G I  + +   + C FV +   E+A++
Sbjct: 31  PERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQ 88
Query: 116 ALHKLNGTVIGKQSVRLSWGR 136
           A+ +LNGT +    ++++  R
Sbjct: 89  AVAELNGTQVESVQLKVNIAR 109

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 117
           +F+GGL    TDE LR  F Q+G +    +         +G GFV +A  E  + A+   
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 118 -HKLNGTVI 125
            HK++G V+
Sbjct: 76  PHKVDGRVV 84

>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 = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 117
           +F+GGL    TDE LR  F Q+G +    +         +G GFV +A  E  + A+   
Sbjct: 15  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 118 -HKLNGTVI 125
            HK++G V+
Sbjct: 75  PHKVDGRVV 83

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 117
           +F+GGL    TDE LR  F Q+G +    +         +G GFV +A  E  + A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 118 -HKLNGTVI 125
            HK++G V+
Sbjct: 69  PHKVDGRVV 77

>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 = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 117
           +F+GGL    TDE LR  F Q+G +    +         +G GFV +A  E  + A+   
Sbjct: 17  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 118 -HKLNGTVI 125
            HK++G V+
Sbjct: 77  PHKVDGRVV 85

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 117
           +F+GGL    TDE LR  F Q+G +    +         +G GFV +A  E  + A+   
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 118 -HKLNGTVI 125
            HK++G V+
Sbjct: 76  PHKVDGRVV 84

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 39/66 (59%), Gaps = 5/66 (7%)
Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEAL 117
           S+  +FVG L+   +++D+R+ F  +G I    I  G     KGC FV++++   A+ A+
Sbjct: 14  SHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAI 73
Query: 118 HKLNGT 123
           + L+G+
Sbjct: 74  NALHGS 79

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI------PVGKGCGFVQFANRENAEEAL--- 117
           +F+GGL    TDE LR  F Q+G +    +         +G GFV +A  E  + A+   
Sbjct: 14  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 118 -HKLNGTVI 125
            HK++G V+
Sbjct: 74  PHKVDGRVV 82

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANRENA 113
           S    +FVG +    +++DLR+ F QYG +  + +        P  KGC FV F  R+ A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 114 EEALHKLNGTVI 125
            EA + L+   +
Sbjct: 61  LEAQNALHNMKV 72

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANRENA 113
           S    +FVG +    +++DLR+ F QYG +  + +        P  KGC FV F  R+ A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 114 EEALHKLNGTVI 125
            EA + L+   +
Sbjct: 61  LEAQNALHNMKV 72

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/103 (25%), Positives = 53/103 (51%), Gaps = 11/103 (10%)
Query: 48  SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-------VGK 100
           S+G+ GQ P+ +   + + I V  +       ++R+ FS +GE+ +V++P         +
Sbjct: 2   SSGSSGQVPKKQ---TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHR 58
Query: 101 GCGFVQFANRENAEEALHKL-NGTVIGKQSVRLSWGRNPANKQ 142
           G GFV F  +++A++A + L + T +  + + L W  +    Q
Sbjct: 59  GFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide Repeat Containing 4 Variant Length = 102

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLN 121
           +FVG L    TDED+R+ F  +G I    +  G     KGC FV+F     A+ A++ L+
Sbjct: 15  LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 122 GT 123
            +
Sbjct: 75  SS 76

>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 = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 8/78 (10%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKL 120
           I+VG L  + T E +++ FSQ+G++ +VK+         KG GFV+    E+  EA+ KL
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAKL 62
Query: 121 NGTVIGKQSVRLSWGRNP 138
           + T    +++R++   NP
Sbjct: 63  DNTDFMGRTIRVTEA-NP 79

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/85 (36%), Positives = 46/85 (54%), Gaps = 11/85 (12%)
Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK---------GCGFVQFANR 110
           G S ++ +F+  L+ + T+E L+  FS+ G I S  I   K         G GFV++   
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 111 ENAEEALHKLNG-TVIG-KQSVRLS 133
           E A++AL +L G TV G K  VR+S
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRIS 85

>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 = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANREN 112
           D     +FVG +    +++DLR+ F QYG +  + +        P  KGC FV F  R+ 
Sbjct: 12  DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 71
Query: 113 AEEALHKLNGTVI 125
           A EA + L+   +
Sbjct: 72  ALEAQNALHNMKV 84

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEAL 117
           +F+G +    T+ D+R  FS +G+I   +I  G     +GC FV F  R  A+ A+
Sbjct: 98  LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 7/82 (8%)
Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------GKGCGFVQFANREN 112
           G S ++ IF+G LDP + ++ L   FS +G I      +        KG  F+ FA+ + 
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 113 AEEALHKLNGTVIGKQSVRLSW 134
           ++ A+  +NG  +  + + +S+
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSY 82

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 6/59 (10%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHK 119
           IFVGGL P+  +E +R+ F  +GE+ S+++P+       +G  F+ F   E  ++ + K
Sbjct: 4   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 9/68 (13%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PV---GKGCGFVQFANRENAEEAL--- 117
           +F+GGL+ + T+++LR+ F +YG +  +KI   P     +G GF+ F    + +E +   
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 118 HKLNGTVI 125
           H L+G VI
Sbjct: 66  HILDGKVI 73

>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of Nucleolysin Tiar Length = 103

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/97 (29%), Positives = 47/97 (48%), Gaps = 4/97 (4%)
Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG----FV 105
           G+ G     E D    T++VG L  +VT+  + Q FSQ G   S K+           FV
Sbjct: 1   GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFV 60
Query: 106 QFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           +F    +A  AL  +NG  I  + V+++W   P++++
Sbjct: 61  EFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQK 97

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/86 (32%), Positives = 44/86 (51%), Gaps = 4/86 (4%)
Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI--ASVKIPVGK--GCGFVQFANRENA 113
           S G S    IFV  L  + T + L+  F++ G +  A +K+  GK  GCG V+F + E A
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVA 61
Query: 114 EEALHKLNGTVIGKQSVRLSWGRNPA 139
           E A   +NG  +  + + +   RN +
Sbjct: 62  ERACRMMNGMKLSGREIDVRIDRNAS 87

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 6/59 (10%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHK 119
           IFVGGL P+  +E +R+ F  +GE+ S+++P+       +G  F+ F   E  ++ + K
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENA 113
           G S ++ +++ GL P  TD+DL +    YG+I S K  +       KG GFV F +   A
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 114 EEALHKLNGTVIGKQSVRLS 133
           ++A+  L  + +  Q  + S
Sbjct: 61  QKAVTALKASGVQAQMAKQS 80

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 117
           +T ++V  L   +TD+ L   F +YG I    I   K      G  FV++  RE A+EA+
Sbjct: 89  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Query: 118 HKLNGTV 124
             LN  +
Sbjct: 149 SALNNVI 155

>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical Protein Flj11016 Length = 115

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQY----GEIASVKIPVGK--GCGFVQFANRENAEEAL 117
           N  +++  L P VT+ DL   F+++    G     ++  G+  G  F+ F N+E A +AL
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
Query: 118 HKLNGTVIGKQSVRLSWGRN 137
           H +NG  +  + + + +G+N
Sbjct: 85  HLVNGYKLYGKILVIEFGKN 104

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 4/84 (4%)
Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI--ASVKIPVGK--GCGFVQFANRENAEE 115
           G S ++ IFV  L  + T + L+  F++ G +  A +K+  GK  GCG V+F + E AE 
Sbjct: 1   GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAER 60
Query: 116 ALHKLNGTVIGKQSVRLSWGRNPA 139
           A   +NG  +  + + +   RN +
Sbjct: 61  ACRMMNGMKLSGREIDVRIDRNAS 84

>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 = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 10/68 (14%)
Query: 68  FVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL---- 117
           FVGGL  + + +DL+  F+++GE+    I         +G GF+ F +  + E+ L    
Sbjct: 15  FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 118 HKLNGTVI 125
           H+L+G VI
Sbjct: 75  HRLDGRVI 82

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEA 116
           S+  +FVG L P +T   +   F+ +G I+  ++         KG GFV F N+ +AE A
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 117 LHKLNGTVIGKQSVRLSW 134
           + ++ G  +G + +R +W
Sbjct: 65  IQQMGGQWLGGRQIRTNW 82

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL--- 117
           +FVGGLD + T E LR  FSQYGE+    I   K      G GFV+F +       L   
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 118 -HKLNG 122
            H L+G
Sbjct: 79  PHTLDG 84

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
           S G S    +F+G L    T++++R  F QYG++    I   K  GFV   ++  AE+A+
Sbjct: 2   SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAI 59
Query: 118 HKLN 121
             L+
Sbjct: 60  RNLH 63

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 117
           +T ++V  L   +TD+ L   F +YG I    I   K      G  FV++  RE A+EA+
Sbjct: 100 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
Query: 118 HKLNGTV 124
             LN  +
Sbjct: 160 SALNNVI 166

>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2 Length = 240

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 64  NTTIFVGGLD---------PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 114
           N T++VGG+D         P   +  +R  FS+ G+I  ++    K CGFV+F  + NAE
Sbjct: 134 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 193
Query: 115 EALHKLNGTVI 125
            A   ++   +
Sbjct: 194 FAKEAMSNQTL 204

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 10/74 (13%)
Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGK---GCGFVQFANRENAEE 115
           SS   +F+GGL    T E LR+ F Q+GE+     ++ P+ K   G GFV F ++   ++
Sbjct: 23  SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 82
Query: 116 AL----HKLNGTVI 125
            L    H+L+   I
Sbjct: 83  VLAQSRHELDSKTI 96

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 6/76 (7%)
Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 117
           + T++VGGLD  V++  L + F Q G + +  +P  +      G GFV+F + E+A+ A+
Sbjct: 15  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 118 HKLNGTVIGKQSVRLS 133
             ++   +  + +R++
Sbjct: 75  KIMDMIKLYGKPIRVN 90

>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast Length = 229

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 64  NTTIFVGGLD---------PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 114
           N T++VGG+D         P   +  +R  FS+ G+I  ++    K CGFV+F  + NAE
Sbjct: 136 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 195
Query: 115 EALHKLNGTVI 125
            A   ++   +
Sbjct: 196 FAKEAMSNQTL 206

>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 = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 117
           +T ++V  L   +TD+ L   F +YG I    I   K      G  FV++  RE A+EA+
Sbjct: 13  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 118 HKLNGTV 124
             LN  +
Sbjct: 73  SALNNVI 79

>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna Selenocysteine Associated Protein Length = 99

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 48/91 (52%), Gaps = 16/91 (17%)
Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGE-IASVKIP------VGKGCGFVQFANRENAEEALH 118
           ++++G L+P + +  + + F+  GE + SVKI       +  G  FV+FA+   AE+ LH
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 119 KLNGTVIGKQSVRLSWGRNPANKQFRADYGN 149
           K+NG  +         G  PA K+F+ +Y  
Sbjct: 71  KINGKPLP--------GATPA-KRFKLNYAT 92

>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From Hypothetical Rna Binding Protein Bc052180 Length = 97

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 36/69 (52%)
Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
            T ++VGGL PN +   L + F ++G I ++    G    ++Q+ + + A+ A  K+ G 
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGF 76
Query: 124 VIGKQSVRL 132
            +G    RL
Sbjct: 77  PLGGPDRRL 85

>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains Of The Yeast Splicing Factor Prp24 Length = 292

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 9/77 (11%)
Query: 67  IFVGGLDPNVTDEDL-RQPFSQYGEIASVKIPVGKG-------CGFVQFANRENAEEALH 118
           I +  L   + DE+L R+ F  +G I  + IP G+        C F  F N+++AE AL 
Sbjct: 213 IXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAERALQ 272
Query: 119 KLNGTVIGKQSVRLSWG 135
             N +++G + + +S  
Sbjct: 273 X-NRSLLGNREISVSLA 288

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEA---- 116
           IFVGGL  N T ED++  F Q+G++    +   K      G GFV F + +  E+     
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 117 LHKLNGTVI 125
            H++N  ++
Sbjct: 62  FHEINNKMV 70

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
           ++T + VG + P  T+++LR  F +YG +  ++  + K   FV     E+A EA+  L+ 
Sbjct: 9   ASTKLHVGNISPTCTNQELRAKFEEYGPV--IECDIVKDYAFVHMERAEDAVEAIRGLDN 66
Query: 123 TVI--GKQSVRLSWGR 136
           T     +  V+LS  R
Sbjct: 67  TEFQGKRMHVQLSTSR 82

>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 = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 55  GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC------GFVQFA 108
           G Q EG      +F+  L     D+DL Q F  +G + S K+ + K        GFV + 
Sbjct: 17  GSQKEG-PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYD 75
Query: 109 NRENAEEALHKLNGTVIGKQSVRLSWGRN 137
           N  +A+ A+  +NG  IG + +++   R+
Sbjct: 76  NPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEE 115
           +SNT + V  L  ++TD +L   F   G I + +I          G  FV F +  +++ 
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 116 ALHKLNGTVIGKQSVRLSWGR 136
           A+  LNG  +  + +++S+ R
Sbjct: 61  AIKVLNGITVRNKRLKVSYAR 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	198
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-43
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-41
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-39
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-38
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-38
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-36
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-36
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-35
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	4e-33
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-32
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-28
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-28
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-28
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-27
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-20
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-26
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-25
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-23
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-24
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-21
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-24
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-22
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-21
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-24
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-24
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-20
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-23
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-23
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-23
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-23
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-23
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-22
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	8e-23
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-22
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-22
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-22
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-22
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-22
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-17
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-22
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-22
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-20
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-22
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-22
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-21
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	6e-22
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-22
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-22
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	9e-22
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-21
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-20
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-21
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-21
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-21
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-21
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-21
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-21
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-21
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-20
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-21
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-21
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-21
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-21
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-21
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-21
1x5o_A	114	RNA binding motif, single-stranded interacting pro	6e-21
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	6e-21
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	7e-21
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	7e-21
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	8e-21
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-16
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	8e-21
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-21
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-19
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-21
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-20
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-20
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-20
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-20
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-20
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-20
2div_A	99	TRNA selenocysteine associated protein; structural	2e-20
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-20
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-20
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-20
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-20
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-20
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-20
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-20
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-20
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-20
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	8e-20
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	8e-20
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	9e-20
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	9e-20
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-20
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-19
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-17
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-19
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-19
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-19
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-19
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-19
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-19
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	8e-13
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-19
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-19
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-19
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-19
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-19
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-19
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-19
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	5e-19
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	5e-19
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-19
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-18
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-18
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-18
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-18
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-18
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-18
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-18
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-18
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-18
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-18
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	6e-18
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-18
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	7e-18
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	8e-18
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-17
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-17
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-17
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-17
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-17
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-17
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-17
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-17
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-17
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	6e-17
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	7e-17
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	9e-17
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-16
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-16
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	9e-16
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-16
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-16
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-16
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-16
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-16
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-16
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-16
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	4e-16
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	4e-16
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-16
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-16
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	8e-16
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-15
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-15
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-15
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-15
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-15
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-15
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	3e-15
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	4e-15
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-15
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	7e-15
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	7e-15
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	8e-15
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	8e-15
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-14
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-14
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-14
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-14
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-14
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-14
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-14
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-12
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-12
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-11
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-11
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-11
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	6e-11
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-10
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-10
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	3e-10
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-10
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	6e-10
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	9e-10
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-08
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	3e-08
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	1e-07
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	1e-06
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	1e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-06
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	2e-06
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	2e-06
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	1e-05
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-05
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	4e-05
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	6e-05
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	7e-05

>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 =  139 bits (352), Expect = 3e-43
 Identities = 32/109 (29%), Positives = 55/109 (50%), Gaps = 7/109 (6%)

Query: 47  ASNGAPGQGPQ-------SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG 99
            S+G+ G   Q       ++    N T++ GG+   +TD+ +RQ FS +G+I  +++   
Sbjct: 1   GSSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60

Query: 100 KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
           KG  FV+F+  E+A  A+  +NGT I    V+  WG+   +       G
Sbjct: 61  KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPSSG 109

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score =  133 bits (337), Expect = 4e-41
 Identities = 24/99 (24%), Positives = 38/99 (38%), Gaps = 6/99 (6%)

Query: 44  GGYASNGAPGQGPQS------EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP 97
           G       P   PQ+            TT ++G +    T+ DL   F  +G I   K  
Sbjct: 1   GSQTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY 60

Query: 98  VGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
             KGC F+++   E A   +  L       +++R  WG+
Sbjct: 61  PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK 99

>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 =  129 bits (327), Expect = 1e-39
 Identities = 32/88 (36%), Positives = 51/88 (57%), Gaps = 4/88 (4%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 109
           G+ G   +   D + TT++VGGL   +T+ DLR  F Q+GEI ++ +   + C F+QFA 
Sbjct: 1   GSSGSSGE---DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFAT 57

Query: 110 RENAEEALHK-LNGTVIGKQSVRLSWGR 136
           R+ AE A  K  N  ++  + + + WGR
Sbjct: 58  RQAAEVAAEKSFNKLIVNGRRLNVKWGR 85

>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 =  127 bits (322), Expect = 1e-38
 Identities = 27/99 (27%), Positives = 51/99 (51%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 109
           G+ G     +  +  + +FVG L P++T+E++R+ F +YG+   V I   KG GF++   
Sbjct: 1   GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLET 60

Query: 110 RENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
           R  AE A  +L+   +  + +R+ +  + A+       G
Sbjct: 61  RTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPSSG 99

>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 =  125 bits (316), Expect = 6e-38
 Identities = 24/93 (25%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 109
           G+ G   +        T++V G D  +T   LR  FS +G I  + +   + C FV +  
Sbjct: 1   GSSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEK 58

Query: 110 RENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
            E+A++A+ +LNGT +    ++++  R      
Sbjct: 59  MESADQAVAELNGTQVESVQLKVNIARKQPMLD 91

>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 =  121 bits (306), Expect = 3e-36
 Identities = 30/103 (29%), Positives = 48/103 (46%), Gaps = 4/103 (3%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFV 105
           G+ G     E D    T++VG L  +VT+  + Q FSQ G   S K+           FV
Sbjct: 1   GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFV 60

Query: 106 QFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
           +F    +A  AL  +NG  I  + V+++W   P++++     G
Sbjct: 61  EFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGPSSG 103

>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 =  118 bits (299), Expect = 3e-35
 Identities = 24/97 (24%), Positives = 46/97 (47%), Gaps = 1/97 (1%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 109
           G+ G     +  SS   ++V  L  + ++E + + F+     A  ++   +   FV F+N
Sbjct: 1   GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSN 60

Query: 110 RENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRAD 146
           RE+A EA+  LNG V+    + ++  + P +K     
Sbjct: 61  REDAVEAMKALNGKVLDGSPIEVTLAK-PVDKDSSGP 96

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score =  113 bits (285), Expect = 4e-33
 Identities = 25/89 (28%), Positives = 46/89 (51%), Gaps = 2/89 (2%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENA 113
              + EG+ SNT +FV     +V + +L + F  +G +  VKI    G  FV+F   E+A
Sbjct: 21  MHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESA 78

Query: 114 EEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
            +A+ +++G     Q + + + + PA + 
Sbjct: 79  AKAIEEVHGKSFANQPLEVVYSKLPAKRY 107

>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 =  111 bits (279), Expect = 3e-32
 Identities = 27/102 (26%), Positives = 49/102 (48%), Gaps = 2/102 (1%)

Query: 57  QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEA 116
            S G +    +FV  L   VT+E L + FSQ+G++  VK    K   F+ F  R+ A +A
Sbjct: 4   GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKA 61

Query: 117 LHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGG 158
           + ++NG  +  +++ + + + P  K+       Q +     G
Sbjct: 62  MEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103

>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 =  101 bits (253), Expect = 3e-28
 Identities = 28/106 (26%), Positives = 49/106 (46%), Gaps = 3/106 (2%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGKGC 102
           G      A     +++  S N+ +F+G L+   V   D+   FS+YG +A   +   KG 
Sbjct: 7   GMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--KGY 64

Query: 103 GFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
            FVQ++N  +A  A+   NG V+  Q++ ++    P   +     G
Sbjct: 65  AFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPSSG 110

>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 =  100 bits (252), Expect = 3e-28
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
            T ++VGGL PN +   L + F ++G I ++    G    ++Q+ + + A+ A  K+ G 
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGF 76

Query: 124 VIGKQSVRL--SWGRNP 138
            +G    RL   + ++ 
Sbjct: 77  PLGGPDRRLRVDFAKSG 93

>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 = 99.9 bits (249), Expect = 9e-28
 Identities = 18/81 (22%), Positives = 30/81 (37%)

Query: 55  GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 114
           G       S T I    L       ++++ FS++G +  V +P G     V+F     A 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEAR 60

Query: 115 EALHKLNGTVIGKQSVRLSWG 135
           +A   L  +      + L W 
Sbjct: 61  KAFRHLAYSKFHHVPLYLEWA 81

>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 =  103 bits (258), Expect = 2e-27
 Identities = 26/87 (29%), Positives = 49/87 (56%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENA 113
             P  +  +    +FVG L  ++T+ED ++ F +YGE + V I   +G GF++  +R  A
Sbjct: 12  LKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLA 71

Query: 114 EEALHKLNGTVIGKQSVRLSWGRNPAN 140
           E A  +L+GT++  + +R+ +  + A 
Sbjct: 72  EIAKAELDGTILKSRPLRIRFATHGAA 98

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 84.0 bits (208), Expect = 5e-20
 Identities = 27/133 (20%), Positives = 42/133 (31%), Gaps = 7/133 (5%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVG--KGCGFVQFANRENAEEA 116
           +    + V  L P V++E L Q FSQ+G +    +     G   G GFV+FA +  A +A
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKA 153

Query: 117 LHKLN-GTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIPPPND-P 174
           L +   G  +   + R                  +                    P    
Sbjct: 154 LERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFE 213

Query: 175 SMYAAAAAAYGAY 187
             YA+   A    
Sbjct: 214 FEYASRWKALDEM 226

>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 = 95.5 bits (238), Expect = 6e-26
 Identities = 34/115 (29%), Positives = 59/115 (51%), Gaps = 7/115 (6%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCG 103
           G+ G   Q +  S++  +FVG L P +T ED++  F+ +G I+  ++         KG G
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSW-GRNPANKQFRADYGNQWSGAYYG 157
           FV F N+ +AE A+ ++ G  +G + +R +W  R P   +   +   + SG   G
Sbjct: 61  FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115

>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 = 97.0 bits (242), Expect = 2e-25
 Identities = 31/115 (26%), Positives = 51/115 (44%), Gaps = 13/115 (11%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFAN 109
           Q   S   S    IF+  LD ++ ++ L   FS +G I S K+       KG GFV F  
Sbjct: 93  QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFET 152

Query: 110 RENAEEALHKLNGTVIGKQSVRLSWGRNPAN---------KQFRADYGNQWSGAY 155
           +E AE A+ K+NG ++  + V +   ++            K+F       ++G+ 
Sbjct: 153 QEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAGSS 207

>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 = 92.3 bits (230), Expect = 1e-23
 Identities = 30/106 (28%), Positives = 49/106 (46%), Gaps = 7/106 (6%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCG 103
           G  G    S       +++VG L P+VT+  L + FS  G I S+++          G  
Sbjct: 1   GPLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYA 60

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGN 149
           +V F    +AE AL  +N  VI  + VR+ W +   + + ++  GN
Sbjct: 61  YVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLR-KSGVGN 105

>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 = 93.8 bits (234), Expect = 1e-24
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 6/87 (6%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEE 115
           +SNT + V  L  ++TD +L   F   G I + +I          G  FV F +  +++ 
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 116 ALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           A+  LNG  +  + +++S+ R      
Sbjct: 61  AIKVLNGITVRNKRLKVSYARPGGESI 87

>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 = 85.7 bits (213), Expect = 2e-21
 Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 6/82 (7%)

Query: 57  QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANR 110
                  +T ++V  L   +TD+ L   F +YG I    I         +G  FV++  R
Sbjct: 82  PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR 141

Query: 111 ENAEEALHKLNGTVIGKQSVRL 132
           E A+EA+  LN  +    S  L
Sbjct: 142 EEAQEAISALNNVIPEGGSQPL 163

>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 = 96.2 bits (240), Expect = 1e-24
 Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 6/95 (6%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDED-LRQPFSQYGEIASVKIPVG-----KGCGFVQF 107
            G  +     +  + V  L P   D D L +  S        ++  G     KG   +++
Sbjct: 174 AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEY 233

Query: 108 ANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
              E AEEA  + +G  +G   +R+S+       +
Sbjct: 234 ETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGR 268

>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 = 91.2 bits (227), Expect = 1e-22
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
            +   I + GL  +VT++++    S Y  +    +   KG  FV   N E AE A++  +
Sbjct: 20  RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFH 78

Query: 122 GTVIGKQSVRLSWGRNPAN 140
            + + ++ + +      A 
Sbjct: 79  QSRLRERELSVQLQPTDAL 97

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 87.3 bits (217), Expect = 3e-21
 Identities = 18/96 (18%), Positives = 38/96 (39%), Gaps = 10/96 (10%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEE 115
            ++  + V  L P++T +   +    +G +    +         KG GF ++  +++A  
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152

Query: 116 ALHKLNGTVIGKQSVRLSW----GRNPANKQFRADY 147
           A   L G  +G +++ + W       PA    R   
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLC 188

>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 = 90.8 bits (226), Expect = 2e-24
 Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 1/92 (1%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
           S G S    +++G L P VT +DLRQ F       + ++ +  G  FV + ++  A  A+
Sbjct: 2   SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAI 61

Query: 118 HKLNGTV-IGKQSVRLSWGRNPANKQFRADYG 148
             L+G V +  + + + +  +   +      G
Sbjct: 62  ETLSGKVELHGKIMEVDYSVSKKLRSSGPSSG 93

>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 = 91.9 bits (229), Expect = 6e-24
 Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 6/86 (6%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEA 116
           S T + V  L  N+T E+ R  F   GEI S K+          G GFV + + ++AE+A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 117 LHKLNGTVIGKQSVRLSWGRNPANKQ 142
           ++ LNG  +  +++++S+ R  +   
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSASI 86

>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 = 81.5 bits (202), Expect = 5e-20
 Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 57  QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANR 110
            S     +  ++V GL   +T ++L Q FSQYG I + +I V       +G GF++F  R
Sbjct: 81  PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKR 140

Query: 111 ENAEEALHKLNGTVIGKQS 129
             AEEA+  LNG      +
Sbjct: 141 IEAEEAIKGLNGQKPSGAT 159

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 93.3 bits (231), Expect = 1e-23
 Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 9/97 (9%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVT---------DEDLRQPFSQYGEIASVKIPVGKGCGF 104
            G        N T++VGG+D  +          +  +R  FS+ G+I  ++    K CGF
Sbjct: 124 MGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGF 183

Query: 105 VQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANK 141
           V+F  + NAE A   ++   +   S +    R     
Sbjct: 184 VKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTG 220

>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 = 2e-23
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 5/81 (6%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGF 104
           G+ G          +  +FVG L+   ++ED+ + F  +G I    +  G     KGC F
Sbjct: 1   GSSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAF 60

Query: 105 VQFANRENAEEALHKLNGTVI 125
           V+F++   A+ A+H L+G+  
Sbjct: 61  VKFSSHTEAQAAIHALHGSQT 81

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 88.1 bits (219), Expect = 4e-23
 Identities = 26/104 (25%), Positives = 53/104 (50%), Gaps = 11/104 (10%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------G 99
            S+G+ GQ P+ +   + + I V  +       ++R+ FS +GE+ +V++P         
Sbjct: 1   GSSGSSGQVPKKQ---TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAH 57

Query: 100 KGCGFVQFANRENAEEALHKL-NGTVIGKQSVRLSWGRNPANKQ 142
           +G GFV F  +++A++A + L + T +  + + L W  +    Q
Sbjct: 58  RGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 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 = 87.8 bits (218), Expect = 6e-23
 Identities = 26/109 (23%), Positives = 50/109 (45%), Gaps = 4/109 (3%)

Query: 44  GGYASNGAPGQGP-QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV---G 99
           G   S+G  G G  +    +++  I+VG L P++  +D+   F +YG I  + +     G
Sbjct: 1   GSSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG 60

Query: 100 KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
               FV+F +  +AE+A++  +G       +R+ + R+          G
Sbjct: 61  PPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSSG 109

>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 = 89.2 bits (222), Expect = 8e-23
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 5/75 (6%)

Query: 56  PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANR 110
            +      +  +F+G +    T+ D+R  FS +G+I   +I  G     +GC FV F  R
Sbjct: 87  SEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTR 146

Query: 111 ENAEEALHKLNGTVI 125
             A+ A+  ++    
Sbjct: 147 AMAQTAIKAMHQAQT 161

>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 = 87.7 bits (218), Expect = 3e-22
 Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 9/89 (10%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--------PVGKGCGFVQFANRENA 113
           S    +FVG +    +++DLR+ F QYG +  + +        P  KGC FV F  R+ A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 114 EEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
            EA + L+   +          + PA+ +
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMK-PADSE 88

>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 = 86.5 bits (215), Expect = 8e-23
 Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 2/91 (2%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
           S G S    +F+G L    T++++R  F QYG++    I   K  GFV   ++  AE+A+
Sbjct: 2   SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAI 59

Query: 118 HKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
             L+   +   ++ +   +N +        G
Sbjct: 60  RNLHHYKLHGVNINVEASKNKSKASSGPSSG 90

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 86.8 bits (215), Expect = 1e-22
 Identities = 20/96 (20%), Positives = 42/96 (43%), Gaps = 1/96 (1%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFV 105
           +S  +    P  EG      ++VG L  +    DL++   + G +       G +   F+
Sbjct: 2   SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFL 61

Query: 106 QFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANK 141
            + +   A++A+  L G  +G  ++R++  R   +K
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRDK 97

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 87.5 bits (217), Expect = 2e-22
 Identities = 24/94 (25%), Positives = 47/94 (50%), Gaps = 6/94 (6%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GK 100
              G+ G G      ++   ++VGGL   V D+ L   F  +G+I  ++IP+       +
Sbjct: 46  VDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 105

Query: 101 GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW 134
           G  FV+F   E+A  A+  +N + +  +++R++ 
Sbjct: 106 GFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139

>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 = 86.5 bits (215), Expect = 2e-22
 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 4/79 (5%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEE 115
           G   +  IF+  LD ++ ++ L   FS +G I S K+       KG GFV F  +E AE 
Sbjct: 1   GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAER 60

Query: 116 ALHKLNGTVIGKQSVRLSW 134
           A+ K+NG ++  + V +  
Sbjct: 61  AIEKMNGMLLNDRKVFVGR 79

>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 = 85.8 bits (213), Expect = 2e-22
 Identities = 32/103 (31%), Positives = 47/103 (45%), Gaps = 4/103 (3%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFV 105
           G+ G    SE  S+   + V  +     D DLRQ F Q+G+I  V+I       KG GFV
Sbjct: 1   GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFV 60

Query: 106 QFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
            F N  +A+ A  KL+GTV+  + + ++              G
Sbjct: 61  TFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPSSG 103

>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 = 88.5 bits (220), Expect = 2e-22
 Identities = 20/102 (19%), Positives = 46/102 (45%), Gaps = 8/102 (7%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGK 100
            S   PG       DS++  +F+GGL   + D+ +++  + +G + +  +       + K
Sbjct: 98  PSVYVPGVVSTVVPDSAHK-LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK 156

Query: 101 GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           G  F ++ +    ++A+  LNG  +G + + +    +   K 
Sbjct: 157 GYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA-SVGAKN 197

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 74.3 bits (183), Expect = 6e-17
 Identities = 16/116 (13%), Positives = 42/116 (36%), Gaps = 13/116 (11%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----------KGCGFVQFA 108
           G  +   ++VG +   +T+E +   F+    +  +    G           K   F++F 
Sbjct: 1   GAMARR-LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR 59

Query: 109 NRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGY 164
           + +   +A+   +G +   QS+++    +       ++  + +        V D  
Sbjct: 60  SVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSA 114

>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 = 84.9 bits (211), Expect = 3e-22
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENA 113
           G S ++ +++ GL P  TD+DL +    YG+I S K  +       KG GFV F +   A
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 114 EEALHKLNGTVIGKQSVRLS 133
           ++A+  L  + +  Q  + S
Sbjct: 61  QKAVTALKASGVQAQMAKQS 80

>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 = 87.2 bits (217), Expect = 3e-22
 Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 6/87 (6%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----G--KGCGFVQF 107
              Q         +FVG L+ NV DE LR  F  +    S  +      G  +G GFV F
Sbjct: 77  FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF 136

Query: 108 ANRENAEEALHKLNGTVIGKQSVRLSW 134
            ++++A+ A+  + G  +  + +R++W
Sbjct: 137 TSQDDAQNAMDSMQGQDLNGRPLRINW 163

>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 = 82.2 bits (204), Expect = 3e-20
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 5/82 (6%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-----GCGFVQFANRENAEEALHKL 120
            ++VG LD  +T++ L+Q F   G IA++KI + K        FV++    +A  AL  L
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 121 NGTVIGKQSVRLSWGRNPANKQ 142
           NG  I    V+++W        
Sbjct: 62  NGKQIENNIVKINWAFQSQQSS 83

>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 = 85.4 bits (212), Expect = 4e-22
 Identities = 24/101 (23%), Positives = 45/101 (44%), Gaps = 9/101 (8%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GK 100
            S+G+ G   +++    N TI V  L  +  + DL++ F  +G I+ + +         K
Sbjct: 1   GSSGSSGPNRRAD---DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSK 57

Query: 101 GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANK 141
           G  F+ F  RE+A  A+  ++G       + + W +   N 
Sbjct: 58  GFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS 98

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 88.5 bits (220), Expect = 4e-22
 Identities = 19/93 (20%), Positives = 45/93 (48%), Gaps = 6/93 (6%)

Query: 48  SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KG 101
               P     +E   +   I+V  +  +++D+D++  F  +G+I S  +         KG
Sbjct: 109 GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKG 168

Query: 102 CGFVQFANRENAEEALHKLNGTVIGKQSVRLSW 134
            GF+++   +++++A+  +N   +G Q +R+  
Sbjct: 169 YGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGK 201

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 86.2 bits (214), Expect = 2e-21
 Identities = 23/111 (20%), Positives = 50/111 (45%), Gaps = 7/111 (6%)

Query: 42  LIGGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV--- 98
           + GG           +    +  + ++VG +   + ++ +RQ F+ +G I S+ +     
Sbjct: 7   MTGGQQMGRGSA-AQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSV 65

Query: 99  ---GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRAD 146
               KG  FV++   E A+ AL ++N  ++G +++++    N    Q   D
Sbjct: 66  TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIID 116

>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 = 85.4 bits (211), Expect = 6e-22
 Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 6/91 (6%)

Query: 44  GGYASNGAPGQGPQSEG------DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP 97
           G   S+GA     + EG       + +  +  GGL   V+   L     + G + ++ +P
Sbjct: 1   GSSGSSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP 60

Query: 98  VGKGCGFVQFANRENAEEALHKLNGTVIGKQ 128
             K   F ++   E ++ A   LNG  +   
Sbjct: 61  PNKPYSFARYRTTEESKRAYVTLNGKEVVDD 91

>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 = 84.2 bits (209), Expect = 7e-22
 Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 7/93 (7%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKG 101
            S+G+ G  P  E   ++ T+FVG L+  V +E L + F Q G +  V I        K 
Sbjct: 1   GSSGSSGMFPAQE--EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS 58

Query: 102 CGFVQFANRENAEEALHKLNGTVIGKQSVRLSW 134
            GFV F + E+   A+  LNG  +  + + +S 
Sbjct: 59  FGFVCFKHPESVSYAIALLNGIRLYGRPINVSG 91

>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 = 84.2 bits (209), Expect = 9e-22
 Identities = 24/105 (22%), Positives = 48/105 (45%), Gaps = 6/105 (5%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCG 103
           G+ G        + + T++VGGLD  V++  L + F Q G + +  +P        +G G
Sbjct: 1   GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
           FV+F + E+A+ A+  ++   +  + +R++              G
Sbjct: 61  FVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSSG 105

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 84.7 bits (210), Expect = 9e-22
 Identities = 29/78 (37%), Positives = 39/78 (50%), Gaps = 4/78 (5%)

Query: 53  GQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFA 108
           G    +E  S    + V  +     D DLRQ F Q+G+I  V+I       KG GFV F 
Sbjct: 18  GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFE 77

Query: 109 NRENAEEALHKLNGTVIG 126
           N  +A+ A  KL+GTV+ 
Sbjct: 78  NSADADRAREKLHGTVVE 95

>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 = 86.1 bits (214), Expect = 1e-21
 Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 3/83 (3%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG--KGCGFVQFANRE 111
           +G  S+   +  T+    L  N+T+++L++ F    EI  V    G  KG  +++F +  
Sbjct: 89  KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-QDGKSKGIAYIEFKSEA 147

Query: 112 NAEEALHKLNGTVIGKQSVRLSW 134
           +AE+ L +  G  I  +SV L +
Sbjct: 148 DAEKNLEEKQGAEIDGRSVSLYY 170

>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 = 83.4 bits (207), Expect = 1e-20
 Identities = 20/97 (20%), Positives = 44/97 (45%), Gaps = 6/97 (6%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFA 108
              +    ++   +F+G L+PN +  +L+   S+      + +        +  G+V F 
Sbjct: 3   HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFE 62

Query: 109 NRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRA 145
           + E+ E+AL +L G  +    ++L   +   +K+ RA
Sbjct: 63  SAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRA 98

>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 = 85.6 bits (212), Expect = 1e-21
 Identities = 31/118 (26%), Positives = 53/118 (44%), Gaps = 13/118 (11%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQF 107
              Q +    + T++VG L    T+E + + FS+ G+I  + + +        G  FV++
Sbjct: 29  NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88

Query: 108 ANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYG 165
            +R +AE A+  +NGT +  + +R  W             G Q+     GGQV D Y 
Sbjct: 89  YSRADAENAMRYINGTRLDDRIIRTDWDAGFKE-------GRQYGRGRSGGQVRDEYR 139

>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 = 83.4 bits (207), Expect = 1e-21
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 2/84 (2%)

Query: 55  GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 114
           G       ++T + VG + P  T+++LR  F +YG +    I   K   FV     E+A 
Sbjct: 1   GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAV 58

Query: 115 EALHKLNGTVIGKQSVRLSWGRNP 138
           EA+  L+ T    + + +    + 
Sbjct: 59  EAIRGLDNTEFQGKRMHVQLSTSR 82

>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 = 83.8 bits (208), Expect = 1e-21
 Identities = 28/102 (27%), Positives = 47/102 (46%), Gaps = 10/102 (9%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRE 111
           S G S +  +FV  L    ++EDL + FS YG ++ +  P+       KG  FV F   E
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 112 NAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSG 153
           +A +A  +++G V   + + +     P+  +  A      SG
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHV----LPSTIKKEASQSGPSSG 99

>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 = 83.5 bits (207), Expect = 2e-21
 Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 9/86 (10%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---------PVGKGCGFVQFANR 110
           G S ++ +F+  L+ + T+E L+  FS+ G I S  I          +  G GFV++   
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 111 ENAEEALHKLNGTVIGKQSVRLSWGR 136
           E A++AL +L G  +    + +    
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRISE 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 = 83.0 bits (206), Expect = 2e-21
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 6/80 (7%)

Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAE 114
             S+  +FVG L P +T   +   F+ +G I+  ++         KG GFV F N+ +AE
Sbjct: 3   LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62

Query: 115 EALHKLNGTVIGKQSVRLSW 134
            A+ ++ G  +G + +R +W
Sbjct: 63  NAIQQMGGQWLGGRQIRTNW 82

>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 = 88.1 bits (219), Expect = 2e-21
 Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 9/89 (10%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDED-LRQPFSQYGEIASVKIPVG-------KGCGFV 105
                        I +  L   + DE+ LR+ F  +G I  + IP G         C F+
Sbjct: 200 SKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFM 259

Query: 106 QFANRENAEEALHKLNGTVIGKQSVRLSW 134
            F N+++AE AL ++N +++G + + +S 
Sbjct: 260 VFENKDSAERAL-QMNRSLLGNREISVSL 287

>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 = 87.3 bits (217), Expect = 4e-21
 Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 4/72 (5%)

Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEA 116
           +   TT+ V  L  +     + + F   G I  V +            ++FA  + A  A
Sbjct: 38  NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAA 97

Query: 117 LHKLNGTVIGKQ 128
           + K +  V   +
Sbjct: 98  ITKTHKVVGQNE 109

>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 = 85.8 bits (213), Expect = 2e-20
 Identities = 21/104 (20%), Positives = 42/104 (40%), Gaps = 7/104 (6%)

Query: 49  NGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIA-SVKIP-----VGKGC 102
           +   GQ        +  T+++    P+ T  ++R        +A S+++P       +  
Sbjct: 102 HKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRF 161

Query: 103 GFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRAD 146
            ++   ++E+A   + KLNG  I   ++      NP  K  R D
Sbjct: 162 AYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV-SNPLEKSKRTD 204

>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 = 83.0 bits (206), Expect = 2e-21
 Identities = 21/95 (22%), Positives = 38/95 (40%), Gaps = 11/95 (11%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQ 106
            S+G+ G         +   IFVG +    T ++LR  F + G +    +   K   FV 
Sbjct: 1   GSSGSSG---------NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVH 49

Query: 107 FANRENAEEALHKLNGTVIGKQSVRLSWGRNPANK 141
                +A+ A+ +LNG  +  + + +        K
Sbjct: 50  MEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKK 84

>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 = 83.5 bits (207), Expect = 2e-21
 Identities = 27/109 (24%), Positives = 50/109 (45%), Gaps = 13/109 (11%)

Query: 47  ASNGAPGQGPQSEGDSS-------NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV- 98
            S+G+ G+  +     S       N  +++  L P VT+ DL   F+++ E     I   
Sbjct: 1   GSSGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFR 60

Query: 99  -----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
                 +G  F+ F N+E A +ALH +NG  +  + + + +G+N   + 
Sbjct: 61  MMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRS 109

>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 = 83.5 bits (207), Expect = 3e-21
 Identities = 25/108 (23%), Positives = 42/108 (38%), Gaps = 7/108 (6%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGF 104
           G+ G     +     +T+FV  LD  V  + L++ FS  G +    I        +G G 
Sbjct: 1   GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGT 60

Query: 105 VQFANRENAEEALHKLNGTVI-GKQ-SVRLSWGRNPANKQFRADYGNQ 150
           V F     A +A+   NG ++  +   V++     P    F  +   Q
Sbjct: 61  VTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQ 108

>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 = 82.2 bits (204), Expect = 4e-21
 Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 7/86 (8%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------GKGCGFVQFANRENAEE 115
             T + +G L  NVT + + + FS YG+I  + +PV        KG  +V+F N + AE+
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 116 ALHKLNGTVIGKQSVRLSWGRNPANK 141
           AL  ++G  I  Q +  +    P  +
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPWPR 88

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 82.2 bits (204), Expect = 4e-21
 Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 4/84 (4%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENA 113
           S G S    IFV  L  + T + L+  F++ G +    I +     KGCG V+F + E A
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVA 61

Query: 114 EEALHKLNGTVIGKQSVRLSWGRN 137
           E A   +NG  +  + + +   RN
Sbjct: 62  ERACRMMNGMKLSGREIDVRIDRN 85

>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 = 82.3 bits (204), Expect = 5e-21
 Identities = 25/102 (24%), Positives = 49/102 (48%), Gaps = 6/102 (5%)

Query: 53  GQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQ 106
           G    S   ++   ++VGGL   V D+ L   F  +G+I  ++IP+       +G  FV+
Sbjct: 1   GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60

Query: 107 FANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
           F   E+A  A+  +N + +  +++R++  +    K+     G
Sbjct: 61  FELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGPSSG 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 = 82.7 bits (205), Expect = 6e-21
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 7/78 (8%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVG--KGCGFVQFA 108
              Q E D +N  +++  L  ++ +++L      +G++ S +I     G  +G GF +  
Sbjct: 17  MAKQQEQDPTN--LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARME 74

Query: 109 NRENAEEALHKLNGTVIG 126
           + E  E  +   NG  I 
Sbjct: 75  STEKCEAVIGHFNGKFIK 92

>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 = 82.3 bits (204), Expect = 6e-21
 Identities = 26/89 (29%), Positives = 46/89 (51%), Gaps = 4/89 (4%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFV 105
           G+ G             ++V  LD  + DE LR+ FS +G I S K+ +     KG GFV
Sbjct: 1   GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFV 60

Query: 106 QFANRENAEEALHKLNGTVIGKQSVRLSW 134
            F++ E A +A+ ++NG ++  + + ++ 
Sbjct: 61  CFSSPEEATKAVTEMNGRIVATKPLYVAL 89

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 81.9 bits (203), Expect = 7e-21
 Identities = 20/100 (20%), Positives = 47/100 (47%), Gaps = 6/100 (6%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KG 101
            S+G+ G    S     +  +F+ GL  + T E+L +    +G +  +++        KG
Sbjct: 1   GSSGSSGVFRYSTSLEKHK-LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG 59

Query: 102 CGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANK 141
             +V++ N   A +A+ K++G  I +  ++++   +  + 
Sbjct: 60  LAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 82.1 bits (203), Expect = 7e-21
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENA 113
           G      +    L+ NV +  L+    +YGE+  V+I +        G   V F +   A
Sbjct: 2   GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61

Query: 114 EEALHKLNGTVIGKQSVR 131
           +E +  L+ T +    + 
Sbjct: 62  KETVKNLHLTSVMGNIIH 79

>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 = 83.8 bits (208), Expect = 8e-21
 Identities = 14/84 (16%), Positives = 37/84 (44%), Gaps = 6/84 (7%)

Query: 57  QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANR 110
             +       +F+GGL   + D+ +++  + +G + +  +         KG  F ++ + 
Sbjct: 87  DYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 146

Query: 111 ENAEEALHKLNGTVIGKQSVRLSW 134
              ++A+  LNG  +G + + +  
Sbjct: 147 NVTDQAIAGLNGMQLGDKKLLVQR 170

>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 = 72.6 bits (179), Expect = 2e-16
 Identities = 14/92 (15%), Positives = 35/92 (38%), Gaps = 12/92 (13%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----------KGCGFVQFANR 110
            S   ++VG +   +T+E +   F+    +  +    G           K   F++F + 
Sbjct: 2   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 111 ENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           +   +A+   +G +   QS+++    +     
Sbjct: 62  DETTQAM-AFDGIIFQGQSLKIRRPHDYQPLP 92

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 81.6 bits (202), Expect = 8e-21
 Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 6/96 (6%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI-ASVKIPVG-----KGCG 103
           G+ G    S G    T I V  +   V+ +++   F  Y  I  SV +         G  
Sbjct: 1   GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA 139
            V F +R+ A  A+  LN   IG + V+L  G  P+
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS 96

>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 = 85.4 bits (211), Expect = 8e-21
 Identities = 27/121 (22%), Positives = 48/121 (39%), Gaps = 2/121 (1%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKI-PVGKGCGF 104
             +            + N+ + V  L+P  VT + L   F  YG++  VKI    K    
Sbjct: 17  RGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENAL 76

Query: 105 VQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGY 164
           VQ A+   A+ A+  LNG  +  + +R++  ++   +  R    +Q     YG      +
Sbjct: 77  VQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRF 136

Query: 165 G 165
            
Sbjct: 137 K 137

>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 = 80.4 bits (198), Expect = 5e-19
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 3/90 (3%)

Query: 52  PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--PVGKGCGFVQFAN 109
           PG          + T+ +  + P+V++EDL+  FS  G +          +    +Q  +
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGS 198

Query: 110 RENAEEALHKLNGTVIG-KQSVRLSWGRNP 138
            E A +AL  L+   +G    +R+S+ ++ 
Sbjct: 199 VEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>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 = 81.0 bits (201), Expect = 9e-21
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 120
           +FVG L+ NV DE LR  F  +    S  +         +G GFV F ++++A+ A+  +
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 121 NGTVIGKQSVRLSW 134
            G  +  + +R++W
Sbjct: 64  QGQDLNGRPLRINW 77

>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 = 81.2 bits (201), Expect = 1e-20
 Identities = 26/90 (28%), Positives = 38/90 (42%), Gaps = 6/90 (6%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI-ASVKIPVG-----KGCG 103
           G+ G    S G    T I V  +   V+ +++   F  Y  I  SV +         G  
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLS 133
            V F +R+ A  A+  LN   IG + V+LS
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLS 90

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 80.7 bits (200), Expect = 1e-20
 Identities = 21/81 (25%), Positives = 44/81 (54%), Gaps = 6/81 (7%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEE 115
           ++   ++VGGL   V D+ L   F  +G+I  ++IP+       +G  FV+F   E+A  
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64

Query: 116 ALHKLNGTVIGKQSVRLSWGR 136
           A+  +N + +  +++R++  +
Sbjct: 65  AIDNMNESELFGRTIRVNLAK 85

>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 = 81.6 bits (202), Expect = 1e-20
 Identities = 20/107 (18%), Positives = 49/107 (45%), Gaps = 7/107 (6%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEALHK 119
             +F+GGL+    ++ L+  F ++G I+ V +        +G  F+ F N  +A+ A   
Sbjct: 8   GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67

Query: 120 LNGTVIGKQSVRLSWGRNPANKQF--RADYGNQWSGAYYGGQVYDGY 164
           +NG  +  +++++   + P+ +    R    +  + +  G   +  +
Sbjct: 68  MNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHHHH 114

>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 = 81.1 bits (201), Expect = 1e-20
 Identities = 18/85 (21%), Positives = 41/85 (48%), Gaps = 7/85 (8%)

Query: 64  NTTIFVGGLDPNVTDEDLRQP----FSQYGEIASVKIPVG---KGCGFVQFANRENAEEA 116
           N TI++  L+  +  ++L++     FS++G+I  + +      +G  FV F    +A  A
Sbjct: 8   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67

Query: 117 LHKLNGTVIGKQSVRLSWGRNPANK 141
           L  + G     + +R+ + +  ++ 
Sbjct: 68  LRSMQGFPFYDKPMRIQYAKTDSDI 92

>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 = 1e-20
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-VGKGCGFVQFANRENAEEAL 117
           +    +  ++VG L  N    +L + F  YG + SV +     G  FV+F +  +A +A+
Sbjct: 68  DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAV 127

Query: 118 HKLNGTVIGKQSVRLSWGRNP 138
            +L+G  +    VR+      
Sbjct: 128 RELDGRTLCGCRVRVELSNGE 148

>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 = 80.7 bits (200), Expect = 2e-20
 Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 7/82 (8%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASV-KIPV------GKGCGFVQFANREN 112
           G S ++ IF+G LDP + ++ L   FS +G I    KI         KG  F+ FA+ + 
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 113 AEEALHKLNGTVIGKQSVRLSW 134
           ++ A+  +NG  +  + + +S+
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSY 82

>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 = 80.8 bits (200), Expect = 2e-20
 Identities = 25/96 (26%), Positives = 48/96 (50%), Gaps = 13/96 (13%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGE-IASVKIP------VGKGCGFVQFANR 110
           S       ++++G L+P + +  + + F+  GE + SVKI       +  G  FV+FA+ 
Sbjct: 3   SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62

Query: 111 ENAEEALHKLNGTVIG----KQSVRLSW--GRNPAN 140
             AE+ LHK+NG  +      +  +L++     P++
Sbjct: 63  ATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPSS 98

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 83.8 bits (207), Expect = 2e-20
 Identities = 27/104 (25%), Positives = 46/104 (44%), Gaps = 2/104 (1%)

Query: 63  SNTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKI-PVGKGCGFVQFANRENAEEALHKL 120
            N+ + V  L+P  VT + L   F  YG++  VKI    K    VQ A+   A+ A+  L
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHL 61

Query: 121 NGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGY 164
           NG  +  + +R++  ++   +  R    +Q     YG      +
Sbjct: 62  NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRF 105

>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 = 82.3 bits (203), Expect = 5e-20
 Identities = 20/90 (22%), Positives = 41/90 (45%), Gaps = 3/90 (3%)

Query: 52  PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI--PVGKGCGFVQFAN 109
           PG          + T+ +  + P+V++EDL+  FS  G +          +    +Q  +
Sbjct: 108 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGS 167

Query: 110 RENAEEALHKLNGTVIGK-QSVRLSWGRNP 138
            E A +AL  L+   +G+   +R+S+ ++ 
Sbjct: 168 VEEAVQALIDLHNHDLGENHHLRVSFSKST 197

>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 = 81.2 bits (201), Expect = 2e-20
 Identities = 28/103 (27%), Positives = 48/103 (46%), Gaps = 13/103 (12%)

Query: 47  ASNGAPGQGPQSEGDSSN-------TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG 99
            S+G+ G   QS G + +         +F+  L     D+DL Q F  +G + S K+ + 
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60

Query: 100 ------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
                 K  GFV + N  +A+ A+  +NG  IG + +++   R
Sbjct: 61  KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR 103

>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 = 82.2 bits (203), Expect = 3e-20
 Identities = 23/96 (23%), Positives = 47/96 (48%), Gaps = 7/96 (7%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GK 100
            + G+       + +   T++ V  L    + + LR+ F +YG +  V IP        +
Sbjct: 54  VTEGSHHHHHHMDVEGM-TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESR 112

Query: 101 GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
           G  FV+F ++ +AE+A+  ++G V+  + +R+   R
Sbjct: 113 GFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 148

>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 = 80.3 bits (199), Expect = 3e-20
 Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 55  GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFA 108
           G          T+ V  L    + + LR+ F +YG +  V IP        +G  FV+F 
Sbjct: 4   GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63

Query: 109 NRENAEEALHKLNGTVIGKQSVRLSWGR 136
           +R +A++A   ++G  +  + +R+   R
Sbjct: 64  DRRDAQDAEAAMDGAELDGRELRVQVAR 91

>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 = 80.9 bits (200), Expect = 4e-20
 Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 10/115 (8%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GK 100
                   GPQ   +     +FV G+    T+ED+   F++YGEI ++ + +       K
Sbjct: 7   VEQDGDEPGPQRSVEGWI--LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64

Query: 101 GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG--RNPANKQFRADYGNQWSG 153
           G   V++   + A+ A+  LNG  +  Q + + W   R P   + R       S 
Sbjct: 65  GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSP 119

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 80.9 bits (200), Expect = 4e-20
 Identities = 25/99 (25%), Positives = 46/99 (46%), Gaps = 6/99 (6%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----- 98
           G     G+   G         T++ V  L    + + LR+ F +YG +  V IP      
Sbjct: 27  GQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTK 86

Query: 99  -GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
             +G  FV+F ++ +AE+A+  ++G V+  + +R+   R
Sbjct: 87  ESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 125

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 79.4 bits (196), Expect = 5e-20
 Identities = 20/99 (20%), Positives = 44/99 (44%), Gaps = 6/99 (6%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGKGCG 103
            S+G+ G  P+         + +  + P++  E L     QYG + S +           
Sbjct: 1   GSSGSSGSVPKR---QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVV 57

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
            V +++++ A +AL KLNG  +   ++++++  +    Q
Sbjct: 58  NVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 80.5 bits (199), Expect = 6e-20
 Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 7/94 (7%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GK 100
              G+   G ++  D +   + V GL    T+ DLR+ FS+YG IA V I         +
Sbjct: 30  MGRGSRHVGNRANPDPNCC-LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 88

Query: 101 GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW 134
           G  FV F N ++A+EA  + NG  +  + +R+ +
Sbjct: 89  GFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 79.2 bits (196), Expect = 8e-20
 Identities = 26/97 (26%), Positives = 45/97 (46%), Gaps = 6/97 (6%)

Query: 46  YASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----G-- 99
           Y S    G  P  +       +FV G+    T+ED+   F++YGEI ++ + +    G  
Sbjct: 5   YDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 64

Query: 100 KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
           KG   V++   + A+ A+  LNG  +  Q + + W  
Sbjct: 65  KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 101

>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 = 78.8 bits (195), Expect = 8e-20
 Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 11/96 (11%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----- 98
           G   S+G  G         S +T++V  L  ++T+ DL + FS+YG++  V I       
Sbjct: 1   GSSGSSGMSGGLA-----PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTR 55

Query: 99  -GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS 133
             KG  F+ F ++++A+     +N   +  + ++ S
Sbjct: 56  KSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS 91

>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 = 79.3 bits (196), Expect = 9e-20
 Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 8/82 (9%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCG 103
           G+ G     + D+    +F+G +  N+ ++DL+  F ++G+I  + +         KGC 
Sbjct: 1   GSSGSSGMKDHDAIK--LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCA 58

Query: 104 FVQFANRENAEEALHKLNGTVI 125
           F+ +  RE+A +A   L+    
Sbjct: 59  FLTYCERESALKAQSALHEQKT 80

>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 = 79.3 bits (196), Expect = 9e-20
 Identities = 25/93 (26%), Positives = 48/93 (51%), Gaps = 6/93 (6%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCG 103
            A       +G +    ++VG L  N+T++ LR  F  +G I S+++ +       KG G
Sbjct: 12  AAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYG 71

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
           F+ F++ E A++AL +LNG  +  + +++    
Sbjct: 72  FITFSDSECAKKALEQLNGFELAGRPMKVGHVT 104

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 79.3 bits (196), Expect = 9e-20
 Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 8/96 (8%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----G--K 100
             +     GPQ   +     +FV  +     ++++++ F  YGEI ++ + +    G  K
Sbjct: 11  EDDDELEPGPQRSVEGW--ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 68

Query: 101 GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
           G   V++   + A  A   LNG  I  Q++++ W  
Sbjct: 69  GYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF 104

>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 = 81.7 bits (201), Expect = 1e-19
 Identities = 22/116 (18%), Positives = 43/116 (37%), Gaps = 2/116 (1%)

Query: 62  SSNTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVGK-GCGFVQFANRENAEEALHK 119
           + +  + V GLD   +  + +   F  YG +  VK    K G   V+ A+    + A+  
Sbjct: 2   ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITH 61

Query: 120 LNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIPPPNDPS 175
           LN   +  Q + +   + PA    ++      S +Y          ++ P     +
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117

>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 = 76.3 bits (187), Expect = 2e-17
 Identities = 13/88 (14%), Positives = 30/88 (34%), Gaps = 6/88 (6%)

Query: 52  PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFV 105
           P Q  ++     +  +        VT+E+  +   + G      + V          G +
Sbjct: 111 PEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLL 170

Query: 106 QFANRENAEEALHKLNGTVIGKQSVRLS 133
           ++ ++ +A E L  LN   +   +    
Sbjct: 171 EWDSKSDALETLGFLNHYQMKNPNGPYP 198

>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 = 78.8 bits (195), Expect = 1e-19
 Identities = 30/93 (32%), Positives = 44/93 (47%), Gaps = 6/93 (6%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCG 103
           G+ G          N  + V GL    T+ DLR+ FS+YG IA V I         +G  
Sbjct: 1   GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
           FV F N ++A+EA  + NG  +  + +R+S   
Sbjct: 61  FVYFENVDDAKEAKERANGMELDGRRIRVSGPS 93

>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 = 78.9 bits (195), Expect = 1e-19
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 5/81 (6%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANREN 112
             G  +   + V  LD  V+D D+++ F+++G +    +         G   V F  + +
Sbjct: 23  GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKAD 82

Query: 113 AEEALHKLNGTVIGKQSVRLS 133
           A +A+ + NG  +  + + + 
Sbjct: 83  ALKAMKQYNGVPLDGRPMNIQ 103

>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 = 80.6 bits (199), Expect = 1e-19
 Identities = 22/102 (21%), Positives = 44/102 (43%), Gaps = 8/102 (7%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GK 100
             +     GPQ   +     +FV  +     ++++++ F  YGEI ++ + +       K
Sbjct: 57  EDDDELEPGPQRSVEGW--ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 114

Query: 101 GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           G   V++   + A  A   LNG  I  Q++++ W      K+
Sbjct: 115 GYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 156

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 79.6 bits (196), Expect = 1e-19
 Identities = 16/98 (16%), Positives = 38/98 (38%), Gaps = 7/98 (7%)

Query: 51  APGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQP----FSQYGEIASVKI---PVGKGCG 103
           +P  G        +  + +  ++P V  E L+       S  G+I  + +       G  
Sbjct: 16  SPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKA 75

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANK 141
           ++ FA +E+A+  +    G       + +++   P ++
Sbjct: 76  YIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQ 113

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 78.0 bits (193), Expect = 2e-19
 Identities = 17/92 (18%), Positives = 42/92 (45%), Gaps = 6/92 (6%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALH 118
             +++G +  + T+E +    S  G + ++K+         KG  F++F + E++  A+ 
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 119 KLNGTVIGKQSVRLSWGRNPANKQFRADYGNQ 150
            LNG  +G + ++  +  N        ++ + 
Sbjct: 63  NLNGYQLGSRFLKCGYSSNSDISGVSLEHHHH 94

>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 = 82.6 bits (203), Expect = 2e-19
 Identities = 23/140 (16%), Positives = 47/140 (33%), Gaps = 7/140 (5%)

Query: 64  NTTIFVGGLDPNVTDEDLRQP----FSQYGEIASVKIPVG---KGCGFVQFANRENAEEA 116
           N TI++  L+  +  ++L++     FSQ+G+I  + +      +G  FV F    +A  A
Sbjct: 9   NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68

Query: 117 LHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGYAIPPPNDPSM 176
           L  + G     + +R+ + +  ++   +              +                 
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128

Query: 177 YAAAAAAYGAYPVYGSHQQQ 196
            A         PV G     
Sbjct: 129 GATPVVGAVQGPVPGMPPMT 148

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 64.5 bits (156), Expect = 8e-13
 Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 2/73 (2%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKI-PVGKGCGFVQFANRENAEEALHKLNGTV 124
            +F+  L     +  L   F+Q+     V++ P      FV+F N   A  A   L G  
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFK 268

Query: 125 IGK-QSVRLSWGR 136
           I +  ++++S+ +
Sbjct: 269 ITQNNAMKISFAK 281

>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 = 78.6 bits (194), Expect = 2e-19
 Identities = 17/92 (18%), Positives = 39/92 (42%), Gaps = 5/92 (5%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANREN 112
            EG  +   + V  LD  V+D D+++ F+++G +    +         G   V F  R +
Sbjct: 29  GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRAD 88

Query: 113 AEEALHKLNGTVIGKQSVRLSWGRNPANKQFR 144
           A +A+ +  G  +  + + +    +  + +  
Sbjct: 89  ALKAMKQYKGVPLDGRPMDIQLVASQIDLEHH 120

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 77.6 bits (192), Expect = 2e-19
 Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 6/95 (6%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENA 113
           G S ++ ++VG L  N+T++ LR  F  +G+I ++ +         KG GF+ F++ E A
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 114 EEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
             AL +LNG  +  + +R+       +       G
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVTERLDGGSGPSSG 95

>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 = 78.1 bits (193), Expect = 3e-19
 Identities = 24/114 (21%), Positives = 43/114 (37%), Gaps = 14/114 (12%)

Query: 48  SNGAPGQGPQ-------SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-- 98
           S+G+ G+ P        S  +    T+F   L   +   DL   FS  G++  V+I    
Sbjct: 2   SSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 61

Query: 99  ----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
                KG  +V+F   ++   A+  L G  +    + +   +   N+      G
Sbjct: 62  NSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNRLSGPSSG 114

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 77.2 bits (191), Expect = 4e-19
 Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAE 114
           ++   +I+VG +D   T E+L   F   G +  V I         KG  +++F+++E+  
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 115 EALHKLNGTVIGKQSVRLSWGR 136
            +L  L+ ++   + +++   R
Sbjct: 63  TSL-ALDESLFRGRQIKVIPKR 83

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

 Score = 77.3 bits (191), Expect = 4e-19
 Identities = 26/88 (29%), Positives = 43/88 (48%), Gaps = 4/88 (4%)

Query: 64  NTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
            + +F+G L   NV+ EDL + FS YG I  + I      GF+QF N ++  +A+   + 
Sbjct: 10  KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIECESQ 67

Query: 123 TVIGKQSVRLSWGRNPANKQF-RADYGN 149
            +   + + L    + A  QF   D+G 
Sbjct: 68  EMNFGKKLILEVSSSNARPQFDHGDHGT 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 = 78.2 bits (193), Expect = 4e-19
 Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 7/89 (7%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----- 98
           G Y          + + +    +++VG +D   T +DL   FS  G I  + I       
Sbjct: 16  GAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSG 75

Query: 99  -GKGCGFVQFANRENAEEALHKLNGTVIG 126
             KG  +++FA R + + A+  ++ TV  
Sbjct: 76  HPKGYAYIEFAERNSVDAAV-AMDETVFR 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 = 77.4 bits (191), Expect = 5e-19
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCG 103
           G+ G        +   T+F+  L  +  +E L +   Q+G++  V++ +       KGC 
Sbjct: 1   GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60

Query: 104 FVQFANRENAEEALHKLN 121
           F QF  +E A++ L   +
Sbjct: 61  FAQFMTQEAAQKCLAAAS 78

>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 = 77.0 bits (190), Expect = 5e-19
 Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 3/98 (3%)

Query: 43  IGGYASNGAPGQGPQSEGDSSNTTIFVGGLD-PNVTDEDLRQPFSQYGEIASVKIPVGKG 101
           +G    +     G    G    + +F+G L   NV+ EDL + FS YG I  + I     
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NA 58

Query: 102 CGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA 139
            GF+QF N ++  +A+   +  +   + + L    + A
Sbjct: 59  FGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA 96

>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 = 77.3 bits (191), Expect = 5e-19
 Identities = 28/102 (27%), Positives = 50/102 (49%), Gaps = 6/102 (5%)

Query: 53  GQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQ 106
           G    S   S    +FVGGL  +  ++ L Q FS+YG+I+ V +         +G GFV 
Sbjct: 1   GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60

Query: 107 FANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
           F N ++A++A+  +NG  +  + +R+      ++ +     G
Sbjct: 61  FENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSSG 102

>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 = 76.7 bits (189), Expect = 6e-19
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 1/80 (1%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHK 119
           G S ++ I V  L  +   +++      Y  +    +   K   FV   N E A+ A+  
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 120 LNGTVIGKQSVRLSWGRNPA 139
            +      + + +      A
Sbjct: 60  FHQYSFRGKDLIVQLQPTDA 79

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 78.4 bits (193), Expect = 1e-18
 Identities = 17/90 (18%), Positives = 37/90 (41%), Gaps = 5/90 (5%)

Query: 49  NGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCG 103
           +         EG  +   + V  LD  V+D D+++ F+++G +    +         G  
Sbjct: 73  DLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTA 132

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLS 133
            V F  R +A +A+ +  G  +  + + + 
Sbjct: 133 DVHFERRADALKAMKQYKGVPLDGRPMDIQ 162

>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 = 76.6 bits (189), Expect = 1e-18
 Identities = 14/74 (18%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV---GKGCGFVQFANRENAEEALHKL 120
           N  +++  L   +T E++   F +YG I  +++      +G  +V + +  +A+ A+  L
Sbjct: 8   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67

Query: 121 NGTVIGKQSVRLSW 134
           +G  +  + + + +
Sbjct: 68  SGFNVSNRYLVVLY 81

>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 = 76.1 bits (188), Expect = 1e-18
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 8/75 (10%)

Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV---G--KGCGFVQFANRENA 113
           EG     T+FVGG+D  + + ++R  F++YG +  VKI     G  KG GFV F N  + 
Sbjct: 4   EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63

Query: 114 EEAL---HKLNGTVI 125
           ++ +      +G  +
Sbjct: 64  QKIVESQINFHGKKL 78

>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 = 76.2 bits (188), Expect = 1e-18
 Identities = 26/101 (25%), Positives = 46/101 (45%), Gaps = 2/101 (1%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG--KGCGFVQF 107
           G+ G    S     + T+ +  L  + T+E L++ F +   I   +   G  KG  F++F
Sbjct: 1   GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEF 60

Query: 108 ANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
           A+ E+A+EAL+  N   I  +++RL       +       G
Sbjct: 61  ASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSSG 101

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 76.1 bits (188), Expect = 1e-18
 Identities = 26/95 (27%), Positives = 46/95 (48%), Gaps = 6/95 (6%)

Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAE 114
           D S  ++FVG +    T+E L+  FS+ G + S ++         KG GF ++ ++E A 
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 115 EALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGN 149
            A+  LNG     +++R+    +  NK+     G 
Sbjct: 65  SAMRNLNGREFSGRALRVDNAASEKNKEELKSLGT 99

>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 = 76.1 bits (188), Expect = 1e-18
 Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 6/86 (6%)

Query: 56  PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVG--KGCGFVQFANR 110
            +    ++   +F+G L+PN +  +L+   S+      + +     G  +  G+V F + 
Sbjct: 9   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 68

Query: 111 ENAEEALHKLNGTVIGKQSVRLSWGR 136
           E+ E+AL +L G  +    ++L   +
Sbjct: 69  EDLEKAL-ELTGLKVFGNEIKLEKPK 93

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

 Score = 76.2 bits (188), Expect = 1e-18
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-GKGCGFVQFANRENAEEALHKLNGTVI 125
           ++VG L       +L + FS YG + +V I     G  FV+F +  +AE+A+  L+G VI
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62

Query: 126 GKQSVRLSWGRNP 138
               VR+      
Sbjct: 63  CGSRVRVELSTGM 75

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 76.3 bits (188), Expect = 2e-18
 Identities = 26/95 (27%), Positives = 44/95 (46%), Gaps = 7/95 (7%)

Query: 48  SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KG 101
           +  A   G Q EG      +F+  L    TD DL   F  +G + S K+ +       K 
Sbjct: 25  AAAAAAAGKQIEG-PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKC 83

Query: 102 CGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
            GFV F N ++A+ A+  +NG  +G + +++   +
Sbjct: 84  FGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>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 = 79.0 bits (194), Expect = 2e-18
 Identities = 26/153 (16%), Positives = 43/153 (28%), Gaps = 10/153 (6%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYG--EIASVKIPV--- 98
                  AP       G      +++G L    TDEDL +     G  +I  +K      
Sbjct: 50  DDVGKGAAPNVVYTYTGKRIA--LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA 107

Query: 99  ---GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAY 155
               KG   V   +  ++++ +  L    +  Q+  ++        QF            
Sbjct: 108 NGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQ 167

Query: 156 YGGQVYDGYGYAIPPPNDPSMYAAAAAAYGAYP 188
             G+   G          P          GA P
Sbjct: 168 MSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVP 200

>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 = 75.9 bits (187), Expect = 5e-18
 Identities = 26/112 (23%), Positives = 46/112 (41%), Gaps = 8/112 (7%)

Query: 33  QFNIVFLLVLIGGYASNGAPGQGP--QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGE 90
           Q++       +            P   +        + V  +   V +  LRQ F +YG 
Sbjct: 9   QYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGP 68

Query: 91  IASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
           I SVKI         +G GFV+F +  +A++A+  LNG  I  + ++++   
Sbjct: 69  IESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA 120

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 74.6 bits (184), Expect = 6e-18
 Identities = 28/85 (32%), Positives = 40/85 (47%), Gaps = 7/85 (8%)

Query: 57  QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQ-YGEIASVKI---PVG--KGCGFVQFANR 110
            S       ++FVG L P+V D  L + F + Y      K+     G  KG GFV+F + 
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDE 61

Query: 111 ENAEEALHKLNGTV-IGKQSVRLSW 134
              + AL +  G V +G + VRLS 
Sbjct: 62  LEQKRALTECQGAVGLGSKPVRLSV 86

>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 = 74.4 bits (183), Expect = 7e-18
 Identities = 16/102 (15%), Positives = 39/102 (38%), Gaps = 7/102 (6%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIA-SVKIPV-----GKGCG 103
           G+ G   + + +S+     +  +  ++T  D+ Q          +V + V     G G  
Sbjct: 1   GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRA 145
            VQF N ++A ++  +L+   +  +   +        ++   
Sbjct: 61  LVQFKNEDDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEK 101

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 73.9 bits (182), Expect = 7e-18
 Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 5/73 (6%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC-GFVQFANRENAEEA 116
           S G S   ++FV G    V    L + F  +G +ASV +   KG    V+  +    E  
Sbjct: 2   SSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAV 61

Query: 117 L----HKLNGTVI 125
           L    H L G  +
Sbjct: 62  LSQSQHSLGGHRL 74

>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 = 73.8 bits (182), Expect = 8e-18
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 57  QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-GKGCGFVQFANRENAEE 115
                   + +FVG    ++T E+L+Q F QYGE+  V IP   +   FV FA+ + A+ 
Sbjct: 4   SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS 63

Query: 116 AL---HKLNGTVI 125
                  + G  +
Sbjct: 64  LCGEDLIIKGISV 76

>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 = 74.1 bits (182), Expect = 1e-17
 Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 2/89 (2%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 109
           G+ G        S +  + V GL  +V + DL +   ++G I  V +   K    V+F N
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFEN 60

Query: 110 RENAEEALH--KLNGTVIGKQSVRLSWGR 136
            ++A+E +         I  Q    ++  
Sbjct: 61  IDSAKECVTFAADVPVYIAGQQAFFNYST 89

>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 = 73.4 bits (181), Expect = 1e-17
 Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 10/90 (11%)

Query: 46  YASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------G 99
           +  + +      S   SS   +F+GGL    T E LR+ F Q+GE+    +         
Sbjct: 7   HHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRS 66

Query: 100 KGCGFVQFANRENAEEAL----HKLNGTVI 125
           +G GFV F ++   ++ L    H+L+   I
Sbjct: 67  RGFGFVTFMDQAGVDKVLAQSRHELDSKTI 96

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 73.1 bits (180), Expect = 1e-17
 Identities = 22/89 (24%), Positives = 41/89 (46%), Gaps = 3/89 (3%)

Query: 56  PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG--KGCGFVQFANRENA 113
             S+   +  T+    L  N+T+++L++ F    EI  V    G  KG  +++F +  +A
Sbjct: 8   CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-QDGKSKGIAYIEFKSEADA 66

Query: 114 EEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           E+ L +  G  I  +SV L +       +
Sbjct: 67  EKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 73.6 bits (181), Expect = 2e-17
 Identities = 26/113 (23%), Positives = 44/113 (38%), Gaps = 14/113 (12%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS--------VKIPVG-- 99
           G+ G     + DS N+ I+V GL+ +VT +DL   F Q G +          + I +   
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 100 ----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
               KG   V + +   A+ A+   +G       +++S  R           G
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSSG 113

>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 = 72.6 bits (179), Expect = 2e-17
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-GKGCGFVQFANRENAEEAL- 117
           G S ++ +FVG    ++T+++LR+ FSQYG++  V IP   +   FV FA+ + A+    
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 118 --HKLNGTVI 125
               + G  +
Sbjct: 61  EDLIIKGISV 70

>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 = 72.7 bits (179), Expect = 2e-17
 Identities = 25/95 (26%), Positives = 37/95 (38%), Gaps = 14/95 (14%)

Query: 53  GQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS--------VKIPV------ 98
           G        S N TIFV GL  NVT E +   F Q G I +        + +        
Sbjct: 2   GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61

Query: 99  GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS 133
            KG   V F +  +A+ A+   +G       +++S
Sbjct: 62  LKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS 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 = 73.1 bits (180), Expect = 2e-17
 Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 6/86 (6%)

Query: 49  NGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGC 102
           +        S+ D++ T IFVGGL  + TD  LR+ F  +G+I    +         +G 
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGY 61

Query: 103 GFVQFANRENAEEALHKLNGTVIGKQ 128
           GFV  A+R  AE A    N  + G++
Sbjct: 62  GFVTMADRAAAERACKDPNPIIDGRK 87

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 72.5 bits (178), Expect = 4e-17
 Identities = 13/73 (17%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEE 115
           D  N ++++ G   + T +D+++     G++ ++++        KG  FV F + E+A++
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 67

Query: 116 ALHKLNGTVIGKQ 128
            +           
Sbjct: 68  FVETPGQKYKETD 80

>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 = 72.6 bits (178), Expect = 4e-17
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 12/82 (14%)

Query: 66  TIFVGGLDPNVTDEDL---RQPFSQYGEIASVKIPVGK---------GCGFVQFANRENA 113
            +FV GL   + D ++    + F ++G+I  V I                +V +   E+A
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 114 EEALHKLNGTVIGKQSVRLSWG 135
             A+  +N  V+  ++++ S G
Sbjct: 77  LRAIQCVNNVVVDGRTLKASLG 98

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 72.0 bits (177), Expect = 4e-17
 Identities = 15/96 (15%), Positives = 36/96 (37%), Gaps = 16/96 (16%)

Query: 53  GQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYG--EIASVKIP------VGKGCGF 104
           G       D    TI +  + P+   + +    S Y    + ++++         +G  F
Sbjct: 2   GHHHHHHMD----TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAF 57

Query: 105 VQFANRENAEEALHKLNGT----VIGKQSVRLSWGR 136
           VQ ++  +A + L  L        I  +++ + + +
Sbjct: 58  VQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAK 93

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 73.4 bits (180), Expect = 6e-17
 Identities = 23/107 (21%), Positives = 37/107 (34%), Gaps = 9/107 (8%)

Query: 48  SNGAPGQGPQSEGDSS-NTTIFVGGLDPNVTDEDLRQPFSQYG--EIASVKIPV------ 98
           +N  P       G  +    ++VG      TD+ L Q     G  ++  +K         
Sbjct: 38  NNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQ 97

Query: 99  GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRA 145
            KG   V  A+  +  + L  L G V+  + V +         QF A
Sbjct: 98  SKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEA 144

>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 = 72.9 bits (179), Expect = 7e-17
 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 11/94 (11%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----------KGCGFVQFANREN 112
           N  I+V  L  +V ++DL+  F +Y + +S    +            KG  F+   N + 
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 113 AEEALHKLNGTVIGKQSVRLSWGRNPANKQFRAD 146
           A +AL + NG V+  + + + + R+   KQ   +
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFARSARPKQDPKE 138

>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 = 71.4 bits (175), Expect = 9e-17
 Identities = 26/112 (23%), Positives = 45/112 (40%), Gaps = 4/112 (3%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQ 106
            S+G+ G  P      S   + V GL P+ + +DL+    + G++    +    G G V+
Sbjct: 1   GSSGSSGGPPSR---RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVE 56

Query: 107 FANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGG 158
           F  +E+   A+ KL+ T         ++ R   +      YG   S     G
Sbjct: 57  FVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSSG 108

>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 = 71.1 bits (175), Expect = 1e-16
 Identities = 26/106 (24%), Positives = 47/106 (44%), Gaps = 9/106 (8%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------GKGC 102
           G+ G        S   T F+G L  +VT+E +++ F     I++V++P         KG 
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF 59

Query: 103 GFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
           G+ +F + ++   AL  LN   +G + +R+       +K      G
Sbjct: 60  GYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKDSGPSSG 104

>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 = 73.5 bits (181), Expect = 1e-16
 Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 10/85 (11%)

Query: 51  APGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGF 104
           +     +     +   IFVGG+  +  +  LR  F QYG+I  ++I   +      G  F
Sbjct: 91  SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 150

Query: 105 VQFANRENAEEAL----HKLNGTVI 125
           V F + ++ ++ +    H +NG   
Sbjct: 151 VTFDDHDSVDKIVIQKYHTVNGHNC 175

>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 = 71.2 bits (175), Expect = 9e-16
 Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 10/79 (12%)

Query: 57  QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANR 110
             +       +F+GGL    TDE LR  F Q+G +    +          G GFV +A  
Sbjct: 6   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65

Query: 111 ENAEEAL----HKLNGTVI 125
           E  + A+    HK++G V+
Sbjct: 66  EEVDAAMNARPHKVDGRVV 84

>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 = 70.7 bits (174), Expect = 1e-16
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 9/85 (10%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVG---KGCG 103
           G+ G           + + V GL    T++DL++ FS +GE+  V++         KG G
Sbjct: 1   GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60

Query: 104 FVQFANRENAEEAL---HKLNGTVI 125
           FV+F   E   + +   H ++G   
Sbjct: 61  FVRFTEYETQVKVMSQRHMIDGRWC 85

>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 = 70.7 bits (174), Expect = 2e-16
 Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 10/81 (12%)

Query: 55  GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFA 108
           G      S +  IFVGG+  N  + +LR+ F ++G +  V +         +G GF+ F 
Sbjct: 1   GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60

Query: 109 NRENAEEAL----HKLNGTVI 125
           + ++ ++A+    H + G  +
Sbjct: 61  DEQSVDQAVNMHFHDIMGKKV 81

>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 = 72.6 bits (179), Expect = 2e-16
 Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 9/69 (13%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL-- 117
            +F+GGL+ + T+++LR+ F +YG +  +KI          G GF+ F    + +E +  
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64

Query: 118 -HKLNGTVI 125
            H L+G VI
Sbjct: 65  QHILDGKVI 73

>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 = 71.8 bits (177), Expect = 2e-16
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 10/77 (12%)

Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANREN 112
           +       IFVGG+ P+V  ++  + FSQ+G I   ++ +       +G GFV + + + 
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 113 AEEAL----HKLNGTVI 125
            +              I
Sbjct: 142 VDRVCQNKFIDFKDRKI 158

>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 = 71.1 bits (174), Expect = 2e-16
 Identities = 17/95 (17%), Positives = 39/95 (41%), Gaps = 3/95 (3%)

Query: 45  GYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF 104
           G    G+     +S G  S   I +  L  +VT+ ++      +G++ ++ +  GK   F
Sbjct: 13  GLVPRGSHMGDSRSAGVPSRV-IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAF 71

Query: 105 VQFANRENAEEAL--HKLNGTVIGKQSVRLSWGRN 137
           ++    E A   +  +     V+  Q + + +  +
Sbjct: 72  IEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106

>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 = 69.9 bits (172), Expect = 2e-16
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 10/78 (12%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK---GCGFVQFANRE 111
           S+ +     +FVGGL  + + +DL+  F+++GE+    I   P      G GF+ F +  
Sbjct: 5   SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAA 64

Query: 112 NAEEAL----HKLNGTVI 125
           + E+ L    H+L+G VI
Sbjct: 65  SVEKVLDQKEHRLDGRVI 82

>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 = 70.3 bits (173), Expect = 2e-16
 Identities = 29/85 (34%), Positives = 37/85 (43%), Gaps = 10/85 (11%)

Query: 51  APGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK---GCGF 104
           +   G  + G      +FVGGLD + T E LR  FSQYGE+    I          G GF
Sbjct: 3   SGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGF 62

Query: 105 VQFANRENAEEAL----HKLNGTVI 125
           V+F +       L    H L+G  I
Sbjct: 63  VKFKDPNCVGTVLASRPHTLDGRNI 87

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 69.8 bits (171), Expect = 4e-16
 Identities = 15/94 (15%), Positives = 34/94 (36%), Gaps = 2/94 (2%)

Query: 45  GYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGF 104
           G+  +             ++  + + GL   V + DL +   ++G I+ V +   K    
Sbjct: 2   GHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQAL 61

Query: 105 VQFANRENAEEALHKLNGT--VIGKQSVRLSWGR 136
           V+F +   A  A++        I      +++  
Sbjct: 62  VEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST 95

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 69.0 bits (170), Expect = 4e-16
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL--- 117
           IFVGGL  N T ED++  F Q+G++    +         +G GFV F + +  E+     
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 118 -HKLNGTVI 125
            H++N  ++
Sbjct: 62  FHEINNKMV 70

>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 = 68.7 bits (169), Expect = 4e-16
 Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL--- 117
           IFVGGL P+  +E +R+ F  +GE+ S+++P+       +G  F+ F   E  ++ +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 118 -HKLNGTVI 125
            H +  +  
Sbjct: 62  YHNVGLSKC 70

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 69.7 bits (171), Expect = 6e-16
 Identities = 28/120 (23%), Positives = 46/120 (38%), Gaps = 23/120 (19%)

Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS--------VKIPV------GKGCGFVQ 106
           +S N TIFV GL  NVT E +   F Q G I +        + +         KG   V 
Sbjct: 4   NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 107 FANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYDGYGY 166
           F +  +A+ A+   +G       +++    + A    RAD+         G    + + +
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGNPIKV----SFA--TRRADFNRGGGNGRGG---LEHHHH 114

>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 = 68.8 bits (169), Expect = 8e-16
 Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 9/93 (9%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCG 103
           G+ G    +     + T+FV GL  + T+E L++ F         +I         KG G
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFG 57

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
           FV F + E+A+ A   +    I    V L W +
Sbjct: 58  FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90

>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 = 68.7 bits (168), Expect = 1e-15
 Identities = 19/105 (18%), Positives = 37/105 (35%), Gaps = 12/105 (11%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGE-IASVKIP-------VGKGCGFVQFANRENAE 114
            N  +F+GG+      E++ +  ++  E +  V +          +G  FV++ +   A 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 115 EALHKLN--GTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYG 157
            A  KL      +    + + W     +     D     SG   G
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDWAEPEIDVD--EDVMETVSGPSSG 109

>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 = 68.0 bits (167), Expect = 1e-15
 Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 12/84 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYG--EIASVKIPV----G--KGCGFVQFANRENAEEALH 118
           +++G L    TDEDL +     G  +I  +K       G  KG   V   +  ++++ + 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 119 KLNGTVIGKQSVRLSWGRNPANKQ 142
            L    +  Q+  +     P+NK 
Sbjct: 64  LLPKRELHGQNPVV----TPSNKL 83

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 68.3 bits (167), Expect = 1e-15
 Identities = 12/86 (13%), Positives = 32/86 (37%), Gaps = 2/86 (2%)

Query: 51  APGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANR 110
                        +  I +  L  +VT+ ++      +G++ ++ +  GK   F++    
Sbjct: 3   GSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTE 62

Query: 111 ENAEEAL--HKLNGTVIGKQSVRLSW 134
           E A   +  +     V+  Q + + +
Sbjct: 63  EAANTMVNYYTSVTPVLRGQPIYIQF 88

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 68.2 bits (167), Expect = 1e-15
 Identities = 26/114 (22%), Positives = 49/114 (42%), Gaps = 11/114 (9%)

Query: 50  GAPGQ-GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCG 103
           G+ G  G     +  +  + V G+  +  + D+R  F     + +V +         G G
Sbjct: 1   GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNG 59

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYG 157
            V+F + ++  EAL K N  ++ ++ V +S       +Q+ A  G+  SG   G
Sbjct: 60  LVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT---ERQWVAAGGHITSGPSSG 109

>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 = 68.7 bits (168), Expect = 1e-15
 Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 1/87 (1%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 109
           GAP          S   + V GL P+ + +DL+    + G++    +    G G V+F  
Sbjct: 2   GAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVR 60

Query: 110 RENAEEALHKLNGTVIGKQSVRLSWGR 136
           +E+   A+ KL+ T         ++ R
Sbjct: 61  KEDMTYAVRKLDNTKFRSHEGETAYIR 87

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 67.1 bits (165), Expect = 2e-15
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK---GCGFVQFANRENAEEAL--- 117
           +F+GGL    T E LR+ F Q+GE+    +   P+ K   G GFV F ++   ++ L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 118 -HKLNGTVI 125
            H+L+   I
Sbjct: 63  RHELDSKTI 71

>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 = 67.7 bits (166), Expect = 3e-15
 Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 10/85 (11%)

Query: 51  APGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI---PVGK---GCGF 104
                 +         +F+GGL    T+E LR  + Q+G++    +   P  K   G GF
Sbjct: 14  TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 73

Query: 105 VQFANRENAEEAL----HKLNGTVI 125
           V F++    + A+    H ++G V+
Sbjct: 74  VTFSSMAEVDAAMAARPHSIDGRVV 98

>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 = 4e-15
 Identities = 25/89 (28%), Positives = 44/89 (49%), Gaps = 7/89 (7%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIA-SVKIPVG-----KGCG 103
           G+ G    S   +++  + + GL    + E++ Q FS    +   + +PV       G  
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRL 132
           FVQFA++E AE+AL K +   IG + + +
Sbjct: 61  FVQFASQEIAEKALKK-HKERIGHRYIEI 88

>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 = 67.6 bits (165), Expect = 6e-15
 Identities = 21/94 (22%), Positives = 35/94 (37%), Gaps = 7/94 (7%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---- 99
           GG       G    +   ++   + + GL    T+ D+   FS       V I +G    
Sbjct: 26  GGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGR 84

Query: 100 -KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL 132
             G   V+FA  E A  A+ K +   +  + + L
Sbjct: 85  VTGEADVEFATHEEAVAAMSK-DRANMQHRYIEL 117

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 66.5 bits (163), Expect = 7e-15
 Identities = 24/105 (22%), Positives = 42/105 (40%), Gaps = 8/105 (7%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCG 103
           G+ G   +        T +VG L  N    D+   F     I SV++         KG  
Sbjct: 1   GSSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFC 59

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
           +V+F   ++ +EAL   +G ++G +S+R+         +     G
Sbjct: 60  YVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDKSGPSSG 103

>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 = 66.1 bits (162), Expect = 7e-15
 Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 9/82 (10%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------GKGCGFVQFANRENAEEALH 118
           T F+G L  +VT+E +++ F     I++V++P         KG G+ +F + ++   AL 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL- 78

Query: 119 KLNGTVIGKQSVRLSWGRNPAN 140
            LN   +G + +R+       +
Sbjct: 79  SLNEESLGNRRIRVDVADQAQD 100

>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 = 65.8 bits (161), Expect = 8e-15
 Identities = 18/92 (19%), Positives = 41/92 (44%), Gaps = 7/92 (7%)

Query: 55  GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFAN 109
           G      ++  T+ + G   NVT++++ +  +      +++I         G  FV F+N
Sbjct: 1   GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSN 59

Query: 110 RENAEEALHKLNGTVIGKQSVRLSWGRNPANK 141
            E  ++AL K N   +G + + +   ++  + 
Sbjct: 60  EEEVKQAL-KCNREYMGGRYIEVFREKSGPSS 90

>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 = 66.4 bits (162), Expect = 8e-15
 Identities = 13/87 (14%), Positives = 35/87 (40%), Gaps = 2/87 (2%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 109
           G+ G        + +  + +  L   VT+ ++      +G++ ++ +  GK   F++ A 
Sbjct: 1   GSSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELAT 60

Query: 110 RENAEEAL--HKLNGTVIGKQSVRLSW 134
            E A   +  +      +  Q + + +
Sbjct: 61  EEAAITMVNYYSAVTPHLRNQPIYIQY 87

>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 = 66.8 bits (163), Expect = 1e-14
 Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 7/96 (7%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI-ASVKIPVG--- 99
                    G+G  S   +++  + + GL    T E++ Q FS    +   + +PV    
Sbjct: 22  ASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEG 81

Query: 100 --KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS 133
              G  FVQFA++E AE+AL   +   IG + + + 
Sbjct: 82  KITGEAFVQFASQELAEKAL-GKHKERIGHRYIEVF 116

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 65.5 bits (160), Expect = 1e-14
 Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 12/76 (15%)

Query: 64  NTTIFVGGLDPNVTDE-------DLRQPFSQYGEIASVKIPV----GKGCGFVQFANREN 112
           ++ I V  + P V  +        + + FS++G+I +   P      KG  F+++A+  +
Sbjct: 1   DSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAH 59

Query: 113 AEEALHKLNGTVIGKQ 128
           A +A+   +G  + KQ
Sbjct: 60  AVDAVKNADGYKLDKQ 75

>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 = 65.9 bits (161), Expect = 1e-14
 Identities = 22/88 (25%), Positives = 36/88 (40%), Gaps = 7/88 (7%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGF 104
           G+ G    S   ++   + + GL    T+ D+   FS       V I +G      G   
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEAD 59

Query: 105 VQFANRENAEEALHKLNGTVIGKQSVRL 132
           V+FA  E+A  A+ K +   +  + V L
Sbjct: 60  VEFATHEDAVAAMAK-DKANMQHRYVEL 86

>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 = 70.3 bits (171), Expect = 1e-14
 Identities = 27/132 (20%), Positives = 50/132 (37%), Gaps = 8/132 (6%)

Query: 52  PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFV 105
           P   P ++GD+  T +FV  ++ + T+  LR+ F  YG I  + +         +G  F+
Sbjct: 91  PHNDPNAQGDAFKT-LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149

Query: 106 QFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFR-ADYGNQWSGAYYGGQVYDGY 164
           ++ +  +   A    +G  I  + V +   R    K +R    G    G   GG   +  
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIR 209

Query: 165 GYAIPPPNDPSM 176
                  +    
Sbjct: 210 HSGRDDTSRYDE 221

>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 = 65.3 bits (160), Expect = 2e-14
 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 7/64 (10%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 119
            I+VG L  + T E +++ FSQ+G++ +VK+         KG GFV+    E+  EA+ K
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 120 LNGT 123
           L+ T
Sbjct: 62  LDNT 65

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 65.1 bits (159), Expect = 2e-14
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 12/82 (14%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDE-------DLRQPFSQYGEIASVKIPV----GKGCGFVQ 106
            E D  ++ I V  + P V  +        + + FS++G+I +   P      KG  F++
Sbjct: 9   QEADGIDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLE 67

Query: 107 FANRENAEEALHKLNGTVIGKQ 128
           +A+  +A +A+   +G  + KQ
Sbjct: 68  YASPAHAVDAVKNADGYKLDKQ 89

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 64.1 bits (156), Expect = 6e-14
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 3/97 (3%)

Query: 45  GYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI---ASVKIPVGKG 101
            ++S   P     S+  +    I +  L    + +DL+    +       +SV      G
Sbjct: 9   HHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG 68

Query: 102 CGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP 138
            G ++F + E   EAL +LN        + +    NP
Sbjct: 69  TGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP 105

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 63.7 bits (155), Expect = 1e-13
 Identities = 16/93 (17%), Positives = 36/93 (38%), Gaps = 7/93 (7%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIA-SVKIPVG-----K 100
            S     +        +   +++ GL     ++ +   F +   +  S+ I  G      
Sbjct: 8   KSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT 67

Query: 101 GCGFVQFANRENAEEALHKLNGTVIGKQSVRLS 133
           G GFV+F N  + + AL   +   +G + +++ 
Sbjct: 68  GEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVH 99

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 60.1 bits (146), Expect = 1e-12
 Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 12/77 (15%)

Query: 64  NTTIFVGGL------DPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRE 111
           +  I V G          V  + L   FS+ G++ +++ P+       KG  FV+  +  
Sbjct: 6   DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMN 65

Query: 112 NAEEALHKLNGTVIGKQ 128
           +A++ +   +G  +  +
Sbjct: 66  DAKKIIKSFHGKRLDLK 82

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 60.7 bits (147), Expect = 2e-12
 Identities = 23/98 (23%), Positives = 38/98 (38%), Gaps = 10/98 (10%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI----ASVKIPVG 99
            G +  G   +  Q     +   + + GL    T E++   F Q+  I      +     
Sbjct: 3   SGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY 62

Query: 100 -----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL 132
                 G  FV FA  E A+ AL K +  ++GK+ + L
Sbjct: 63  PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL 99

>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 = 58.4 bits (141), Expect = 1e-11
 Identities = 19/93 (20%), Positives = 38/93 (40%), Gaps = 10/93 (10%)

Query: 48  SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQY---GEIASVKIPVG----- 99
           S+G+ G     EG      + + GL  + + ED++   S       +A V          
Sbjct: 2   SSGSSGMMLGPEGGE-GYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQ 60

Query: 100 KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL 132
            G  FV+  + ++ + AL K +   +G + + +
Sbjct: 61  SGEAFVELESEDDVKLALKK-DRESMGHRYIEV 92

>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 = 57.6 bits (139), Expect = 2e-11
 Identities = 16/87 (18%), Positives = 36/87 (41%), Gaps = 10/87 (11%)

Query: 55  GPQSEGDSSN-TTIFVGGLDPNVTDEDLRQPFSQY---GEIASVKIPVG-----KGCGFV 105
           G + E +  +   I   GL  + T ED+   FS          +   +      +G   +
Sbjct: 1   GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALI 60

Query: 106 QFANRENAEEALHKLNGTVIGKQSVRL 132
           +  + ++ ++AL K +   +G++ V +
Sbjct: 61  EMESEQDVQKALEK-HRMYMGQRYVEV 86

>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 = 56.3 bits (136), Expect = 3e-11
 Identities = 14/76 (18%), Positives = 34/76 (44%), Gaps = 12/76 (15%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQY-----------GEIASVKIPVGKGCGFVQFANRENAEE 115
           ++VG +   +T+E +   F+               + +V+I   K   F++F + +   +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 116 ALHKLNGTVIGKQSVR 131
           A+   +G +   QS++
Sbjct: 69  AM-AFDGIIFQGQSLK 83

>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 = 55.8 bits (134), Expect = 6e-11
 Identities = 21/92 (22%), Positives = 45/92 (48%), Gaps = 8/92 (8%)

Query: 58  SEGDSSNT-TIFVGGLDPNVTDEDLRQP----FSQYGEIASVKIPV---GKGCGFVQFAN 109
           S G S N   + V  +D  ++ ++L+Q     F+++G++ SV++      +    VQ  N
Sbjct: 2   SSGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMEN 61

Query: 110 RENAEEALHKLNGTVIGKQSVRLSWGRNPANK 141
            ++A  A++ L+   IG + + +S     +  
Sbjct: 62  LQDAIGAVNSLHRYKIGSKKILVSLATGASGP 93

>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 = 57.5 bits (138), Expect = 1e-10
 Identities = 12/70 (17%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALH 118
           N ++++ G   + T +D+++     G++ ++++        KG  FV F + E+A++ + 
Sbjct: 109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 168

Query: 119 KLNGTVIGKQ 128
                     
Sbjct: 169 TPGQKYKETD 178

>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 = 56.3 bits (135), Expect = 2e-10
 Identities = 35/144 (24%), Positives = 58/144 (40%), Gaps = 14/144 (9%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV--GKGCGF 104
           AS  A   G    G S    I V  L   VT + L Q FS++G +  +       +    
Sbjct: 29  ASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQAL 88

Query: 105 VQFANRENAEEALHKLNGTVI--GKQSVRLSWGRNPANKQFRADYGNQWSGAYYGGQVYD 162
           +Q+A+  +A+ A   L+G  I     ++R+ + +   +   +  Y N  S  Y    +  
Sbjct: 89  LQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK-LTSLNVK--YNNDKSRDYTRPDLPS 145

Query: 163 GYGYAIPPPNDPSMYAAAAAAYGA 186
           G        + PS+    AAA+G 
Sbjct: 146 G-------DSQPSLDQTMAAAFGL 162

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 54.6 bits (131), Expect = 3e-10
 Identities = 23/77 (29%), Positives = 31/77 (40%), Gaps = 11/77 (14%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPF-----SQYGEIASVKIPVGKGCGFVQFANREN 112
           S G S    + V GL P V DE L   F     S  G + S +       G + F    +
Sbjct: 2   SSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCG--GVLTFREPAD 59

Query: 113 AEEAL----HKLNGTVI 125
           AE  L    H+L+G  +
Sbjct: 60  AERVLAQADHELHGAQL 76

>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 = 54.2 bits (130), Expect = 6e-10
 Identities = 15/94 (15%), Positives = 31/94 (32%), Gaps = 9/94 (9%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQY---GEIASVKIPVG---- 99
                 G             + + GL  + + ED++   S        A V         
Sbjct: 27  GQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR 86

Query: 100 -KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL 132
             G  FV+  + ++ + AL K +   +G + + +
Sbjct: 87  QSGEAFVELGSEDDVKMALKK-DRESMGHRYIEV 119

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 53.4 bits (128), Expect = 6e-10
 Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 8/70 (11%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG--------KGCGFVQFAN 109
           S G S +  +FVGGL P++ ++++   F ++G +                KG  F+ F  
Sbjct: 2   SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61

Query: 110 RENAEEALHK 119
             + +  +  
Sbjct: 62  ESSVQALIDA 71

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 53.5 bits (128), Expect = 9e-10
 Identities = 24/96 (25%), Positives = 41/96 (42%), Gaps = 4/96 (4%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV--GKGCGF 104
           AS  A   G    G S    I V  L   VT + L Q FS++G +  +       +    
Sbjct: 11  ASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQAL 70

Query: 105 VQFANRENAEEALHKLNGTVI--GKQSVRLSWGRNP 138
           +Q+A+  +A+ A   L+G  I     ++R+ + +  
Sbjct: 71  LQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 106

>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 = 50.3 bits (120), Expect = 1e-08
 Identities = 16/93 (17%), Positives = 32/93 (34%), Gaps = 4/93 (4%)

Query: 44  GGYASNGAPGQGPQSEGDSSNTTIFVGGL-DPNVTDEDLRQPFSQYGEIASVKIPVGKGC 102
            G    G P Q    + +     I +  L     +D  + +    YG+I +  +   K  
Sbjct: 6   SGKKPEGKPDQKFDQKQELGRV-IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQ 64

Query: 103 GFVQFANRENAEEAL--HKLNGTVIGKQSVRLS 133
            F++   RE+A   +            + V++ 
Sbjct: 65  AFIEMETREDAMAMVDHCLKKALWFQGRCVKVD 97

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 121

 Score = 49.2 bits (117), Expect = 3e-08
 Identities = 23/64 (35%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 68  FVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGK 127
           F G LD     EDL   FS +GEI  +    G   G + F  +E A+EAL K      G 
Sbjct: 23  FSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILF--KEKAKEALGKAKDANNGN 80

Query: 128 QSVR 131
             +R
Sbjct: 81  LQLR 84

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 46.6 bits (110), Expect = 1e-07
 Identities = 14/71 (19%), Positives = 29/71 (40%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHK 119
               ++ + +  L   +    LR    Q+G + S    + +G    ++  RE A +A   
Sbjct: 3   MAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMA 62

Query: 120 LNGTVIGKQSV 130
           LN  V+   ++
Sbjct: 63  LNNCVLANTTI 73

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A* Length = 345

 Score = 47.1 bits (111), Expect = 1e-06
 Identities = 14/65 (21%), Positives = 26/65 (40%)

Query: 70  GGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQS 129
           GGL   V+   L     + G + ++ +P  K   F ++   E ++ A   LNG  +    
Sbjct: 26  GGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDL 85

Query: 130 VRLSW 134
            +   
Sbjct: 86  GQKIT 90

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 8/46 (17%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 79  EDLRQPFSQYGEIASVKIPVGKGCG--FVQFANRENAEEALHKLNG 122
           +D+ +  +++G +  + +      G  +V+  +   A  A++ L+G
Sbjct: 32  DDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHG 77

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 45.1 bits (106), Expect = 1e-06
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 1/75 (1%)

Query: 52  PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIA-SVKIPVGKGCGFVQFANR 110
           PG      G +    + +      +T + L    +  G++   V          V+F + 
Sbjct: 13  PGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESV 72

Query: 111 ENAEEALHKLNGTVI 125
             A++A   LNG  I
Sbjct: 73  LCAQKAKAALNGADI 87

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 44.0 bits (103), Expect = 2e-06
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 75  NVTDEDLRQPFSQYGEIASVKIPVGK-GCGFVQFANRENAEEALHKLNGTVIGKQSVRLS 133
             + + L +   +YGE+ ++ +   K G   V+FA  + AE A+    G V     +++S
Sbjct: 28  GYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVGLVDNP--LKIS 85

Query: 134 WGRNPANKQ 142
           W        
Sbjct: 86  WLEGQPQDA 94

>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 Length = 119

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 52  PGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRE 111
            G    SE    +T + V G         L Q F+QYG I    +        +++ ++ 
Sbjct: 12  QGDSLTSEDHLDDTWVTVFGFPQASASYILLQ-FAQYGNILKHVMSNTGNWMHIRYQSKL 70

Query: 112 NAEEALHKLNGTVIG 126
            A +AL K +G + G
Sbjct: 71  QARKALSK-DGRIFG 84

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 41.7 bits (98), Expect = 1e-05
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 8/52 (15%)

Query: 79  EDLRQPFSQYGEIASVKIPVGK--------GCGFVQFANRENAEEALHKLNG 122
           ED+R   S+YG + S++IP           G  FV+F +  + ++A+  L G
Sbjct: 30  EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81

>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 = 40.6 bits (95), Expect = 3e-05
 Identities = 15/88 (17%), Positives = 32/88 (36%), Gaps = 3/88 (3%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDE-DLRQPFSQYGEIASVKIPVGKGCGFVQFA 108
           G+ G   Q     +   + +            L Q    +G I++  I       F++ A
Sbjct: 1   GSSGSSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMA 60

Query: 109 NRENAEEAL--HKLNGTVIGKQSVRLSW 134
             E+A+ A+  +     ++  + VR+  
Sbjct: 61  TTEDAQAAVDYYTTTPALVFGKPVRVHL 88

>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 = 40.5 bits (95), Expect = 4e-05
 Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 79  EDLRQPFSQYGEIASVKIPVG--KGCGFVQFANRENAEEALHKLNG 122
           EDLR   S++G+I  + +      G   V F + E A+  +  L+G
Sbjct: 41  EDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDG 86

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118

 Score = 40.1 bits (94), Expect = 6e-05
 Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 10/54 (18%)

Query: 79  EDLRQPFSQYGEIASVKIPV----------GKGCGFVQFANRENAEEALHKLNG 122
            ++ +   ++G +  V I                 FV+F+      +A+  LNG
Sbjct: 40  GEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG 93

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 39.5 bits (92), Expect = 7e-05
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 17/76 (22%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPF------------SQYGEIASVKI-----PVGKGCGFVQ 106
           N++    GL   V+D ++++ +             +YGE+  + +         G  +V+
Sbjct: 15  NSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVK 74

Query: 107 FANRENAEEALHKLNG 122
           F   E+AE+A+  LN 
Sbjct: 75  FRREEDAEKAVIDLNN 90

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	198
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.88
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.88
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.88
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.87
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.87
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.87
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.87
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.87
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.87
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.87
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.87
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.86
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.86
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.86
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.86
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.86
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.85
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.85
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.85
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.85
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.85
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.85
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.85
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.85
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.85
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.85
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.85
1x5p_A	97	Negative elongation factor E; structure genomics,	99.85
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.85
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.85
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.85
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.85
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.85
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.85
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.85
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.84
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.84
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.84
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.84
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.84
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.84
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.84
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.84
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.84
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.84
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.84
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.84
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.84
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.84
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.84
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.84
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.84
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.84
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.84
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.83
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.83
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.83
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.83
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.83
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.83
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.83
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.83
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.83
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.83
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.83
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.82
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.82
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.82
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.82
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.82
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.82
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.82
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.82
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.82
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.82
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.82
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.82
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.82
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.82
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.82
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.81
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.81
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.81
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.81
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.81
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.81
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.81
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.81
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.81
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.81
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.81
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.81
2div_A	99	TRNA selenocysteine associated protein; structural	99.8
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.8
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.8
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.8
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.8
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.8
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.8
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.8
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.8
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.8
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.79
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.79
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.79
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.79
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.79
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.79
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.79
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.79
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.79
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.79
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.79
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.79
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.79
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.79
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.79
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.78
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.78
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.78
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.78
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.78
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.78
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.78
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.78
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.78
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.78
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.78
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.78
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.78
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.78
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.77
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.77
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.77
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.77
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.76
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.76
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.62
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.76
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.76
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.76
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.76
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.75
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.75
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.75
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.75
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.74
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.74
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.74
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.74
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.73
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.73
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.73
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.72
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.72
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.72
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.71
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.71
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.71
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.7
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.7
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.7
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.7
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.69
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.69
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.69
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.69
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.68
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.67
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.67
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.67
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.67
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.66
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.65
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.65
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.64
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.64
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.64
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.64
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.64
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.63
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.63
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.63
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.62
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.62
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.62
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.61
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.6
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.6
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.6
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.6
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.58
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.58
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.58
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.57
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.56
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.53
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.51
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.5
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.48
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.45
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.42
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.36
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.36
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.16
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.91
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.81
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.3
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.23
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.87
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.62
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.57
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.26
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.23
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	97.07
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.98
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.52
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	94.46
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	93.26

>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=99.88  E-value=1.4e-21  Score=136.52  Aligned_cols=82  Identities=22%  Similarity=0.380  Sum_probs=75.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCC-----eEeEEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGK-----QSVRLS  133 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g-----~~l~v~  133 (198)
                      ......++|||+|||+++++++|+++|++||.|.+|+|+.+ +||||+|.+.++|++||+.||+..|+|     +.|+|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~   88 (108)
T 1x4c_A           10 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   88 (108)
T ss_dssp             CCCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEE
Confidence            33456889999999999999999999999999999999988 999999999999999999999999999     999999


Q ss_pred             eccCCCCC
Q 029166          134 WGRNPANK  141 (198)
Q Consensus       134 ~a~~~~~~  141 (198)
                      +++++...
T Consensus        89 ~a~~~~~~   96 (108)
T 1x4c_A           89 VDGPRSPS   96 (108)
T ss_dssp             ESSCCSCC
T ss_pred             eCCCCCCC
Confidence            99986544

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.88  E-value=5.7e-23  Score=162.12  Aligned_cols=134  Identities=22%  Similarity=0.313  Sum_probs=98.4

Q ss_pred             ccchhhhc--chhhhhhhhhhhhccCCCCccccchhhhhh-h-----hcCCCCCCC-CCCCCCCCCCCCCCCeEEEcCCC
Q 029166            3 KRRHCCER--KGEREERTLLYKLCFHRNSSYCQFNIVFLL-V-----LIGGYASNG-APGQGPQSEGDSSNTTIFVGGLD   73 (198)
Q Consensus         3 ~~~~~c~~--~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~-~-----~~~~~~~~~-~~~~~~~~~~~~~~~~lfV~~l~   73 (198)
                      .++++|+|  +++|.+    +..|+++|..-...+..... .     ..+...... ....+.....+...++|||+||+
T Consensus        68 ~~~~~C~ffakG~C~~----G~~C~y~H~lPt~~d~~~~~~~~~~~D~fGr~k~~~~~d~~~g~gs~~~~~rtLfVgnL~  143 (240)
T 3u1l_A           68 GQLFFCLFFAKGMCCL----GPKCEYLHHIPDEEDIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGID  143 (240)
T ss_dssp             TCCSBCHHHHTTCCSC----GGGCSSBBSCCCHHHHHHHHHHCSSBCTTSSBCGGGTC---------CCCCCEEEEECTT
T ss_pred             CCCeEcCccccCCCCC----CCCCCccCCCCCccchhhhcccccCcccccchhcccchhcccCcCccccCCceeecCCCC
Confidence            46899999  999999    99999998754433322111 0     001110000 00111122345678999999999


Q ss_pred             CCC---------CHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCcee------------CCeEeEE
Q 029166           74 PNV---------TDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI------------GKQSVRL  132 (198)
Q Consensus        74 ~~~---------~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~------------~g~~l~v  132 (198)
                      ..+         +|++|+++|++||+|.+|+|+.+||||||+|.+.++|+.|++.|++..|            .|+.|.|
T Consensus       144 ~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V  223 (240)
T 3u1l_A          144 GALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLV  223 (240)
T ss_dssp             GGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEE
T ss_pred             hhhhcccccccCcHHHHHHHHHccCCEEEEEEECCCCEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEE
Confidence            998         7999999999999999999999999999999999999999999999999            8999999


Q ss_pred             EeccCCCC
Q 029166          133 SWGRNPAN  140 (198)
Q Consensus       133 ~~a~~~~~  140 (198)
                      +||+...+
T Consensus       224 ~wA~~~pn  231 (240)
T 3u1l_A          224 KWANEDPD  231 (240)
T ss_dssp             EECC----
T ss_pred             EEccCCCC
Confidence            99986544

>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=99.88  E-value=2.4e-21  Score=133.86  Aligned_cols=84  Identities=14%  Similarity=0.248  Sum_probs=75.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHh--CCceeCCeEeEEEec
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL--NGTVIGKQSVRLSWG  135 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l--~~~~~~g~~l~v~~a  135 (198)
                      .....+.++|||+|||+.+++++|+++|++||.|.+|.|+++|+||||+|.+.++|++|++.|  ++..|.|+.|.|+|+
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a   88 (101)
T 2cq1_A            9 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYS   88 (101)
T ss_dssp             CCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEC
T ss_pred             CccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEc
Confidence            344456789999999999999999999999999999999999999999999999999999976  577899999999999


Q ss_pred             cCCCCC
Q 029166          136 RNPANK  141 (198)
Q Consensus       136 ~~~~~~  141 (198)
                      +.+..+
T Consensus        89 ~~~~~~   94 (101)
T 2cq1_A           89 NHKELK   94 (101)
T ss_dssp             SCSSCC
T ss_pred             CcccCc
Confidence            876544

>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=99.87  E-value=3.7e-21  Score=132.97  Aligned_cols=87  Identities=33%  Similarity=0.513  Sum_probs=78.9

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .......+.++|||+|||+++++++|+++|++||.|.+|+|+.+    ++||||+|.+.++|++|++.||+..|+|+.|+
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cq3_A            7 GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE   86 (103)
T ss_dssp             CCSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34455667899999999999999999999999999999999876    79999999999999999999999999999999


Q ss_pred             EEeccCCCCCC
Q 029166          132 LSWGRNPANKQ  142 (198)
Q Consensus       132 v~~a~~~~~~~  142 (198)
                      |++++++....
T Consensus        87 v~~a~~~~~~~   97 (103)
T 2cq3_A           87 VNNATARVMTN   97 (103)
T ss_dssp             EEECCSSCCCC
T ss_pred             EEEcccCCCCC
Confidence            99998865443

>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=99.87  E-value=1.7e-21  Score=133.80  Aligned_cols=84  Identities=29%  Similarity=0.532  Sum_probs=77.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ......+.++|||+|||+.+++++|+++|++||.|.+|++.++++||||+|.+.++|++|++.|++..|+|+.|+|+|++
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpj_A            8 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   87 (99)
T ss_dssp             CSCCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcC
Confidence            34445667899999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      ++..
T Consensus        88 ~~~~   91 (99)
T 2cpj_A           88 HSAS   91 (99)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7543

>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=99.87  E-value=1e-21  Score=135.86  Aligned_cols=79  Identities=15%  Similarity=0.188  Sum_probs=73.0

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCC--ceeCCeEeEEEeccC
Q 029166           61 DSSNTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG--TVIGKQSVRLSWGRN  137 (198)
Q Consensus        61 ~~~~~~lfV~~l~~-~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~--~~~~g~~l~v~~a~~  137 (198)
                      ..+.++|||+|||+ +++|++|+++|++||.|.+|.|+++++||||+|++.++|++|++.|++  ..|.|+.|.|+||+.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   91 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   91 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCC
Confidence            34678999999999 999999999999999999999999999999999999999999998875  469999999999986


Q ss_pred             CC
Q 029166          138 PA  139 (198)
Q Consensus       138 ~~  139 (198)
                      ..
T Consensus        92 ~~   93 (102)
T 1x4d_A           92 YK   93 (102)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>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=6.6e-22  Score=137.14  Aligned_cols=82  Identities=16%  Similarity=0.282  Sum_probs=74.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhC--CceeCCeEeEEEeccCC
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN--GTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~--~~~~~g~~l~v~~a~~~  138 (198)
                      ..+.++|||+|||++++|++|+++|++||.|++|+|+++||||||+|++.++|++|++.|+  +..|+|+.|+|+||+++
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~   92 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK   92 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCC
Confidence            3457899999999999999999999999999999999999999999999999999999886  47899999999999876


Q ss_pred             CCCC
Q 029166          139 ANKQ  142 (198)
Q Consensus       139 ~~~~  142 (198)
                      ....
T Consensus        93 ~~~~   96 (105)
T 1sjq_A           93 ELKT   96 (105)
T ss_dssp             SCCC
T ss_pred             CCCc
Confidence            5443

>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=99.87  E-value=4.5e-21  Score=132.69  Aligned_cols=81  Identities=30%  Similarity=0.573  Sum_probs=74.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      ...+.++|||+|||+++++++|+++|++||.|.+|+++  ++||||+|.+.++|++|++.||+..|+|+.|+|+|++++.
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   84 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPD   84 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCc
Confidence            34457899999999999999999999999999999987  6799999999999999999999999999999999998766


Q ss_pred             CCC
Q 029166          140 NKQ  142 (198)
Q Consensus       140 ~~~  142 (198)
                      .+.
T Consensus        85 ~~~   87 (103)
T 2dgu_A           85 QKR   87 (103)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            543

>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=99.87  E-value=4.6e-21  Score=132.52  Aligned_cols=85  Identities=32%  Similarity=0.501  Sum_probs=77.4

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ........++|||+|||+.+++++|+++|++||.|.+|+|+.+    ++||||+|.+.++|++|++.|++..|.|+.|+|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A            8 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CCCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            3445567899999999999999999999999999999999884    699999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 029166          133 SWGRNPANK  141 (198)
Q Consensus       133 ~~a~~~~~~  141 (198)
                      +|++++..+
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cqi_A           88 NWATTPSSQ   96 (103)
T ss_dssp             EECCCTTCC
T ss_pred             EECCCCccc
Confidence            999986543

>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=99.87  E-value=2.5e-21  Score=134.49  Aligned_cols=84  Identities=21%  Similarity=0.278  Sum_probs=75.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCC--ceeCCeEeEEEec
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG--TVIGKQSVRLSWG  135 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~--~~~~g~~l~v~~a  135 (198)
                      .....+.++|||+|||++++|++|+++|++||.|.+|.|+++|+||||+|.+.++|++|++.|++  ..|+|+.|.|+|+
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a   88 (104)
T 1wex_A            9 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEc
Confidence            34455678999999999999999999999999999999999999999999999999999998865  4599999999999


Q ss_pred             cCCCCC
Q 029166          136 RNPANK  141 (198)
Q Consensus       136 ~~~~~~  141 (198)
                      +.+..+
T Consensus        89 ~~~~~~   94 (104)
T 1wex_A           89 TSKRIT   94 (104)
T ss_dssp             SSSSCC
T ss_pred             cCcccc
Confidence            876543

>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=99.87  E-value=8.9e-22  Score=135.56  Aligned_cols=77  Identities=32%  Similarity=0.557  Sum_probs=71.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ....++|||+|||+++|+++|+++|++||.|.+|+|+++      +|||||+|.+.++|++|++.||+..|+|+.|+|+|
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999999864      58999999999999999999999999999999999


Q ss_pred             ccC
Q 029166          135 GRN  137 (198)
Q Consensus       135 a~~  137 (198)
                      |+|
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            975

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=3.3e-21  Score=133.24  Aligned_cols=87  Identities=29%  Similarity=0.541  Sum_probs=78.2

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .......+.++|||+|||+++++++|+++|++||.|.+|+|+.+    ++||||+|.+.++|++|++.||+..|+|+.|+
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2d9p_A            7 GDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY   86 (103)
T ss_dssp             CCCCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            33445557889999999999999999999999999999999854    79999999999999999999999999999999


Q ss_pred             EEeccCCCCCC
Q 029166          132 LSWGRNPANKQ  142 (198)
Q Consensus       132 v~~a~~~~~~~  142 (198)
                      |+|++++..+.
T Consensus        87 V~~a~~~~~~~   97 (103)
T 2d9p_A           87 VALAQRKEERQ   97 (103)
T ss_dssp             EEECSSCCCCC
T ss_pred             EEEecccccCC
Confidence            99999865543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.86  E-value=4.1e-21  Score=133.49  Aligned_cols=86  Identities=24%  Similarity=0.531  Sum_probs=78.2

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-------CcEEEEEeCCHHHHHHHHHHh-CCceeCC
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-------KGCGFVQFANRENAEEALHKL-NGTVIGK  127 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-------kg~afV~f~~~~~a~~a~~~l-~~~~~~g  127 (198)
                      .........++|||+|||+++++++|+++|++||.|.+|+|+.+       ++||||+|.+.++|++|++.| |+..|+|
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g   86 (107)
T 2cph_A            7 GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG   86 (107)
T ss_dssp             CSSCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS
T ss_pred             cccccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECC
Confidence            34455667899999999999999999999999999999999876       799999999999999999999 9999999


Q ss_pred             eEeEEEeccCCCCC
Q 029166          128 QSVRLSWGRNPANK  141 (198)
Q Consensus       128 ~~l~v~~a~~~~~~  141 (198)
                      +.|+|+|++++...
T Consensus        87 ~~l~v~~a~~~~~~  100 (107)
T 2cph_A           87 RRLVLEWADSEVTV  100 (107)
T ss_dssp             CBCEEEECCCCCCC
T ss_pred             CEEEEEeCCCCCCC
Confidence            99999999976543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.86  E-value=1.2e-20  Score=133.01  Aligned_cols=86  Identities=31%  Similarity=0.672  Sum_probs=77.8

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQS  129 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~  129 (198)
                      .......+.++|||+|||+.+++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.|++..|+|+.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (115)
T 2dgo_A            7 GQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ   86 (115)
T ss_dssp             SSCCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEE
T ss_pred             cCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            34455567889999999999999999999999999999999875      589999999999999999999999999999


Q ss_pred             eEEEeccCCCCC
Q 029166          130 VRLSWGRNPANK  141 (198)
Q Consensus       130 l~v~~a~~~~~~  141 (198)
                      |+|+|++++...
T Consensus        87 l~V~~a~~~~~~   98 (115)
T 2dgo_A           87 IRTNWATRKPPA   98 (115)
T ss_dssp             CEEEESSCCCCC
T ss_pred             EEEEEccCCCCC
Confidence            999999876544

>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=99.86  E-value=5.2e-21  Score=130.88  Aligned_cols=82  Identities=23%  Similarity=0.531  Sum_probs=76.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeC--CeEeEEEecc
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG--KQSVRLSWGR  136 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~--g~~l~v~~a~  136 (198)
                      ....+.++|||+|||+++++++|+++|++||.|.+|++..+++||||+|.+.++|++|++.||+..|+  ++.|+|+|++
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~   91 (97)
T 1why_A           12 GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECC
Confidence            34456789999999999999999999999999999999999999999999999999999999999999  9999999999


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      ++..
T Consensus        92 ~~~~   95 (97)
T 1why_A           92 SGPS   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=6.2e-21  Score=131.54  Aligned_cols=84  Identities=26%  Similarity=0.542  Sum_probs=76.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ....+.++|||+|||+.+++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.||+..|+|+.|+|
T Consensus         7 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2cqb_A            7 GMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV   86 (102)
T ss_dssp             CSCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            34456789999999999999999999999999999999764      799999999999999999999999999999999


Q ss_pred             EeccCCCCCC
Q 029166          133 SWGRNPANKQ  142 (198)
Q Consensus       133 ~~a~~~~~~~  142 (198)
                      +|++++..+.
T Consensus        87 ~~a~~~~~~~   96 (102)
T 2cqb_A           87 NLAKPMRIKE   96 (102)
T ss_dssp             EECCCCCCCC
T ss_pred             EeCCCCCCCC
Confidence            9999865543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.85  E-value=4.2e-21  Score=131.91  Aligned_cols=79  Identities=18%  Similarity=0.291  Sum_probs=73.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCce--eCCeEeEEEeccC
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTV--IGKQSVRLSWGRN  137 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~--~~g~~l~v~~a~~  137 (198)
                      ...++++|||+|||+.+++++|+++|++||.|.+|.++++||||||+|++.++|.+|++.|++..  |.|+.|.|.+++.
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~   96 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS   96 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSC
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccc
Confidence            34567899999999999999999999999999999999999999999999999999999998764  8899999999987


Q ss_pred             C
Q 029166          138 P  138 (198)
Q Consensus       138 ~  138 (198)
                      +
T Consensus        97 k   97 (100)
T 3r27_A           97 Q   97 (100)
T ss_dssp             S
T ss_pred             c
Confidence            5

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.85  E-value=3.1e-20  Score=130.51  Aligned_cols=82  Identities=23%  Similarity=0.362  Sum_probs=74.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ......++|||+|||+++++++|+++|++||.|.+|+|+.+     ++||||+|.+.++|++|++.||+..|+|+.|+|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34456789999999999999999999999999999999875     6899999999999999999999999999999999


Q ss_pred             eccCCCC
Q 029166          134 WGRNPAN  140 (198)
Q Consensus       134 ~a~~~~~  140 (198)
                      +++....
T Consensus        90 ~a~~~~~   96 (114)
T 2do0_A           90 MDERALP   96 (114)
T ss_dssp             ECSCCCC
T ss_pred             EcccCCC
Confidence            9986543

>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=99.85  E-value=4.8e-21  Score=127.75  Aligned_cols=79  Identities=39%  Similarity=0.736  Sum_probs=74.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHh-CCceeCCeEeEEEecc
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL-NGTVIGKQSVRLSWGR  136 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l-~~~~~~g~~l~v~~a~  136 (198)
                      +..+.+.++|||+|||.++++++|+++|++||.|.+|+++++++||||+|.+.++|++|++.| ++..++|+.|+|+||+
T Consensus         6 ~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             CCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            344566789999999999999999999999999999999999999999999999999999999 9999999999999985

>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=99.85  E-value=3e-20  Score=129.75  Aligned_cols=84  Identities=23%  Similarity=0.474  Sum_probs=76.3

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC---CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~---kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ......+.++|||+|||+++++++|+++|++||.|.+|+|..+   ++||||+|.+.++|++|++.||+..|+|+.|+|+
T Consensus        15 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           15 RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             SCCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3455567789999999999999999999999999999999774   6899999999999999999999999999999999


Q ss_pred             eccCCCC
Q 029166          134 WGRNPAN  140 (198)
Q Consensus       134 ~a~~~~~  140 (198)
                      |+++...
T Consensus        95 ~a~~~~~  101 (109)
T 1x4a_A           95 FPRSGRG  101 (109)
T ss_dssp             CCCCCCC
T ss_pred             EcccCCC
Confidence            9987543

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

Probab=99.85  E-value=2.3e-20  Score=128.11  Aligned_cols=84  Identities=26%  Similarity=0.447  Sum_probs=75.8

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccC--CceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           55 GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQY--GEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        55 ~~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~--G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ........+.++|||+|||+.+++++|+++|++|  |.|.+|++.  ++||||+|.+.++|++|++.||+..|+|+.|+|
T Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A            6 SGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             CCCCSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cccccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3445556678999999999999999999999999  999999875  789999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 029166          133 SWGRNPAN  140 (198)
Q Consensus       133 ~~a~~~~~  140 (198)
                      +|++++..
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpd_A           84 TLAKPVDK   91 (99)
T ss_dssp             ECCCCCCC
T ss_pred             EECCCCCC
Confidence            99987643

>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=99.85  E-value=1.1e-20  Score=131.00  Aligned_cols=84  Identities=26%  Similarity=0.531  Sum_probs=76.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCC---eEe
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGK---QSV  130 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g---~~l  130 (198)
                      ......++|||+|||.++++++|+++|++||.|.+|+|+.+     ++||||+|.+.++|++|++.||+..+.+   +.|
T Consensus        10 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             CSCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            34456899999999999999999999999999999999876     7999999999999999999999999988   999


Q ss_pred             EEEeccCCCCCC
Q 029166          131 RLSWGRNPANKQ  142 (198)
Q Consensus       131 ~v~~a~~~~~~~  142 (198)
                      +|+|++++..+.
T Consensus        90 ~V~~a~~~~~~~  101 (105)
T 2dnh_A           90 VVKFADTDKESG  101 (105)
T ss_dssp             EEEESCSSCCCS
T ss_pred             EEEECccCcccC
Confidence            999999876543

>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=9.7e-21  Score=127.78  Aligned_cols=79  Identities=25%  Similarity=0.509  Sum_probs=73.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCCC
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPAN  140 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~~  140 (198)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+++  ++||||+|.+.++|++|++.||+..|+|+.|+|+|++++..
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            4467899999999999999999999999999999998  79999999999999999999999999999999999987654


Q ss_pred             C
Q 029166          141 K  141 (198)
Q Consensus       141 ~  141 (198)
                      .
T Consensus        83 ~   83 (90)
T 2dnq_A           83 A   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.85  E-value=1.5e-20  Score=132.53  Aligned_cols=84  Identities=26%  Similarity=0.486  Sum_probs=76.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .....+.++|||+|||+++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.||+..|+|+.|+
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   98 (115)
T 2cpz_A           19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   98 (115)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            444556789999999999999999999999999999999875      48999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 029166          132 LSWGRNPANK  141 (198)
Q Consensus       132 v~~a~~~~~~  141 (198)
                      |+|++++...
T Consensus        99 V~~a~~~~~~  108 (115)
T 2cpz_A           99 VQLKRSKNDS  108 (115)
T ss_dssp             EECCCCSCCC
T ss_pred             EEEcCCCCcC
Confidence            9999876543

>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=99.85  E-value=1.2e-20  Score=130.86  Aligned_cols=85  Identities=25%  Similarity=0.465  Sum_probs=76.8

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      ........++|||+|||+++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.|++..|+|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (105)
T 1x5u_A            8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   87 (105)
T ss_dssp             CCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            3445567889999999999999999999999999999999774      5899999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 029166          131 RLSWGRNPANK  141 (198)
Q Consensus       131 ~v~~a~~~~~~  141 (198)
                      +|++++++...
T Consensus        88 ~v~~a~~~~~~   98 (105)
T 1x5u_A           88 RVNKASAHNKN   98 (105)
T ss_dssp             EEEETTTTSCC
T ss_pred             EEEECCCCCcC
Confidence            99999876543

>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=99.85  E-value=9.6e-21  Score=132.30  Aligned_cols=81  Identities=33%  Similarity=0.675  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCCC
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPAN  140 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~~  140 (198)
                      ....++|||+|||..+++++|+++|++||.|.+|+|+.+++||||+|.+.++|++|++.|++..|+|+.|+|+|++++..
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            44578999999999999999999999999999999999999999999999999999999999999999999999987654


Q ss_pred             C
Q 029166          141 K  141 (198)
Q Consensus       141 ~  141 (198)
                      .
T Consensus       102 ~  102 (109)
T 1x4g_A          102 M  102 (109)
T ss_dssp             S
T ss_pred             C
Confidence            3

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.2e-20  Score=130.31  Aligned_cols=84  Identities=25%  Similarity=0.494  Sum_probs=76.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .....+.++|||+|||+++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.||+..|+|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (103)
T 2cq0_A            9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN   88 (103)
T ss_dssp             CCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            344556799999999999999999999999999999999865      58999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 029166          132 LSWGRNPANK  141 (198)
Q Consensus       132 v~~a~~~~~~  141 (198)
                      |+|++++...
T Consensus        89 v~~a~~~~~~   98 (103)
T 2cq0_A           89 VEWAKPSTNS   98 (103)
T ss_dssp             EEESSCCCCS
T ss_pred             EEECCCCCCC
Confidence            9999876544

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.7e-20  Score=126.69  Aligned_cols=82  Identities=26%  Similarity=0.484  Sum_probs=74.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      .....+.++|||+||  ++++++|+++|++||.|.+|.|..+++||||+|.+.++|++|++.|++..|+|+.|+|+|+++
T Consensus         9 ~~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~   86 (97)
T 1x5p_A            9 RRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   86 (97)
T ss_dssp             CCCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSS
T ss_pred             cCCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCC
Confidence            344456789999996  899999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCCC
Q 029166          138 PANK  141 (198)
Q Consensus       138 ~~~~  141 (198)
                      +...
T Consensus        87 ~~~~   90 (97)
T 1x5p_A           87 QPML   90 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=1.8e-20  Score=128.59  Aligned_cols=82  Identities=24%  Similarity=0.498  Sum_probs=74.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ....+.++|||+|||.++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++ |++..|+|+.|+|
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V   83 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEV   83 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEE
Confidence            34456789999999999999999999999999999999864      6999999999999999999 9999999999999


Q ss_pred             EeccCCCCC
Q 029166          133 SWGRNPANK  141 (198)
Q Consensus       133 ~~a~~~~~~  141 (198)
                      ++++++..+
T Consensus        84 ~~a~~~~~~   92 (99)
T 2dgs_A           84 KRAEPRDSK   92 (99)
T ss_dssp             EECCCCCCC
T ss_pred             EECCCCccc
Confidence            999976544

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.85  E-value=7.4e-21  Score=141.07  Aligned_cols=83  Identities=27%  Similarity=0.471  Sum_probs=75.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ....+.++|||+|||+++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++||+.||+..|+++.|+|
T Consensus        34 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  113 (156)
T 1h2v_Z           34 KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TTTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34456789999999999999999999999999999999764      589999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 029166          133 SWGRNPANK  141 (198)
Q Consensus       133 ~~a~~~~~~  141 (198)
                      +|+++....
T Consensus       114 ~~a~~~~~~  122 (156)
T 1h2v_Z          114 DWDAGFKEG  122 (156)
T ss_dssp             EEESCCCTT
T ss_pred             EECCCCCCc
Confidence            999875543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.7e-20  Score=130.67  Aligned_cols=83  Identities=34%  Similarity=0.510  Sum_probs=75.1

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQS  129 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~  129 (198)
                      .....+.+.++|||+|||+++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++||+.+++ .|+|+.
T Consensus         9 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~   87 (116)
T 2cqd_A            9 HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRK   87 (116)
T ss_dssp             CCCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEE
T ss_pred             CCCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEE
Confidence            34555667899999999999999999999999999999999874      58999999999999999999998 899999


Q ss_pred             eEEEeccCCC
Q 029166          130 VRLSWGRNPA  139 (198)
Q Consensus       130 l~v~~a~~~~  139 (198)
                      |+|+|++...
T Consensus        88 l~V~~a~~~~   97 (116)
T 2cqd_A           88 ANVNLAYLGA   97 (116)
T ss_dssp             CEEEESTTTC
T ss_pred             EEEEEcccCC
Confidence            9999998653

>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=99.85  E-value=2.1e-20  Score=130.77  Aligned_cols=85  Identities=21%  Similarity=0.451  Sum_probs=76.8

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhC------Cce
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLN------GTV  124 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~------~~~  124 (198)
                      .+......++|||+|||+++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.|+      +..
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~   87 (111)
T 1x4h_A            8 LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   87 (111)
T ss_dssp             CCCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             CCCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcE
Confidence            3445566889999999999999999999999999999999853      7999999999999999999999      999


Q ss_pred             eCCeEeEEEeccCCCCC
Q 029166          125 IGKQSVRLSWGRNPANK  141 (198)
Q Consensus       125 ~~g~~l~v~~a~~~~~~  141 (198)
                      |+|+.|+|+|++++...
T Consensus        88 ~~g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           88 LDGRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SSSCEEEEECCCCCCCC
T ss_pred             EcCEEEEEEECCCCccC
Confidence            99999999999876544

>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=134.51  Aligned_cols=83  Identities=16%  Similarity=0.281  Sum_probs=75.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhC--CceeCCeEeEEEeccC
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN--GTVIGKQSVRLSWGRN  137 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~--~~~~~g~~l~v~~a~~  137 (198)
                      ...+.++|||+|||++++|++|+++|++||.|.+|+|+++|+||||+|++.++|++|++.|+  +..|.|+.|+|+||++
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  106 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH  106 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccC
Confidence            34457899999999999999999999999999999999999999999999999999999887  4689999999999987


Q ss_pred             CCCCC
Q 029166          138 PANKQ  142 (198)
Q Consensus       138 ~~~~~  142 (198)
                      +..+.
T Consensus       107 k~~~~  111 (119)
T 2ad9_A          107 KELKT  111 (119)
T ss_dssp             SSCCC
T ss_pred             CCCCc
Confidence            65543

>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=99.85  E-value=2.1e-20  Score=128.15  Aligned_cols=81  Identities=27%  Similarity=0.455  Sum_probs=74.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.||+..|+|+.|+|++
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            345789999999999999999999999999999999875      49999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 029166          135 GRNPANK  141 (198)
Q Consensus       135 a~~~~~~  141 (198)
                      ++++...
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9986543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=2.2e-20  Score=131.19  Aligned_cols=85  Identities=27%  Similarity=0.435  Sum_probs=76.5

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceE--------EEEEeCC------CcEEEEEeCCHHHHHHHHHHhCC
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIA--------SVKIPVG------KGCGFVQFANRENAEEALHKLNG  122 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~--------~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~  122 (198)
                      ......+.++|||+|||+++++++|+++|++||.|.        .|+|+.+      ++||||+|.+.++|++|++.||+
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g   87 (113)
T 2cpe_A            8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG   87 (113)
T ss_dssp             CCCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CcccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCC
Confidence            345566789999999999999999999999999998        6888765      68999999999999999999999


Q ss_pred             ceeCCeEeEEEeccCCCCC
Q 029166          123 TVIGKQSVRLSWGRNPANK  141 (198)
Q Consensus       123 ~~~~g~~l~v~~a~~~~~~  141 (198)
                      ..|+|+.|+|++++++...
T Consensus        88 ~~~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           88 KDFQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             CEETTEECEEECSSCCCCS
T ss_pred             CccCCCEEEEEECCCCCCC
Confidence            9999999999999876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1e-20  Score=129.01  Aligned_cols=80  Identities=30%  Similarity=0.584  Sum_probs=74.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEE-EEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASV-KIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v-~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .+.++|||+|||+++++++|+++|++||.|.++ +|+.+      ++||||+|.+.++|++|++.||+..|+|+.|+|+|
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            457899999999999999999999999999999 88875      69999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 029166          135 GRNPANK  141 (198)
Q Consensus       135 a~~~~~~  141 (198)
                      ++++..+
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9876544

>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=99.84  E-value=2.6e-20  Score=128.96  Aligned_cols=82  Identities=28%  Similarity=0.509  Sum_probs=73.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-------KGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      .....+.++|||+|||+++++++|+++|++|| |.+|+|+.+       ++||||+|.+.++|++|| .|++..|+|+.|
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            34445678999999999999999999999999 999999754       689999999999999999 899999999999


Q ss_pred             EEEeccCCCCC
Q 029166          131 RLSWGRNPANK  141 (198)
Q Consensus       131 ~v~~a~~~~~~  141 (198)
                      +|++++++..+
T Consensus        87 ~V~~a~~~~~~   97 (104)
T 1wi8_A           87 RVDVADQAQDK   97 (104)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99999886543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.84  E-value=2.3e-20  Score=135.76  Aligned_cols=84  Identities=29%  Similarity=0.473  Sum_probs=76.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .......++|||+|||.++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.||+..|+|+.|+
T Consensus        36 ~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  115 (139)
T 1u6f_A           36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             SCCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            345566789999999999999999999999999999999764      68999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 029166          132 LSWGRNPANK  141 (198)
Q Consensus       132 v~~a~~~~~~  141 (198)
                      |+++++...+
T Consensus       116 v~~a~~~~~~  125 (139)
T 1u6f_A          116 VALAASGHQR  125 (139)
T ss_dssp             EEESSCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999976544

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.84  E-value=9.2e-21  Score=126.36  Aligned_cols=74  Identities=19%  Similarity=0.301  Sum_probs=71.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      .+..|||+||++.+||++|+++|.+||+|.++++..+||||||+|.++++|++|++.||+..+.|+.|+|++|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999994

>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=2.8e-20  Score=125.97  Aligned_cols=80  Identities=25%  Similarity=0.484  Sum_probs=73.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ......++|||+|||+++++++|+++|++||.|.+|+++  ++||||+|.+.++|++|++.||+..|+|+.|+|++++++
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   82 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSR   82 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCC
Confidence            345567899999999999999999999999999999997  569999999999999999999999999999999999876


Q ss_pred             CC
Q 029166          139 AN  140 (198)
Q Consensus       139 ~~  140 (198)
                      ..
T Consensus        83 ~~   84 (92)
T 2dgt_A           83 LR   84 (92)
T ss_dssp             CS
T ss_pred             CC
Confidence            44

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=2.9e-20  Score=127.75  Aligned_cols=84  Identities=19%  Similarity=0.419  Sum_probs=76.3

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      ......+.++|||+|||.++++++|+++|++||.|.+|+|+.+     ++||||+|.+.++|++|++.||+..|+|+.|+
T Consensus        10 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   89 (100)
T 2do4_A           10 RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIK   89 (100)
T ss_dssp             CCSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEE
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3445566789999999999999999999999999999999875     49999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 029166          132 LSWGRNPAN  140 (198)
Q Consensus       132 v~~a~~~~~  140 (198)
                      |+|++++..
T Consensus        90 v~~a~~~~~   98 (100)
T 2do4_A           90 VAISNSGPS   98 (100)
T ss_dssp             EEECCCCSC
T ss_pred             EEECCCCCC
Confidence            999987654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=2.6e-20  Score=126.75  Aligned_cols=79  Identities=30%  Similarity=0.564  Sum_probs=73.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .+.++|||+|||..+++++|+++|++||.|.+|+++.+      ++||||+|.+.++|++|++.||+..|+|+.|+|+|+
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            35789999999999999999999999999999999875      589999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      +++..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.4e-20  Score=129.70  Aligned_cols=83  Identities=30%  Similarity=0.597  Sum_probs=75.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ....+.++|||+|||+++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.||+..|+|+.|+|
T Consensus         7 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   86 (102)
T 1x5s_A            7 GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   86 (102)
T ss_dssp             CCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34456789999999999999999999999999999999874      689999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 029166          133 SWGRNPANK  141 (198)
Q Consensus       133 ~~a~~~~~~  141 (198)
                      ++++++...
T Consensus        87 ~~a~~~~~~   95 (102)
T 1x5s_A           87 DQAGKSSDN   95 (102)
T ss_dssp             EEEECCCCC
T ss_pred             EECCCCCCC
Confidence            999876543

>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=99.84  E-value=1.9e-20  Score=127.97  Aligned_cols=79  Identities=20%  Similarity=0.351  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHhccCCceEEEEEeCC---CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           62 SSNTTIFVGGLDPNVTDEDLR----QPFSQYGEIASVKIPVG---KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~----~~F~~~G~i~~v~i~~~---kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .+.++|||+|||+++++++|+    ++|++||.|.+|+|+.+   ++||||+|.+.++|++|++.||+..|+|+.|+|++
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   86 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL   86 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            456899999999999999999    99999999999999876   79999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 029166          135 GRNPAN  140 (198)
Q Consensus       135 a~~~~~  140 (198)
                      |++...
T Consensus        87 a~~~~~   92 (96)
T 2dgx_A           87 ATGASG   92 (96)
T ss_dssp             CCCSSC
T ss_pred             cCCCCC
Confidence            987644

>2dnm_A SRP46 splicing factor; 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=129.87  Aligned_cols=84  Identities=25%  Similarity=0.463  Sum_probs=75.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      +....+.++|||+|||+++++++|+++|++||.|.+|.|+.+      ++||||+|.+.++|++|++.||+..|+|+.|+
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            344556789999999999999999999999999999999764      68999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 029166          132 LSWGRNPANK  141 (198)
Q Consensus       132 v~~a~~~~~~  141 (198)
                      |+++++....
T Consensus        87 V~~a~~~~~~   96 (103)
T 2dnm_A           87 VQVARYGRRD   96 (103)
T ss_dssp             EEECSSCCSC
T ss_pred             EEECCcCCCC
Confidence            9999875443

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.84  E-value=1.1e-20  Score=133.42  Aligned_cols=77  Identities=32%  Similarity=0.593  Sum_probs=72.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      .++|||+|||+++++++|+++|++||.|.+|+|+.+    ||||||+|.+.++|++||+.|++..|+|+.|+|++++++.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~   84 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   84 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCcc
Confidence            568999999999999999999999999999999874    6899999999999999999999999999999999998754


Q ss_pred             C
Q 029166          140 N  140 (198)
Q Consensus       140 ~  140 (198)
                      .
T Consensus        85 ~   85 (115)
T 4f25_A           85 E   85 (115)
T ss_dssp             C
T ss_pred             c
Confidence            4

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.84  E-value=8.6e-21  Score=130.67  Aligned_cols=77  Identities=26%  Similarity=0.485  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ...++|||+|||.++++++|+++|++||.|.++++.++++||||+|.+.++|++|++.||+..|+|+.|+|+|++++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            44689999999999999999999999999999999999999999999999999999999999999999999999863

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=1.9e-20  Score=128.23  Aligned_cols=80  Identities=28%  Similarity=0.508  Sum_probs=73.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC---------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV---------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~---------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      .+.++|||+|||+++++++|+++|++||.|.+|+|+.         .++||||+|.+.++|++|++.||+..|+|+.|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4578999999999999999999999999999999874         3589999999999999999999999999999999


Q ss_pred             EeccCCCCC
Q 029166          133 SWGRNPANK  141 (198)
Q Consensus       133 ~~a~~~~~~  141 (198)
                      ++++++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>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=99.84  E-value=2.3e-20  Score=130.95  Aligned_cols=80  Identities=15%  Similarity=0.210  Sum_probs=73.5

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhC--CceeCCeEeEEEeccC
Q 029166           61 DSSNTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN--GTVIGKQSVRLSWGRN  137 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~-~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~--~~~~~g~~l~v~~a~~  137 (198)
                      ..+.++|||+|||++ +++++|+++|++||.|.+|.|+++|+||||+|.+.++|++|++.|+  +..|.|+.|+|+||+.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  101 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK  101 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcc
Confidence            556789999999998 9999999999999999999999999999999999999999999885  4669999999999986


Q ss_pred             CCC
Q 029166          138 PAN  140 (198)
Q Consensus       138 ~~~  140 (198)
                      +..
T Consensus       102 ~~~  104 (112)
T 1x4f_A          102 YKK  104 (112)
T ss_dssp             CSS
T ss_pred             ccc
Confidence            544

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.84  E-value=9.3e-21  Score=135.59  Aligned_cols=85  Identities=25%  Similarity=0.500  Sum_probs=77.1

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      .+....+.++|||+|||+.+++++|+++|++||.|.+|.|+.+      ++||||+|.+.++|++|++.||+..|+|+.|
T Consensus        15 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   94 (126)
T 3ex7_B           15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   94 (126)
T ss_dssp             CBCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEE
Confidence            3455566889999999999999999999999999999999865      7999999999999999999999999999999


Q ss_pred             EEEeccCCCCC
Q 029166          131 RLSWGRNPANK  141 (198)
Q Consensus       131 ~v~~a~~~~~~  141 (198)
                      +|+|++++...
T Consensus        95 ~v~~a~~~~~~  105 (126)
T 3ex7_B           95 SVDWCFVRGPP  105 (126)
T ss_dssp             EEEESEESSSC
T ss_pred             EEEEecCCCCC
Confidence            99999876544

>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=99.84  E-value=3.6e-20  Score=131.00  Aligned_cols=81  Identities=22%  Similarity=0.511  Sum_probs=74.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ..+.++|||+|||.++++++|+++|++||.|.+|.|+.+     ++||||+|.+.++|++|++.||+..|+|+.|+|+|+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            345789999999999999999999999999999999885     499999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 029166          136 RNPANK  141 (198)
Q Consensus       136 ~~~~~~  141 (198)
                      +++...
T Consensus        84 ~~~~~~   89 (116)
T 2fy1_A           84 KKPSFQ   89 (116)
T ss_dssp             CCSSCS
T ss_pred             CCCCCC
Confidence            876543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=5.6e-20  Score=124.79  Aligned_cols=79  Identities=25%  Similarity=0.442  Sum_probs=72.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .....+.++|||+|||..+++++|+++|++||.|.+|+++.+      ++||||+|.+.++|++|++.||+..|+|+.|+
T Consensus        10 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   89 (94)
T 2e5h_A           10 GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIK   89 (94)
T ss_dssp             CSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            344556789999999999999999999999999999999774      68999999999999999999999999999999


Q ss_pred             EEecc
Q 029166          132 LSWGR  136 (198)
Q Consensus       132 v~~a~  136 (198)
                      |+||+
T Consensus        90 v~~ak   94 (94)
T 2e5h_A           90 ASIAI   94 (94)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99985

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.84  E-value=5.8e-20  Score=126.98  Aligned_cols=82  Identities=26%  Similarity=0.437  Sum_probs=73.6

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .....+.++|||+|||+++++++|+++|++|| |.+|+|+.+      ++||||+|.+.++|++|+ .||+..|+|+.|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   86 (103)
T 2dng_A            9 ELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLR   86 (103)
T ss_dssp             CCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEE
Confidence            34455678999999999999999999999997 999999865      589999999999999999 8999999999999


Q ss_pred             EEeccCCCCC
Q 029166          132 LSWGRNPANK  141 (198)
Q Consensus       132 v~~a~~~~~~  141 (198)
                      |++++++...
T Consensus        87 V~~a~~~~~~   96 (103)
T 2dng_A           87 VDIAEGRKQD   96 (103)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEecCCCCC
Confidence            9999876543

>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=99.84  E-value=1e-20  Score=128.36  Aligned_cols=79  Identities=24%  Similarity=0.455  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCc-eEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCC-ceeCCeEeEEEeccCCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGE-IASVKIPVGKGCGFVQFANRENAEEALHKLNG-TVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~-i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~-~~~~g~~l~v~~a~~~~  139 (198)
                      ...++|||+|||+++++++|+++|++||. |..+.+ .+++||||+|.+.++|++|++.||+ ..|+|+.|+|+|++++.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~   84 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   84 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcc
Confidence            45789999999999999999999999999 555544 5689999999999999999999999 99999999999998765


Q ss_pred             CC
Q 029166          140 NK  141 (198)
Q Consensus       140 ~~  141 (198)
                      .+
T Consensus        85 ~~   86 (93)
T 2cqh_A           85 LR   86 (93)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>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=99.83  E-value=4.4e-20  Score=129.49  Aligned_cols=81  Identities=22%  Similarity=0.402  Sum_probs=74.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHH---HHhccCCceEEEEEeCCC---------cEEEEEeCCHHHHHHHHHHhCCceeC
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLR---QPFSQYGEIASVKIPVGK---------GCGFVQFANRENAEEALHKLNGTVIG  126 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~---~~F~~~G~i~~v~i~~~k---------g~afV~f~~~~~a~~a~~~l~~~~~~  126 (198)
                      ......++|||+|||+++++++|+   ++|++||.|.+|.|++++         |||||+|.+.++|++|++.||+..|+
T Consensus        10 ~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   89 (111)
T 2cpi_A           10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   89 (111)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             ccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEEC
Confidence            444567899999999999999999   999999999999998643         79999999999999999999999999


Q ss_pred             CeEeEEEeccCCC
Q 029166          127 KQSVRLSWGRNPA  139 (198)
Q Consensus       127 g~~l~v~~a~~~~  139 (198)
                      |+.|+|+||+++.
T Consensus        90 gr~l~V~~a~~k~  102 (111)
T 2cpi_A           90 GRTLKASLGTTKY  102 (111)
T ss_dssp             TEEEEEESCCCCS
T ss_pred             CEEEEEEeccccc
Confidence            9999999998764

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.83  E-value=3.6e-20  Score=122.87  Aligned_cols=76  Identities=29%  Similarity=0.621  Sum_probs=71.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      +.+|||+|||.++++++|+++|++||.|.++.++.+      ++||||+|.+.++|++|++.||+..++|+.|+|+|+++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            368999999999999999999999999999999865      69999999999999999999999999999999999987


Q ss_pred             CC
Q 029166          138 PA  139 (198)
Q Consensus       138 ~~  139 (198)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.83  E-value=3.3e-20  Score=130.09  Aligned_cols=78  Identities=21%  Similarity=0.262  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .+.++|||+||+++++|++|+++|++||.|.+|+|+.+      +|||||+|.+.++|++|++.||+..|+|+.|+|+++
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            45789999999999999999999999999999999763      689999999999999999999999999999999999


Q ss_pred             cCCC
Q 029166          136 RNPA  139 (198)
Q Consensus       136 ~~~~  139 (198)
                      ....
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            7543

>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=99.83  E-value=7.5e-20  Score=127.95  Aligned_cols=79  Identities=32%  Similarity=0.588  Sum_probs=72.7

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           60 GDSSNTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~-~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      .....++|||+|||+. +++++|+++|++||.|.+|+|  .++||||+|.+.++|++|++.|++..|+|+.|+|+|++++
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            3445689999999999 999999999999999999999  6899999999999999999999999999999999999865


Q ss_pred             CC
Q 029166          139 AN  140 (198)
Q Consensus       139 ~~  140 (198)
                      ..
T Consensus       101 ~~  102 (110)
T 1wf1_A          101 KP  102 (110)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.83  E-value=4.1e-20  Score=129.13  Aligned_cols=82  Identities=30%  Similarity=0.600  Sum_probs=73.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ........++|||+|||+++++++|+++|++||.|.+|+++  +|||||+|.+.++|++|++.||+..++|+.|+|+|++
T Consensus        24 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  101 (108)
T 2jvo_A           24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK  101 (108)
T ss_dssp             ----CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCS
T ss_pred             ccCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            34556678999999999999999999999999999999998  8999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      ++..
T Consensus       102 ~~~~  105 (108)
T 2jvo_A          102 LPAK  105 (108)
T ss_dssp             CCC-
T ss_pred             CCCC
Confidence            7643

>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=99.83  E-value=4.3e-20  Score=128.19  Aligned_cols=84  Identities=21%  Similarity=0.459  Sum_probs=75.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCcee---CCe
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVI---GKQ  128 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~---~g~  128 (198)
                      .....+.++|||+|||.++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.||+..+   .++
T Consensus         7 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~   86 (106)
T 2dgp_A            7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNR   86 (106)
T ss_dssp             SCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCc
Confidence            344566789999999999999999999999999999999874      68999999999999999999999987   899


Q ss_pred             EeEEEeccCCCCC
Q 029166          129 SVRLSWGRNPANK  141 (198)
Q Consensus       129 ~l~v~~a~~~~~~  141 (198)
                      .|+|++++++..+
T Consensus        87 ~l~v~~a~~~~~~   99 (106)
T 2dgp_A           87 PIQVKPADSESRG   99 (106)
T ss_dssp             CCEEEECCCCSCC
T ss_pred             eEEEEECCccccc
Confidence            9999999876543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=5.3e-20  Score=125.07  Aligned_cols=80  Identities=35%  Similarity=0.502  Sum_probs=73.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .....+.++|||+|||..+++++|+++|++||.|.+|+++.+      ++||||+|.+.++|++|++.||+..|+|+.|+
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A            9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            444556789999999999999999999999999999999753      58999999999999999999999999999999


Q ss_pred             EEeccC
Q 029166          132 LSWGRN  137 (198)
Q Consensus       132 v~~a~~  137 (198)
                      |+|+++
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999975

>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=8e-20  Score=123.24  Aligned_cols=79  Identities=22%  Similarity=0.440  Sum_probs=73.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      .....++|||+|||+++++++|+++|++||.|.+|+++  ++||||+|.+.++|++|++.||+..++|+.|+|++++++.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            34567899999999999999999999999999999998  5699999999999999999999999999999999998764


Q ss_pred             C
Q 029166          140 N  140 (198)
Q Consensus       140 ~  140 (198)
                      .
T Consensus        83 ~   83 (90)
T 2dnp_A           83 K   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=3.9e-20  Score=129.38  Aligned_cols=83  Identities=34%  Similarity=0.531  Sum_probs=76.1

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .........++|||+|||.++++++|+++|++||.|.+|+++.+    +|||||+|.+.++|++|++.|++..|+|+.|+
T Consensus        21 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  100 (109)
T 2err_A           21 MNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE  100 (109)
T ss_dssp             -CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECE
T ss_pred             CCccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34555667899999999999999999999999999999999875    79999999999999999999999999999999


Q ss_pred             EEeccCC
Q 029166          132 LSWGRNP  138 (198)
Q Consensus       132 v~~a~~~  138 (198)
                      |++++++
T Consensus       101 V~~a~~~  107 (109)
T 2err_A          101 VNNATAR  107 (109)
T ss_dssp             EEECCCS
T ss_pred             EEECCCC
Confidence            9999875

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=3.4e-20  Score=128.26  Aligned_cols=83  Identities=33%  Similarity=0.542  Sum_probs=75.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhcc-CCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCce-eCCeEeEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQ-YGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTV-IGKQSVRL  132 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~-~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~-~~g~~l~v  132 (198)
                      ...+.++|||+|||+++++++|+++|++ ||.|.+|+|+.+     ++||||+|.+.++|++|++.|++.. |+|+.|+|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            3456789999999999999999999999 999999999875     7999999999999999999999999 99999999


Q ss_pred             EeccCCCCCC
Q 029166          133 SWGRNPANKQ  142 (198)
Q Consensus       133 ~~a~~~~~~~  142 (198)
                      ++++++..+.
T Consensus        85 ~~a~~~~~~~   94 (104)
T 2dhg_A           85 SVAIPKASRV   94 (104)
T ss_dssp             CBCCCCCSCC
T ss_pred             EEccCCCcCC
Confidence            9998765443

>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=99.83  E-value=4e-20  Score=123.67  Aligned_cols=77  Identities=31%  Similarity=0.690  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .+.++|||+|||.++++++|+++|++||.|.+|+++.+      ++||||+|.+.++|++|++.||+..++|+.|+|+|+
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            35789999999999999999999999999999999875      589999999999999999999999999999999999


Q ss_pred             cCC
Q 029166          136 RNP  138 (198)
Q Consensus       136 ~~~  138 (198)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            864

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.7e-19  Score=124.18  Aligned_cols=82  Identities=27%  Similarity=0.349  Sum_probs=70.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEe--CCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP--VGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~--~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .....+.++|||+|||+++++++|+++|++||.|.-+...  ..++||||+|.+.++|++|++.||+..|+|+.|+|+|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   88 (101)
T 2fc9_A            9 STWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ   88 (101)
T ss_dssp             CCCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEEC
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEc
Confidence            3455668999999999999999999999999987322110  13799999999999999999999999999999999999


Q ss_pred             cCCC
Q 029166          136 RNPA  139 (198)
Q Consensus       136 ~~~~  139 (198)
                      +++.
T Consensus        89 ~~~~   92 (101)
T 2fc9_A           89 GPRG   92 (101)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            8764

>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=99.82  E-value=5e-20  Score=128.75  Aligned_cols=84  Identities=21%  Similarity=0.470  Sum_probs=76.2

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      .+....+.++|||+|||..+++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.|++..|+|+.|
T Consensus        19 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   98 (110)
T 1oo0_B           19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI   98 (110)
T ss_dssp             CBCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            3445566789999999999999999999999999999999764      5999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 029166          131 RLSWGRNPAN  140 (198)
Q Consensus       131 ~v~~a~~~~~  140 (198)
                      +|+|++++..
T Consensus        99 ~V~~a~~~~~  108 (110)
T 1oo0_B           99 QVDWCFVKGP  108 (110)
T ss_dssp             EEEESEESSC
T ss_pred             EEEEcccCCC
Confidence            9999987543

>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=99.82  E-value=5.7e-20  Score=122.43  Aligned_cols=76  Identities=28%  Similarity=0.626  Sum_probs=71.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ..+.++|||+|||+++++++|+++|++||.|.+++++.+      ++||||+|.+.++|++|++.||+..++|+.|+|+|
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            346789999999999999999999999999999998653      79999999999999999999999999999999999


Q ss_pred             cc
Q 029166          135 GR  136 (198)
Q Consensus       135 a~  136 (198)
                      |+
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>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=99.82  E-value=7.3e-20  Score=122.59  Aligned_cols=77  Identities=34%  Similarity=0.588  Sum_probs=72.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ..++|||+|||.++++++|+++|++||.|.+++++.       .++||||+|.+.++|++|++.||+..++|+.|+|+++
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            468999999999999999999999999999999865       4789999999999999999999999999999999999


Q ss_pred             cCCC
Q 029166          136 RNPA  139 (198)
Q Consensus       136 ~~~~  139 (198)
                      .++.
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.82  E-value=1.4e-20  Score=127.48  Aligned_cols=77  Identities=18%  Similarity=0.334  Sum_probs=69.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCC-ceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHh-CCceeCCeEeEEEec
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYG-EIASVKIPVG------KGCGFVQFANRENAEEALHKL-NGTVIGKQSVRLSWG  135 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G-~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l-~~~~~~g~~l~v~~a  135 (198)
                      +++|||+|||+++||++|+++|++|| .|.+|+|+++      ||||||+|.+.++|++|++.+ ++..++|+.|+|+||
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 8999999763      699999999999999999977 466799999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      +++..
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87654

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.82  E-value=4.2e-20  Score=125.68  Aligned_cols=80  Identities=30%  Similarity=0.432  Sum_probs=72.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      +......++|||+|||+.+++++|+++|++||.|.+|+|+.+     ++||||+|.+.++|++|++.||+..|+|+.|+|
T Consensus        10 ~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (95)
T 2ywk_A           10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV   89 (95)
T ss_dssp             --CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEE
Confidence            344456789999999999999999999999999999999875     689999999999999999999999999999999


Q ss_pred             EeccC
Q 029166          133 SWGRN  137 (198)
Q Consensus       133 ~~a~~  137 (198)
                      +|++.
T Consensus        90 ~~a~~   94 (95)
T 2ywk_A           90 SGPSS   94 (95)
T ss_dssp             ECCCC
T ss_pred             EEcCC
Confidence            99874

>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=99.82  E-value=1.2e-19  Score=124.35  Aligned_cols=81  Identities=27%  Similarity=0.453  Sum_probs=72.1

Q ss_pred             CCCCCCCCCCeEEEcCCCC-CCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           56 PQSEGDSSNTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~-~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .......+.++|||+|||+ ++++++|+++|++||.|.++++.  +|||||+|.+.++|++|++.||+..++|+.|+|++
T Consensus        14 ~~~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   91 (97)
T 2xnq_A           14 LVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEV   91 (97)
T ss_dssp             -----CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEE
T ss_pred             cccCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            3445556789999999998 99999999999999999999984  89999999999999999999999999999999999


Q ss_pred             ccCC
Q 029166          135 GRNP  138 (198)
Q Consensus       135 a~~~  138 (198)
                      ++++
T Consensus        92 a~~~   95 (97)
T 2xnq_A           92 SSSN   95 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9865

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.82  E-value=1.1e-19  Score=128.53  Aligned_cols=79  Identities=27%  Similarity=0.503  Sum_probs=72.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .....+.++|||+|||+++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.||+..|+|+.|+
T Consensus        34 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  113 (118)
T 2khc_A           34 QIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK  113 (118)
T ss_dssp             SCCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344556789999999999999999999999999999999864      68999999999999999999999999999999


Q ss_pred             EEecc
Q 029166          132 LSWGR  136 (198)
Q Consensus       132 v~~a~  136 (198)
                      |+|++
T Consensus       114 V~~ak  118 (118)
T 2khc_A          114 VQLKK  118 (118)
T ss_dssp             EEEC-
T ss_pred             EEecC
Confidence            99985

>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=99.82  E-value=2.1e-20  Score=131.27  Aligned_cols=77  Identities=22%  Similarity=0.392  Sum_probs=73.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      .+.++|||+|||+.+++++|+++|++||.|.+|.|+++++||||+|.+.++|++|++.||+..|+|+.|.|+|++..
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999764

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.82  E-value=9.5e-20  Score=124.31  Aligned_cols=78  Identities=22%  Similarity=0.470  Sum_probs=72.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ++++|||+|||..+++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.|++..++|+.|+|++++
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            3689999999999999999999999999999999865      6999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      ++..
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7543

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

Probab=99.82  E-value=4.1e-20  Score=127.23  Aligned_cols=76  Identities=30%  Similarity=0.547  Sum_probs=72.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCCC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPAN  140 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~~  140 (198)
                      ++|||+|||+++++++|+++|++||.|.+|+++.+ ++||||+|.+.++|++|++.|++..++|+.|+|++++++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   77 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPR   77 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCC
Confidence            58999999999999999999999999999999986 99999999999999999999999999999999999987653

>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=99.82  E-value=5.6e-20  Score=132.42  Aligned_cols=82  Identities=33%  Similarity=0.506  Sum_probs=75.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .....+.++|||+|||+++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++||+.|++..|+|+.|+
T Consensus        40 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~  119 (129)
T 2kxn_B           40 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR  119 (129)
T ss_dssp             SSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            444556789999999999999999999999999999999864      68999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 029166          132 LSWGRNPA  139 (198)
Q Consensus       132 v~~a~~~~  139 (198)
                      |+|++++.
T Consensus       120 V~~a~~~~  127 (129)
T 2kxn_B          120 VDFSITKR  127 (129)
T ss_dssp             ESCCSSSS
T ss_pred             EEEecCCC
Confidence            99998754

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.82  E-value=5.4e-20  Score=124.40  Aligned_cols=80  Identities=30%  Similarity=0.493  Sum_probs=73.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ....++|||+|||.++++++|+++|++||.|.+|+|++    +++||||+|.+.++|++|++.|++..|+|+.|+|++++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            34578999999999999999999999999999999986    36999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      +...
T Consensus        85 ~~~~   88 (92)
T 2dgv_A           85 NASG   88 (92)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=5.2e-20  Score=127.76  Aligned_cols=83  Identities=25%  Similarity=0.518  Sum_probs=75.4

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      .+....+.++|||+|||.++++++|+++|++||.|.+|.|+.+      +|||||+|.+.++|++|++.||+..|+|+.|
T Consensus        16 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   95 (106)
T 1p27_B           16 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   95 (106)
T ss_dssp             CBCCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEE
Confidence            3444556789999999999999999999999999999999764      6999999999999999999999999999999


Q ss_pred             EEEeccCCC
Q 029166          131 RLSWGRNPA  139 (198)
Q Consensus       131 ~v~~a~~~~  139 (198)
                      +|+|++++.
T Consensus        96 ~V~~a~~~~  104 (106)
T 1p27_B           96 SVDWCFVRG  104 (106)
T ss_dssp             EEEESEESS
T ss_pred             EEEeecCCC
Confidence            999998753

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=7.4e-20  Score=126.80  Aligned_cols=83  Identities=29%  Similarity=0.445  Sum_probs=75.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .......++|||+|||+++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++||+. ++..|+|+.|+
T Consensus        10 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~   88 (105)
T 2dh8_A           10 NSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNID   88 (105)
T ss_dssp             CCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEB
T ss_pred             cCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEE
Confidence            345566899999999999999999999999999999999875      48999999999999999998 99999999999


Q ss_pred             EEeccCCCCC
Q 029166          132 LSWGRNPANK  141 (198)
Q Consensus       132 v~~a~~~~~~  141 (198)
                      |++++++...
T Consensus        89 V~~a~~~~~~   98 (105)
T 2dh8_A           89 PKPCTPRGMQ   98 (105)
T ss_dssp             CCCSCCSSCC
T ss_pred             EEEccCCCCC
Confidence            9999876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.81  E-value=5.5e-20  Score=125.60  Aligned_cols=78  Identities=17%  Similarity=0.389  Sum_probs=69.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCc--eEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCc----eeCC
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGE--IASVKIPVG------KGCGFVQFANRENAEEALHKLNGT----VIGK  127 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~--i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~----~~~g  127 (198)
                      ....-.+|||+|||+++|+++|+++|++||.  |.+|+++++      ||||||+|.+.++|++|++.||+.    .|+|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            3445678999999999999999999999995  678888764      699999999999999999999986    5899


Q ss_pred             eEeEEEeccC
Q 029166          128 QSVRLSWGRN  137 (198)
Q Consensus       128 ~~l~v~~a~~  137 (198)
                      +.|.|+||++
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999985

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=2.3e-19  Score=122.70  Aligned_cols=81  Identities=20%  Similarity=0.480  Sum_probs=72.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEe--CCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP--VGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~--~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .......++|||+|||+++++++|+++|++||.|. +.++  .+++||||+|.+.++|++|++.||+..|+|+.|+|+++
T Consensus        13 ~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CSSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            34455678999999999999999999999999985 4544  46899999999999999999999999999999999999


Q ss_pred             cCCC
Q 029166          136 RNPA  139 (198)
Q Consensus       136 ~~~~  139 (198)
                      +++.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.81  E-value=6.1e-20  Score=128.83  Aligned_cols=77  Identities=21%  Similarity=0.264  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCC-ceEEEEEeC--CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYG-EIASVKIPV--GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G-~i~~v~i~~--~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ...++|||+|||+++++++|+++|++|| +|..+.|..  ++|||||+|.+.++|++||+.||+..|+|+.|+|++++.+
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            3468999999999999999999999999 999999863  5899999999999999999999999999999999999754

>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=99.81  E-value=6.2e-20  Score=129.57  Aligned_cols=79  Identities=23%  Similarity=0.409  Sum_probs=67.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeE-----eEEEec
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQS-----VRLSWG  135 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~-----l~v~~a  135 (198)
                      ....++|||+|||+++++++|+++|++||+|.+|.|+.+ +||||+|.+.++|++||+.||+..|+|+.     |+|+.+
T Consensus        13 ~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~   91 (115)
T 3beg_B           13 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   91 (115)
T ss_dssp             ----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccC
Confidence            345789999999999999999999999999999999888 99999999999999999999999999988     777777


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      .+...
T Consensus        92 ~~~~~   96 (115)
T 3beg_B           92 GPRSP   96 (115)
T ss_dssp             C----
T ss_pred             CCCCC
Confidence            66443

>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=99.81  E-value=4.8e-19  Score=122.25  Aligned_cols=82  Identities=23%  Similarity=0.386  Sum_probs=72.9

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      ......+.++|||+|||+++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++  +++.|+|+.|
T Consensus         8 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l   85 (103)
T 2cqg_A            8 VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWC   85 (103)
T ss_dssp             CSCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEE
T ss_pred             CCCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEE
Confidence            3445556789999999999999999999999999999999775      5899999999999999998  4789999999


Q ss_pred             EEEeccCCCC
Q 029166          131 RLSWGRNPAN  140 (198)
Q Consensus       131 ~v~~a~~~~~  140 (198)
                      +|+|++++..
T Consensus        86 ~v~~a~~~~~   95 (103)
T 2cqg_A           86 DCKLPNSKQS   95 (103)
T ss_dssp             EEECCCTTCC
T ss_pred             EEEecCCCCc
Confidence            9999987654

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

Probab=99.81  E-value=6.4e-20  Score=125.28  Aligned_cols=79  Identities=28%  Similarity=0.445  Sum_probs=71.9

Q ss_pred             CCCCCCeEEEcCCCC-CCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           60 GDSSNTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~-~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ...+.++|||+|||+ .+++++|+++|++||.|.+|+|.  ++||||+|.+.++|++|++.|++..+.|+.|+|++++++
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   83 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSN   83 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECC
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcC
Confidence            345688999999998 99999999999999999999996  799999999999999999999999999999999999875


Q ss_pred             CC
Q 029166          139 AN  140 (198)
Q Consensus       139 ~~  140 (198)
                      ..
T Consensus        84 ~~   85 (96)
T 2kvi_A           84 AR   85 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=4.3e-19  Score=122.22  Aligned_cols=83  Identities=28%  Similarity=0.471  Sum_probs=69.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC---CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV---GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~---~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .....+.++|||+|||+++++++|+++|+.|+.|.-+....   +++||||+|.+.++|++||+.||+..|+|+.|+|+|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A            9 NARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SSSSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            34556678999999999999999999999886443332211   258999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 029166          135 GRNPAN  140 (198)
Q Consensus       135 a~~~~~  140 (198)
                      ++++..
T Consensus        89 a~~~~~   94 (102)
T 2fc8_A           89 AKPKGE   94 (102)
T ss_dssp             CCCCCS
T ss_pred             ecCCCC
Confidence            997654

>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=99.81  E-value=8.4e-20  Score=124.94  Aligned_cols=79  Identities=28%  Similarity=0.384  Sum_probs=71.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      .....++|||+|||+++++++|+++|++||.|.++.++.      .++||||+|.+.++|++|++.||+..|+|+.|+|+
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            445578999999999999999999999999998766554      26999999999999999999999999999999999


Q ss_pred             eccCC
Q 029166          134 WGRNP  138 (198)
Q Consensus       134 ~a~~~  138 (198)
                      +++.+
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            99864

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.81  E-value=1.7e-19  Score=123.72  Aligned_cols=81  Identities=30%  Similarity=0.461  Sum_probs=73.6

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEE--------EEEeCC------CcEEEEEeCCHHHHHHHHHHhC
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS--------VKIPVG------KGCGFVQFANRENAEEALHKLN  121 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~--------v~i~~~------kg~afV~f~~~~~a~~a~~~l~  121 (198)
                      .........++|||+|||.++++++|+++|++||.|.+        ++++.+      +|||||+|.+.++|++|++.||
T Consensus         5 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~   84 (99)
T 2la6_A            5 HHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD   84 (99)
T ss_dssp             CSCCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhC
Confidence            34455566899999999999999999999999999999        888764      5899999999999999999999


Q ss_pred             CceeCCeEeEEEecc
Q 029166          122 GTVIGKQSVRLSWGR  136 (198)
Q Consensus       122 ~~~~~g~~l~v~~a~  136 (198)
                      +..++|+.|+|++|+
T Consensus        85 g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           85 GKEFSGNPIKVSFAT   99 (99)
T ss_dssp             TCBSSSSBCEEEECC
T ss_pred             CCEeCCcEEEEEecC
Confidence            999999999999985

>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=99.81  E-value=1.6e-19  Score=126.86  Aligned_cols=80  Identities=21%  Similarity=0.380  Sum_probs=73.4

Q ss_pred             CCCCeEEE--cCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCcee-----CCeEeEEEe
Q 029166           62 SSNTTIFV--GGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI-----GKQSVRLSW  134 (198)
Q Consensus        62 ~~~~~lfV--~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~-----~g~~l~v~~  134 (198)
                      .+.++|||  +||++++++++|+++|++||.|.+|.|+.+|+||||+|.+.++|++|++.||+.+|     .++.|.|.+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~  102 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF  102 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEe
Confidence            34678999  77999999999999999999999999999999999999999999999999999998     689999999


Q ss_pred             ccCCCCC
Q 029166          135 GRNPANK  141 (198)
Q Consensus       135 a~~~~~~  141 (198)
                      ++.....
T Consensus       103 a~~~p~~  109 (114)
T 2cq2_A          103 VEKVQWS  109 (114)
T ss_dssp             ESCCCCS
T ss_pred             cccCccc
Confidence            9865443

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=2e-19  Score=126.89  Aligned_cols=78  Identities=23%  Similarity=0.433  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .+.++|||+|||+++++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|++||+. ++..|+|+.|+|+++
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            34589999999999999999999999999999999875      58999999999999999997 999999999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      +++..
T Consensus       104 ~~~~~  108 (116)
T 1x4b_A          104 VAREE  108 (116)
T ss_dssp             SSCCC
T ss_pred             CCCcc
Confidence            87654

>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=99.81  E-value=1.7e-19  Score=125.89  Aligned_cols=82  Identities=29%  Similarity=0.587  Sum_probs=75.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      +......++|||+|||..+++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|++|++.|++..|+|+.|+
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            444556789999999999999999999999999999999864      58999999999999999999999999999999


Q ss_pred             EEeccCCC
Q 029166          132 LSWGRNPA  139 (198)
Q Consensus       132 v~~a~~~~  139 (198)
                      |++++++.
T Consensus       100 V~~a~~k~  107 (108)
T 2jrs_A          100 VGHVTERT  107 (108)
T ss_dssp             EECSCSSC
T ss_pred             EEEcccCC
Confidence            99998764

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=2.1e-19  Score=123.16  Aligned_cols=79  Identities=29%  Similarity=0.555  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceE-EEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeE----
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIA-SVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQS----  129 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~-~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~----  129 (198)
                      ....++|||+|||+++++++|+++|++||.|. +|+|+++      ++||||+|.+.++|++|++.||+..|+|+.    
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            34578999999999999999999999999999 9999875      389999999999999999999999999999    


Q ss_pred             eEEEeccCCC
Q 029166          130 VRLSWGRNPA  139 (198)
Q Consensus       130 l~v~~a~~~~  139 (198)
                      |+|+||++..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999998653

>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=99.80  E-value=3.5e-19  Score=119.66  Aligned_cols=77  Identities=17%  Similarity=0.279  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      ...++|||+|||+++++++|+++|++| .|.++++.+++|||||+|.+.++|++|++.||+..++|+.|+|+|+....
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEeCCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            346889999999999999999999999 99999998889999999999999999999999999999999999997643

>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=99.80  E-value=3.4e-19  Score=123.77  Aligned_cols=78  Identities=21%  Similarity=0.427  Sum_probs=72.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ....+.++|||+|||+.+++++|+++|++||.|.+|+|+.+     ++||||+|.+.++|++|++.||+..|+|+.|+|+
T Consensus        24 ~~~~~~~~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           24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34456889999999999999999999999999999999854     6999999999999999999999999999999999


Q ss_pred             ecc
Q 029166          134 WGR  136 (198)
Q Consensus       134 ~a~  136 (198)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>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=99.80  E-value=4.9e-20  Score=145.08  Aligned_cols=75  Identities=20%  Similarity=0.294  Sum_probs=69.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCC--ceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYG--EIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G--~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ..++|||+||++++++++|+++|++||  .|++|+|+.+      ||||||+|.+.++|++||+.||+..|+|+.|+|++
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  9999999875      58999999999999999999999999999999999


Q ss_pred             ccC
Q 029166          135 GRN  137 (198)
Q Consensus       135 a~~  137 (198)
                      +++
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>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=99.80  E-value=2.6e-19  Score=122.20  Aligned_cols=80  Identities=23%  Similarity=0.514  Sum_probs=73.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHhccCCceEEEEEeC---CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLR----QPFSQYGEIASVKIPV---GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~----~~F~~~G~i~~v~i~~---~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ..+.++|||+|||.++++++|+    ++|++||.|.+|.+..   +++||||+|.+.++|++|++.||+..++|+.|+|+
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   84 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            4567899999999999999999    9999999999999873   57999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 029166          134 WGRNPAN  140 (198)
Q Consensus       134 ~a~~~~~  140 (198)
                      |++++..
T Consensus        85 ~a~~~~~   91 (97)
T 1nu4_A           85 YAKTDSD   91 (97)
T ss_dssp             ECSSCCT
T ss_pred             EccCCCc
Confidence            9987654

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.80  E-value=9e-20  Score=132.34  Aligned_cols=86  Identities=26%  Similarity=0.500  Sum_probs=77.0

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQS  129 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~  129 (198)
                      ..+......++|||+|||+++++++|+++|++||.|..|+|+.+      ++||||+|.+.++|++|++.|++..|+|+.
T Consensus        39 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~  118 (135)
T 2lea_A           39 RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRE  118 (135)
T ss_dssp             CSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSC
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            34455566789999999999999999999999999999999764      689999999999999999999999999999


Q ss_pred             eEEEeccCCCCC
Q 029166          130 VRLSWGRNPANK  141 (198)
Q Consensus       130 l~v~~a~~~~~~  141 (198)
                      |+|+|+++....
T Consensus       119 l~V~~a~~~~~~  130 (135)
T 2lea_A          119 LRVQMARYGRPP  130 (135)
T ss_dssp             CEEEECCCCCCC
T ss_pred             EEEEECCCCCCC
Confidence            999999876443

>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=99.80  E-value=5.6e-20  Score=129.35  Aligned_cols=79  Identities=23%  Similarity=0.369  Sum_probs=72.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      +...++|||+|||+++++++|+++|++||.|.+|+|+.      .++||||+|.+.++|++|| .||+..|+|+.|+|++
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~  100 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEe
Confidence            34458999999999999999999999999999999975      3689999999999999999 8999999999999999


Q ss_pred             ccCCCC
Q 029166          135 GRNPAN  140 (198)
Q Consensus       135 a~~~~~  140 (198)
                      ++++..
T Consensus       101 a~~~~~  106 (114)
T 2cq4_A          101 SQAEKN  106 (114)
T ss_dssp             HHHHHH
T ss_pred             cCCCcc
Confidence            986543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=6.5e-19  Score=118.90  Aligned_cols=78  Identities=21%  Similarity=0.336  Sum_probs=71.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .....++|||+|||+++++++|+++|++| .|.+|+|+.+     +|||||+|.+.++|++|++ ||+..|+|+.|+|.+
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            34567899999999999999999999999 9999999874     6899999999999999999 999999999999999


Q ss_pred             ccCCC
Q 029166          135 GRNPA  139 (198)
Q Consensus       135 a~~~~  139 (198)
                      ++++.
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98764

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.80  E-value=7.2e-19  Score=127.63  Aligned_cols=79  Identities=27%  Similarity=0.592  Sum_probs=72.1

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      ......+.++|||+|||..+++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.||+..|+|+.|
T Consensus        56 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  135 (140)
T 2ku7_A           56 SGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI  135 (140)
T ss_dssp             SCSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEE
T ss_pred             CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            3445567899999999999999999999999999999999764      7999999999999999999999999999999


Q ss_pred             EEEec
Q 029166          131 RLSWG  135 (198)
Q Consensus       131 ~v~~a  135 (198)
                      +|+||
T Consensus       136 ~v~~A  140 (140)
T 2ku7_A          136 RVNLA  140 (140)
T ss_dssp             EEEC-
T ss_pred             EEEeC
Confidence            99986

>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=99.80  E-value=3e-19  Score=133.71  Aligned_cols=84  Identities=23%  Similarity=0.486  Sum_probs=75.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      +....+.++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|++||+.||+..|.|+.|.
T Consensus        66 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  145 (165)
T 1rk8_A           66 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ  145 (165)
T ss_dssp             CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            444566789999999999999999999999999999999875      69999999999999999999999999999999


Q ss_pred             EEeccCCCCC
Q 029166          132 LSWGRNPANK  141 (198)
Q Consensus       132 v~~a~~~~~~  141 (198)
                      |.|+.++..+
T Consensus       146 V~~a~~~~~~  155 (165)
T 1rk8_A          146 VDWCFVKGPK  155 (165)
T ss_dssp             EEESEECC--
T ss_pred             EEEecCCCCC
Confidence            9999876544

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.79  E-value=3.2e-19  Score=128.05  Aligned_cols=80  Identities=18%  Similarity=0.435  Sum_probs=72.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHhccCCceEEEEEeC---CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLR----QPFSQYGEIASVKIPV---GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~----~~F~~~G~i~~v~i~~---~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ..+.++|||+|||+.+++++|+    ++|++||.|.+|.+.+   +||||||+|.+.++|++|++.||+..|.|+.|+|+
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~  105 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVIT  105 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEE
Confidence            4457899999999999999876    6999999999998864   57999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 029166          134 WGRNPAN  140 (198)
Q Consensus       134 ~a~~~~~  140 (198)
                      ||+.+..
T Consensus       106 ~a~~~~~  112 (127)
T 2a3j_A          106 FSETPQS  112 (127)
T ss_dssp             ECCCCCH
T ss_pred             EccCcch
Confidence            9987654

>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=99.79  E-value=3.6e-19  Score=131.10  Aligned_cols=82  Identities=24%  Similarity=0.475  Sum_probs=76.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      .......++|||+|||+++++++|+++|++||.|.+|+|+.+ +|||||+|.+.++|++|++.||+..|+|+.|+|+|++
T Consensus        67 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  146 (150)
T 2i2y_A           67 RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSN  146 (150)
T ss_dssp             SSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECC
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcC
Confidence            444556789999999999999999999999999999999987 8999999999999999999999999999999999998


Q ss_pred             CCC
Q 029166          137 NPA  139 (198)
Q Consensus       137 ~~~  139 (198)
                      ++.
T Consensus       147 ~~~  149 (150)
T 2i2y_A          147 GEK  149 (150)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>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=99.79  E-value=4.4e-19  Score=119.06  Aligned_cols=75  Identities=24%  Similarity=0.498  Sum_probs=70.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      +.++|||+|||+++++++|+++|++||.|.+++++.+      ++||||+|.+.++|++|+ .||+..++|+.|+|++++
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            3579999999999999999999999999999999764      689999999999999999 899999999999999998


Q ss_pred             CC
Q 029166          137 NP  138 (198)
Q Consensus       137 ~~  138 (198)
                      +.
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.79  E-value=1.9e-19  Score=129.77  Aligned_cols=83  Identities=19%  Similarity=0.441  Sum_probs=74.2

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEE--EEEeCC------CcEEEEEeCCHHHHHHHHHHhCCc----e
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS--VKIPVG------KGCGFVQFANRENAEEALHKLNGT----V  124 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~--v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~----~  124 (198)
                      .+......++|||+|||++++|++|+++|++||.|..  |+|+++      ||||||+|.+. +|++|++.||+.    .
T Consensus        16 ~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~   94 (131)
T 2m2b_A           16 EPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT   94 (131)
T ss_dssp             CCCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc
Confidence            3444566789999999999999999999999999976  888764      59999999999 999999999999    9


Q ss_pred             eCCeEeEEEeccCCCC
Q 029166          125 IGKQSVRLSWGRNPAN  140 (198)
Q Consensus       125 ~~g~~l~v~~a~~~~~  140 (198)
                      |+|+.|+|+++++...
T Consensus        95 ~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           95 IDGKTINVEFAKGSKR  110 (131)
T ss_dssp             GGGCCCCCEECCCSCC
T ss_pred             CCCEEEEEEECCCCCC
Confidence            9999999999987543

>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=99.79  E-value=5.9e-19  Score=122.99  Aligned_cols=79  Identities=20%  Similarity=0.400  Sum_probs=72.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCc-eEEEEEe-------CCCcEEEEEeCCHHHHHHHHHHhC--CceeCCeEeE
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGE-IASVKIP-------VGKGCGFVQFANRENAEEALHKLN--GTVIGKQSVR  131 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~-i~~v~i~-------~~kg~afV~f~~~~~a~~a~~~l~--~~~~~g~~l~  131 (198)
                      .+.++|||+|||+++++++|+++|++||. |.+|.++       .+++||||+|.+.++|++|++.|+  +..++|+.|+
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            45789999999999999999999999998 9999998       458999999999999999999996  5899999999


Q ss_pred             EEeccCCCC
Q 029166          132 LSWGRNPAN  140 (198)
Q Consensus       132 v~~a~~~~~  140 (198)
                      |+|++++..
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987654

>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=99.79  E-value=1.1e-18  Score=120.84  Aligned_cols=80  Identities=29%  Similarity=0.417  Sum_probs=71.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEE-EEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS-VKIPV-----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~-v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .......++|||+|||+++++++|+++|++||.|.+ |+|+.     ++|||||+|.+.++|++||+. ++..|+++.|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~   87 (104)
T 1wg5_A            9 SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIE   87 (104)
T ss_dssp             CSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEE
Confidence            344456789999999999999999999999999987 87765     379999999999999999997 99999999999


Q ss_pred             EEeccCC
Q 029166          132 LSWGRNP  138 (198)
Q Consensus       132 v~~a~~~  138 (198)
                      |.++.++
T Consensus        88 v~~~~~~   94 (104)
T 1wg5_A           88 IFKSSRA   94 (104)
T ss_dssp             EEEECTT
T ss_pred             EEECCHH
Confidence            9998754

>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=99.79  E-value=1.3e-19  Score=127.63  Aligned_cols=80  Identities=16%  Similarity=0.170  Sum_probs=72.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCce-EEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI-ASVKIPV-----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i-~~v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ....+.++|||+|||+++++++|+++|++||.| ..|+|+.     .+|||||+|.+.++|++||+. |+..|+|+.|+|
T Consensus        10 ~~~~~~~~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           10 DVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             SCCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            344567899999999999999999999999999 8888876     479999999999999999986 999999999999


Q ss_pred             EeccCCC
Q 029166          133 SWGRNPA  139 (198)
Q Consensus       133 ~~a~~~~  139 (198)
                      .++.++.
T Consensus        89 ~~a~~~~   95 (114)
T 2cpy_A           89 HVVTLED   95 (114)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9997643

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.79  E-value=1.5e-18  Score=123.78  Aligned_cols=82  Identities=21%  Similarity=0.430  Sum_probs=75.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ......++|||+|||..+++++|+++|++||.|.+|+|+.+     ++||||+|.+.++|++|++.|++..|+|+.|+|+
T Consensus        30 ~~~~~~~~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           30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34556789999999999999999999999999999999874     6999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 029166          134 WGRNPAN  140 (198)
Q Consensus       134 ~a~~~~~  140 (198)
                      +|.+...
T Consensus       110 ~a~~~~~  116 (124)
T 2kt5_A          110 LVASQID  116 (124)
T ss_dssp             EECCTTC
T ss_pred             EeCCCCC
Confidence            9987543

>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=99.79  E-value=6.6e-19  Score=123.88  Aligned_cols=82  Identities=27%  Similarity=0.497  Sum_probs=72.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCce----EEEEEeC--CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI----ASVKIPV--GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i----~~v~i~~--~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ...+.++|||+|||+++++++|+++|++||.|    ..+++..  +++||||+|.+.++|++|++.|++..|+|+.|+|+
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34467899999999999999999999999998    5666554  47999999999999999999999999999999999


Q ss_pred             eccCCCCC
Q 029166          134 WGRNPANK  141 (198)
Q Consensus       134 ~a~~~~~~  141 (198)
                      |++++..+
T Consensus       101 ~a~~~~~~  108 (115)
T 2cpx_A          101 FGKNKKQR  108 (115)
T ss_dssp             ECCCCSCC
T ss_pred             EccCCCCC
Confidence            99986544

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=7.5e-20  Score=126.44  Aligned_cols=82  Identities=30%  Similarity=0.537  Sum_probs=74.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      .+.+.++|||+|||..+++++|+++|++||.|.+|+++.+      ++||||+|.+.++|++|++.||+..++|+.|+|+
T Consensus         4 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   83 (104)
T 1p1t_A            4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             SHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             cCCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            3445689999999999999999999999999999999864      6999999999999999999999999999999999


Q ss_pred             eccCCCCC
Q 029166          134 WGRNPANK  141 (198)
Q Consensus       134 ~a~~~~~~  141 (198)
                      |++++..+
T Consensus        84 ~a~~~~~~   91 (104)
T 1p1t_A           84 NAASEKNK   91 (104)
T ss_dssp             ETTCTTHH
T ss_pred             eCCCccch
Confidence            99876543

>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=99.79  E-value=1.9e-19  Score=123.84  Aligned_cols=82  Identities=27%  Similarity=0.484  Sum_probs=68.9

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-------CcEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 029166           56 PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-------KGCGFVQFANRENAEEALHKLNGTVIGKQ  128 (198)
Q Consensus        56 ~~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-------kg~afV~f~~~~~a~~a~~~l~~~~~~g~  128 (198)
                      .........++|||+|||.++++++|+++|++|| |.+|+|+.+       +|||||+|.+.++|++|+ .|++..|+|+
T Consensus        11 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~   88 (100)
T 2j76_E           11 RSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNR   88 (100)
T ss_dssp             ---------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTB
T ss_pred             CCcCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCe
Confidence            3445556789999999999999999999999999 999999764       589999999999999999 8999999999


Q ss_pred             EeEEEeccCCC
Q 029166          129 SVRLSWGRNPA  139 (198)
Q Consensus       129 ~l~v~~a~~~~  139 (198)
                      .|+|++++++.
T Consensus        89 ~l~V~~a~~~~   99 (100)
T 2j76_E           89 RIRVDVADQAQ   99 (100)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEeccCCC
Confidence            99999998753

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.6e-19  Score=123.32  Aligned_cols=77  Identities=18%  Similarity=0.369  Sum_probs=71.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .+...++|||+|||+++|+++|+++|++||.|.+|.|+.     ++|||||+|.+.++|++|+. +++..++|+.|.|.|
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            445578999999999999999999999999999999987     47999999999999999999 899999999999999


Q ss_pred             ccC
Q 029166          135 GRN  137 (198)
Q Consensus       135 a~~  137 (198)
                      +..
T Consensus        86 ~~~   88 (103)
T 1s79_A           86 KDD   88 (103)
T ss_dssp             HHH
T ss_pred             chH
Confidence            764

>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=99.79  E-value=8.2e-19  Score=117.37  Aligned_cols=76  Identities=22%  Similarity=0.511  Sum_probs=69.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ....+.++|||+|||+++++++|+++|++||.|.+++|+.+      +|||||+|.+.++|++|++ +++..|+|+.|+|
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v   84 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDP   84 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEE
Confidence            44567889999999999999999999999999999999764      5899999999999999996 5888999999999


Q ss_pred             Eec
Q 029166          133 SWG  135 (198)
Q Consensus       133 ~~a  135 (198)
                      ++|
T Consensus        85 ~~A   87 (87)
T 3s7r_A           85 KKA   87 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.79  E-value=1e-18  Score=122.15  Aligned_cols=83  Identities=25%  Similarity=0.427  Sum_probs=69.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      ..+...+.++|||+|||.++++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|++|++.+ +..|+|+.|
T Consensus        18 ~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l   96 (109)
T 2rs2_A           18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTI   96 (109)
T ss_dssp             --------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEE
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEE
Confidence            3445566789999999999999999999999999999999874      689999999999999999976 599999999


Q ss_pred             EEEeccCCCC
Q 029166          131 RLSWGRNPAN  140 (198)
Q Consensus       131 ~v~~a~~~~~  140 (198)
                      +|+++.++..
T Consensus        97 ~V~~a~~~~~  106 (109)
T 2rs2_A           97 DPKVAFPRRA  106 (109)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEccCCCC
Confidence            9999987643

>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=99.79  E-value=1.8e-18  Score=147.93  Aligned_cols=82  Identities=22%  Similarity=0.442  Sum_probs=75.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ....++|||+|||+.+++++|+++|++||.|+.|.|+.+      +|||||+|.+.++|++||..||+..|+|+.|.|+|
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            345689999999999999999999999999999999864      79999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 029166          135 GRNPANKQ  142 (198)
Q Consensus       135 a~~~~~~~  142 (198)
                      +++.....
T Consensus       179 a~~~~~~~  186 (437)
T 3pgw_S          179 ERGRTVKG  186 (437)
T ss_pred             eCCCCCCC
Confidence            98765543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=2.1e-18  Score=123.13  Aligned_cols=77  Identities=18%  Similarity=0.179  Sum_probs=70.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcE-EEEEeCCHHHHHHHHHHhCCceeCC--eEeEEEeccCCCC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC-GFVQFANRENAEEALHKLNGTVIGK--QSVRLSWGRNPAN  140 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~-afV~f~~~~~a~~a~~~l~~~~~~g--~~l~v~~a~~~~~  140 (198)
                      ...|||+||++.+++++|+++|++||.|++|.|....|| |||+|.+.++|++|++.|||..|.|  +.|+|++|+++..
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l  104 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRL  104 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEESSSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSCC
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCcc
Confidence            345789999999999999999999999999998766697 9999999999999999999999987  6999999998654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.78  E-value=6.4e-19  Score=122.30  Aligned_cols=80  Identities=24%  Similarity=0.367  Sum_probs=72.5

Q ss_pred             CCCCCCCeEEEcCCCCCC------CHHHHHHHhccCCceEEEEEeC----CCcEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 029166           59 EGDSSNTTIFVGGLDPNV------TDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNGTVIGKQ  128 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~------~e~~l~~~F~~~G~i~~v~i~~----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~  128 (198)
                      ......++|||+|||+.+      ++++|+++|++||.|.+|.|++    ++|||||+|.+.++|++|++.||+..|+|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           10 EADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             SCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            344457899999999999      7899999999999999999984    479999999999999999999999999998


Q ss_pred             -EeEEEeccCC
Q 029166          129 -SVRLSWGRNP  138 (198)
Q Consensus       129 -~l~v~~a~~~  138 (198)
                       .|+|+++...
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             9999999754

>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=99.78  E-value=9e-20  Score=123.09  Aligned_cols=76  Identities=20%  Similarity=0.299  Sum_probs=65.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCC--ceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYG--EIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G--~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      .+|||+|||+++++++|+++|++||  .|.+++++.+      +|||||+|.+.++|++|++.||+..|+|+.|+|+++.
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  9999998764      5899999999999999999999999999999999998


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      ++..
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7643

>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=99.78  E-value=2.1e-19  Score=122.19  Aligned_cols=76  Identities=26%  Similarity=0.303  Sum_probs=67.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ...++|||+|||+++++++|+++|++||.|.++.++.      .++||||+|.+.++|++|++.||+..|+|+.|+|+++
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            3468999999999999999999999999998776654      3699999999999999999999999999999999998


Q ss_pred             cC
Q 029166          136 RN  137 (198)
Q Consensus       136 ~~  137 (198)
                      .+
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            64

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=2.2e-18  Score=117.07  Aligned_cols=78  Identities=23%  Similarity=0.362  Sum_probs=68.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCc-EEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG-CGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPAN  140 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg-~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~~  140 (198)
                      ...++|||+|||+++++++|+++|++||.|.+|.+.+..+ ||||+|.+.++|++|++ |++..|+|+.|+|+++.++..
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~   84 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEF   84 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCC
Confidence            3467999999999999999999999999999983332222 99999999999999999 999999999999999876543

>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=99.78  E-value=1e-18  Score=120.74  Aligned_cols=79  Identities=23%  Similarity=0.326  Sum_probs=69.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ......++|||+|||++++|++|+++|++||.| +|+|+.+     +|||||+|.+.++|++||+ +|+..|+++.|+|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            344567899999999999999999999999954 8988764     6899999999999999995 79999999999999


Q ss_pred             eccCCC
Q 029166          134 WGRNPA  139 (198)
Q Consensus       134 ~a~~~~  139 (198)
                      ++.+..
T Consensus        88 ~~~~~~   93 (102)
T 1wez_A           88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            987643

>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=99.78  E-value=2.9e-18  Score=120.41  Aligned_cols=80  Identities=18%  Similarity=0.455  Sum_probs=73.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCcee--------
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVI--------  125 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~--------  125 (198)
                      ..+.+.++|||+|||+++++++|+++|++||.|.+|+|+.+     ++||||+|.+.++|++|++.||+..|        
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            44556789999999999999999999999999999999875     68999999999999999999999999        


Q ss_pred             CCeEeEEEeccCC
Q 029166          126 GKQSVRLSWGRNP  138 (198)
Q Consensus       126 ~g~~l~v~~a~~~  138 (198)
                      .++.|.|+|++++
T Consensus       100 ~~~~l~v~~a~p~  112 (114)
T 1x5o_A          100 PTEPLLCKFSGPS  112 (114)
T ss_dssp             CSSCBEEEECCCS
T ss_pred             CCCceeEEccCCC
Confidence            5778999999864

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.78  E-value=2.1e-18  Score=127.91  Aligned_cols=82  Identities=27%  Similarity=0.523  Sum_probs=75.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ......++|||+|||+++++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|++|++.||+..|+|+.|+|
T Consensus        65 ~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  144 (158)
T 2kn4_A           65 MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV  144 (158)
T ss_dssp             CCCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34456789999999999999999999999999999999874      689999999999999999999999999999999


Q ss_pred             EeccCCCC
Q 029166          133 SWGRNPAN  140 (198)
Q Consensus       133 ~~a~~~~~  140 (198)
                      +|++++..
T Consensus       145 ~~a~~~~~  152 (158)
T 2kn4_A          145 QMARYGRP  152 (158)
T ss_dssp             EEECCSSC
T ss_pred             EECCCCCC
Confidence            99987543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.78  E-value=7.9e-19  Score=125.13  Aligned_cols=77  Identities=26%  Similarity=0.508  Sum_probs=71.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      +.++|||+|||.++++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|+ .||+..|+|+.|+|+|++
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            4689999999999999999999999999999999764      699999999999999999 799999999999999998


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      +...
T Consensus       114 ~~~~  117 (124)
T 2jwn_A          114 TNMP  117 (124)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            6543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=2.3e-19  Score=119.59  Aligned_cols=75  Identities=32%  Similarity=0.524  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .+.++|||+|||+++++++|+++|++||.|.+++|+.+      ++||||+|.+.++|++|++.||+..|+|+.|+|.++
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            45789999999999999999999999999999999875      689999999999999999999999999999988776


Q ss_pred             c
Q 029166          136 R  136 (198)
Q Consensus       136 ~  136 (198)
                      +
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=1.6e-18  Score=118.04  Aligned_cols=79  Identities=19%  Similarity=0.334  Sum_probs=71.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEE-EeCCC--cEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVK-IPVGK--GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~-i~~~k--g~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      .....++|||+|||+++++++|+++|++||.|.+++ |+.++  +.|||+|.+.++|++|++.||+..|+|+.|+|+++.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   90 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIP   90 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            344578999999999999999999999999999994 77653  559999999999999999999999999999999998


Q ss_pred             CC
Q 029166          137 NP  138 (198)
Q Consensus       137 ~~  138 (198)
                      ++
T Consensus        91 ~~   92 (96)
T 2e44_A           91 DE   92 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            76

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.78  E-value=1.8e-19  Score=124.02  Aligned_cols=77  Identities=22%  Similarity=0.372  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCC------CCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCC-e
Q 029166           62 SSNTTIFVGGLDP------NVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGK-Q  128 (198)
Q Consensus        62 ~~~~~lfV~~l~~------~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g-~  128 (198)
                      ...++|||+|||.      ++++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|++|++.||+..|+| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3468999999999      9999999999999999999999753      6999999999999999999999999999 9


Q ss_pred             EeEEEeccCC
Q 029166          129 SVRLSWGRNP  138 (198)
Q Consensus       129 ~l~v~~a~~~  138 (198)
                      .|+|.++.+.
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999999753

>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=99.78  E-value=1.1e-18  Score=129.71  Aligned_cols=80  Identities=24%  Similarity=0.266  Sum_probs=71.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC--CcEEEEEeCCHHHHHHHHHHhCCceeCC--eEeEEEecc
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG--KGCGFVQFANRENAEEALHKLNGTVIGK--QSVRLSWGR  136 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~--kg~afV~f~~~~~a~~a~~~l~~~~~~g--~~l~v~~a~  136 (198)
                      .....+|||+||++.+++++|+++|++||+|++|.|..+  ++||||+|.+.++|++|++.|||..|.+  +.|+|+|++
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            344578999999999999999999999999999998643  5799999999999999999999999965  999999999


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      ++..
T Consensus       123 ~~~l  126 (164)
T 1sjr_A          123 LTSL  126 (164)
T ss_dssp             SSSC
T ss_pred             CCcc
Confidence            7643

>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=99.77  E-value=9.8e-19  Score=117.37  Aligned_cols=77  Identities=32%  Similarity=0.511  Sum_probs=66.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPAN  140 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~~  140 (198)
                      ...++|||+|||+++++++|+++|++||.|.+|+|+.+ ++||||+|.+.++|++++..  ...+.++.|+|.+++++..
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~~   80 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCCC
Confidence            34789999999999999999999999999999999875 89999999999999865432  3456899999999987654

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.77  E-value=1.4e-18  Score=129.11  Aligned_cols=76  Identities=22%  Similarity=0.340  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCC--ceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYG--EIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G--~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ..++|||+|||+++++++|+++|++||  .|.+|+|+.+      +|||||+|.+.++|++||+.||+..|+|+.|+|++
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            568999999999999999999999999  9999999864      58999999999999999999999999999999999


Q ss_pred             ccCC
Q 029166          135 GRNP  138 (198)
Q Consensus       135 a~~~  138 (198)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9753

>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=99.77  E-value=1.7e-18  Score=121.76  Aligned_cols=77  Identities=18%  Similarity=0.407  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC---CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~---kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ...++|||+|||+.+++++|+++|++||.|.+|.|+.+   +|||||+|.+.++|++|++.||+..++|+.|+|+|++++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   85 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNAN   85 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            35689999999999999999999999999999999764   689999999999999999999999999999999999864

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.77  E-value=8.5e-19  Score=119.43  Aligned_cols=82  Identities=24%  Similarity=0.387  Sum_probs=71.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEE-eCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI-PVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i-~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      ....+.++|||+|||..+++++|+++|++||.|..+.. ..++|||||+|.+.++|++|++.|++..|+|+.|+|+++++
T Consensus        11 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   90 (96)
T 1fjc_A           11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCC
Confidence            34456789999999999999999999999999877711 12479999999999999999999999999999999999987


Q ss_pred             CCC
Q 029166          138 PAN  140 (198)
Q Consensus       138 ~~~  140 (198)
                      +..
T Consensus        91 ~~~   93 (96)
T 1fjc_A           91 KGG   93 (96)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.76  E-value=5.1e-18  Score=121.78  Aligned_cols=79  Identities=24%  Similarity=0.293  Sum_probs=71.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-CCcE-EEEEeCCHHHHHHHHHHhCCceeCC--eEeEEEeccC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-GKGC-GFVQFANRENAEEALHKLNGTVIGK--QSVRLSWGRN  137 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-~kg~-afV~f~~~~~a~~a~~~l~~~~~~g--~~l~v~~a~~  137 (198)
                      ...-+|||+||++.+++++|+++|++||.|.+|.|.. .++| |||+|.+.++|++|++.|||..|.+  +.|+|+|+++
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~  105 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  105 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSC
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCC
Confidence            4456788999999999999999999999999998865 4688 9999999999999999999999987  8999999997


Q ss_pred             CCC
Q 029166          138 PAN  140 (198)
Q Consensus       138 ~~~  140 (198)
                      ..-
T Consensus       106 ~~l  108 (130)
T 3zzy_A          106 TSL  108 (130)
T ss_dssp             SSC
T ss_pred             Cce
Confidence            644

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.76  E-value=1.9e-18  Score=116.44  Aligned_cols=78  Identities=35%  Similarity=0.506  Sum_probs=62.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCce--eCCeEeEEEec
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTV--IGKQSVRLSWG  135 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~--~~g~~l~v~~a  135 (198)
                      ....+.++|||+|||++++|++|+++|++||.|.+|+|+++ ||||||+|.+.++|++    +++..  +.++.|.|.+|
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNA   81 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEc
Confidence            34556889999999999999999999999999999999874 8999999999999984    44444  56999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      +++..
T Consensus        82 ~~k~~   86 (89)
T 3d2w_A           82 EPKHN   86 (89)
T ss_dssp             C----
T ss_pred             CCCCc
Confidence            87643

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.62  E-value=3.9e-20  Score=130.61  Aligned_cols=81  Identities=31%  Similarity=0.483  Sum_probs=73.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEE--------EEEeCC------CcEEEEEeCCHHHHHHHHHHhCCcee
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS--------VKIPVG------KGCGFVQFANRENAEEALHKLNGTVI  125 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~--------v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~  125 (198)
                      +..+.++|||+|||..+++++|+++|++||.|..        |+|+.+      ++||||+|.+.++|++|++.||+..|
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            3456789999999999999999999999999998        777764      68999999999999999999999999


Q ss_pred             CCeEeEEEeccCCCC
Q 029166          126 GKQSVRLSWGRNPAN  140 (198)
Q Consensus       126 ~g~~l~v~~a~~~~~  140 (198)
                      +|+.|+|++++++..
T Consensus        83 ~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           83 SGNPIKVSFATRRAD   97 (116)
Confidence            999999999987643

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.76  E-value=2.4e-18  Score=121.89  Aligned_cols=78  Identities=17%  Similarity=0.237  Sum_probs=71.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCc---eEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGE---IASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~---i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      ....+.++|||+|||+++++++|+++|++||.   |..|+|+.+     +|||||+|.+.++|++||+ +|+..|+|+.|
T Consensus        12 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i   90 (118)
T 2db1_A           12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYI   90 (118)
T ss_dssp             SCBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEE
Confidence            33456789999999999999999999999998   889998764     6899999999999999999 99999999999


Q ss_pred             EEEeccC
Q 029166          131 RLSWGRN  137 (198)
Q Consensus       131 ~v~~a~~  137 (198)
                      +|.++..
T Consensus        91 ~V~~a~~   97 (118)
T 2db1_A           91 EVFKSHR   97 (118)
T ss_dssp             EEEEECH
T ss_pred             EEEECCH
Confidence            9999864

>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=2.3e-18  Score=115.07  Aligned_cols=72  Identities=22%  Similarity=0.476  Sum_probs=68.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccC----C-------ceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQY----G-------EIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~----G-------~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      .+.++|||+|||+++++++|+++|++|    |       .|.++++.++++||||+|.+.++|++|+ .||+..++|+.|
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l   82 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   82 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEE
Confidence            457899999999999999999999999    8       9999999999999999999999999999 899999999999


Q ss_pred             EEEe
Q 029166          131 RLSW  134 (198)
Q Consensus       131 ~v~~  134 (198)
                      +|+.
T Consensus        83 ~V~r   86 (87)
T 2hzc_A           83 KIRR   86 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9973

>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=99.76  E-value=1.6e-18  Score=125.84  Aligned_cols=79  Identities=16%  Similarity=0.227  Sum_probs=71.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCc---eEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGE---IASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQS  129 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~---i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~  129 (198)
                      .....+.++|||+|||+++|+++|+++|++||.   |.+|+|+.+     +|||||+|.+.++|++||+ ||+..|+|+.
T Consensus        38 ~~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~  116 (136)
T 2hgl_A           38 GPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRY  116 (136)
T ss_dssp             CSSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEE
Confidence            344556789999999999999999999999999   888988764     6899999999999999999 9999999999


Q ss_pred             eEEEeccC
Q 029166          130 VRLSWGRN  137 (198)
Q Consensus       130 l~v~~a~~  137 (198)
                      |+|.++.+
T Consensus       117 i~V~~a~~  124 (136)
T 2hgl_A          117 IEVFKSHR  124 (136)
T ss_dssp             EEEEECCH
T ss_pred             EEEEECCh
Confidence            99999864

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.76  E-value=5.1e-18  Score=116.67  Aligned_cols=80  Identities=23%  Similarity=0.410  Sum_probs=69.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEE-----EEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS-----VKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~-----v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .....++|||+|||+++++++|+++|++||.|..     .....++|||||+|.+.++|++|++ ||+..|+|+.|+|++
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            3445789999999999999999999999997755     2223458999999999999999999 999999999999999


Q ss_pred             ccCCCC
Q 029166          135 GRNPAN  140 (198)
Q Consensus       135 a~~~~~  140 (198)
                      ++++..
T Consensus        92 a~~~~~   97 (101)
T 1fj7_A           92 PKGRDG   97 (101)
T ss_dssp             CSCCCC
T ss_pred             cCCCCC
Confidence            987643

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.75  E-value=1.3e-18  Score=113.20  Aligned_cols=69  Identities=30%  Similarity=0.527  Sum_probs=65.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      +|||+|||+++++++|+++|++||.|.+++++.+      +|||||+|.+.++|++|++ +++..++|+.|+|++|
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            5999999999999999999999999999998764      5899999999999999998 9999999999999986

>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=99.75  E-value=6.6e-19  Score=128.28  Aligned_cols=79  Identities=22%  Similarity=0.315  Sum_probs=69.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ......++|||+|||++++|++|+++|++|| |.+|+|+.+     +|||||+|.+.++|++|| .+|+..|+++.|+|.
T Consensus        41 ~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~  118 (139)
T 2hgn_A           41 VQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELF  118 (139)
T ss_dssp             ----CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEE
Confidence            4455678999999999999999999999999 779999864     799999999999999999 689999999999999


Q ss_pred             eccCCC
Q 029166          134 WGRNPA  139 (198)
Q Consensus       134 ~a~~~~  139 (198)
                      ++.+..
T Consensus       119 ~a~~~~  124 (139)
T 2hgn_A          119 LNSTTG  124 (139)
T ss_dssp             ECCCSC
T ss_pred             ECCCCC
Confidence            987654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=1.2e-18  Score=113.73  Aligned_cols=70  Identities=26%  Similarity=0.526  Sum_probs=66.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ++|||+|||+++++++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++.++ ..++|+.|+|++|
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            47999999999999999999999999999999874      5899999999999999999999 9999999999987

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=8.6e-18  Score=117.49  Aligned_cols=75  Identities=23%  Similarity=0.349  Sum_probs=68.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ..+..+|||+|||+++++++|+++|+.| .|.+|+|+.+     +|||||+|.+.++|++|| .+|+..|+|+.|+|..+
T Consensus        13 ~~~~~~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           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            3446799999999999999999999999 8999999863     799999999999999999 59999999999999988


Q ss_pred             cC
Q 029166          136 RN  137 (198)
Q Consensus       136 ~~  137 (198)
                      .+
T Consensus        91 ~~   92 (109)
T 2dnn_A           91 TE   92 (109)
T ss_dssp             CH
T ss_pred             Cc
Confidence            64

>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=99.74  E-value=4.7e-19  Score=119.32  Aligned_cols=75  Identities=31%  Similarity=0.520  Sum_probs=67.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ++|||+|||.++++++|+++|++||.|.+++++.+      +|||||+|.+.+ |++|++.||+..++|+.|+|++|.+.
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            58999999999999999999999999999999864      689999999999 99999999999999999999999875


Q ss_pred             CC
Q 029166          139 AN  140 (198)
Q Consensus       139 ~~  140 (198)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>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=99.74  E-value=1.2e-17  Score=129.24  Aligned_cols=77  Identities=23%  Similarity=0.416  Sum_probs=72.4

Q ss_pred             CCCeEEEcCCC-CCCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           63 SNTTIFVGGLD-PNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        63 ~~~~lfV~~l~-~~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      +.++|||+||+ +.+++++|+++|++||.|.+|+|+++ +|||||+|.+.++|++||+.||+..+.|+.|+|.+++.+.
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~   81 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA   81 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCc
Confidence            47899999999 89999999999999999999999885 6999999999999999999999999999999999997543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.74  E-value=1.6e-18  Score=114.56  Aligned_cols=69  Identities=25%  Similarity=0.422  Sum_probs=64.0

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHHhccCCceEEEEEeC----CCcEEEEEeCCHHHHHHHHHHhCCceeCCe-EeEE
Q 029166           64 NTTIFVGGLDPNV------TDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENAEEALHKLNGTVIGKQ-SVRL  132 (198)
Q Consensus        64 ~~~lfV~~l~~~~------~e~~l~~~F~~~G~i~~v~i~~----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~-~l~v  132 (198)
                      +++|||+|||..+      ++++|+++|++||.|.+|.|++    ++|||||+|.+.++|++|++.||+..++|+ .|+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            3689999999999      7799999999999999999874    479999999999999999999999999999 8876

>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=99.74  E-value=2.9e-18  Score=122.36  Aligned_cols=78  Identities=15%  Similarity=0.255  Sum_probs=68.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      .....++|||+|||+++++++|+++|++||.|.++.++.      .+|||||+|.+.++|++||+ ||+..|+|+.|+|.
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            345668999999999999999999999999987743332      36999999999999999999 99999999999999


Q ss_pred             eccCC
Q 029166          134 WGRNP  138 (198)
Q Consensus       134 ~a~~~  138 (198)
                      ++.++
T Consensus       100 ~a~~~  104 (124)
T 1wel_A          100 PITKK  104 (124)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            99753

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.5e-17  Score=111.93  Aligned_cols=73  Identities=19%  Similarity=0.310  Sum_probs=65.8

Q ss_pred             CCe-EEEcCCCCCCCHHH----HHHHhccC-CceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           64 NTT-IFVGGLDPNVTDED----LRQPFSQY-GEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        64 ~~~-lfV~~l~~~~~e~~----l~~~F~~~-G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      ..+ |||+|||+.+++++    |+++|++| |+|.+|    ..|+|||+|.+.++|++|++.|++..+.|+.|+|.+|+.
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V----tgG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~   83 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI----TGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPK   83 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC----CTTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCC
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE----ecCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCC
Confidence            444 99999999999988    55899999 599988    249999999999999999999999999999999999997


Q ss_pred             CCC
Q 029166          138 PAN  140 (198)
Q Consensus       138 ~~~  140 (198)
                      .+.
T Consensus        84 ~sd   86 (96)
T 2diu_A           84 NRE   86 (96)
T ss_dssp             SCC
T ss_pred             Ccc
Confidence            654

>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=99.73  E-value=6.4e-18  Score=123.41  Aligned_cols=81  Identities=27%  Similarity=0.470  Sum_probs=70.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEE--------EEEe---CCCcEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS--------VKIP---VGKGCGFVQFANRENAEEALHKLNGTVIGKQS  129 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~--------v~i~---~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~  129 (198)
                      ..+.++|||+|||+.+++++|+++|++||.|..        +.+.   .++|||||+|.+.++|++|++.||+..|+|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            345689999999999999999999999998765        3332   35799999999999999999999999999999


Q ss_pred             eEEEeccCCCCC
Q 029166          130 VRLSWGRNPANK  141 (198)
Q Consensus       130 l~v~~a~~~~~~  141 (198)
                      |+|+||++...+
T Consensus       122 l~V~~a~~~~~~  133 (143)
T 3egn_A          122 MVVQFARSARPK  133 (143)
T ss_dssp             CEEEECCCSCC-
T ss_pred             EEEEECCCCCCc
Confidence            999999875443

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.73  E-value=2e-17  Score=128.35  Aligned_cols=79  Identities=32%  Similarity=0.556  Sum_probs=71.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ..+.++|||+|||++++|++|+++|++||+|.+|+|+++      +|||||+|.+.++|++|++.+++..+.|+.|++.+
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            345689999999999999999999999999999999864      58999999999999999999999999999999999


Q ss_pred             ccCCC
Q 029166          135 GRNPA  139 (198)
Q Consensus       135 a~~~~  139 (198)
                      +....
T Consensus        92 ~~~~~   96 (213)
T 4f02_A           92 SQRDP   96 (213)
T ss_dssp             CCCCT
T ss_pred             ccccc
Confidence            87543

>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=99.72  E-value=6.1e-18  Score=117.70  Aligned_cols=79  Identities=19%  Similarity=0.205  Sum_probs=71.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCc---eEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGE---IASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~---i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      ....+.++|||+|||+++++++|+++|+.||.   |.+|+|+.+     +|||||+|.+.++|++||+ +++..|+|+.|
T Consensus         6 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            34456789999999999999999999999988   899999764     6899999999999999999 99999999999


Q ss_pred             EEEeccCC
Q 029166          131 RLSWGRNP  138 (198)
Q Consensus       131 ~v~~a~~~  138 (198)
                      +|.++.++
T Consensus        85 ~V~~a~~~   92 (107)
T 2lmi_A           85 EVYEINNE   92 (107)
T ss_dssp             CCEECCHH
T ss_pred             EEEECCHH
Confidence            99998753

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.72  E-value=4.4e-18  Score=132.12  Aligned_cols=78  Identities=32%  Similarity=0.574  Sum_probs=72.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ...+|||+|||+++++++|+++|++||.|.+++|+.+    +|||||+|.+.++|++|++.||+..|+|+.|+|+||+++
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            4578999999999999999999999999999999864    699999999999999999999999999999999999875


Q ss_pred             CC
Q 029166          139 AN  140 (198)
Q Consensus       139 ~~  140 (198)
                      .+
T Consensus       182 ~~  183 (213)
T 4f02_A          182 KE  183 (213)
T ss_dssp             HH
T ss_pred             cc
Confidence            43

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.72  E-value=2.5e-17  Score=124.67  Aligned_cols=78  Identities=19%  Similarity=0.402  Sum_probs=72.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ....++|||+|||+.+++++|+++|++||.|++|.|+.+     ++||||+|.+.++|++|++.||+..|+|+.|+|+||
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            345689999999999999999999999999999999764     699999999999999999999999999999999999


Q ss_pred             cCC
Q 029166          136 RNP  138 (198)
Q Consensus       136 ~~~  138 (198)
                      ...
T Consensus       165 ~~~  167 (177)
T 2f3j_A          165 ASQ  167 (177)
T ss_dssp             SSG
T ss_pred             cCC
Confidence            764

>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=99.71  E-value=4.9e-18  Score=110.34  Aligned_cols=69  Identities=28%  Similarity=0.637  Sum_probs=64.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      +|||+|||+++++++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++ +++..++|+.|+|++|
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            5999999999999999999999999999998764      6899999999999999998 5889999999999886

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.71  E-value=1.1e-16  Score=118.42  Aligned_cols=79  Identities=28%  Similarity=0.616  Sum_probs=72.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ......++|||+|||..+++++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++.||+..++|+.|+|
T Consensus        82 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  161 (166)
T 3md3_A           82 SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI  161 (166)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Confidence            34556789999999999999999999999999999999864      689999999999999999999999999999999


Q ss_pred             EeccC
Q 029166          133 SWGRN  137 (198)
Q Consensus       133 ~~a~~  137 (198)
                      +||++
T Consensus       162 ~~a~~  166 (166)
T 3md3_A          162 NWAAK  166 (166)
T ss_dssp             EESCC
T ss_pred             EecCC
Confidence            99963

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.71  E-value=6.2e-18  Score=116.43  Aligned_cols=79  Identities=29%  Similarity=0.535  Sum_probs=71.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .....++|||+|||+++++++|+++|++||.|.+|+|+.+     +|||||+|.+.++|++|++  ++..++|+.|.|.+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGP   82 (102)
T ss_dssp             CEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEE
Confidence            3445689999999999999999999999999999999874     6999999999999999998  99999999999999


Q ss_pred             ccCCCC
Q 029166          135 GRNPAN  140 (198)
Q Consensus       135 a~~~~~  140 (198)
                      +.++..
T Consensus        83 a~~~~~   88 (102)
T 2xs2_A           83 AIRKQN   88 (102)
T ss_dssp             EEECC-
T ss_pred             CCcCcc
Confidence            986543

>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=99.71  E-value=8.2e-17  Score=119.16  Aligned_cols=77  Identities=35%  Similarity=0.621  Sum_probs=72.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCC------cEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~k------g~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      +.++|||+|||+++++++|+++|++||.|.++++++++      |||||+|.+.++|++|++.|++..+.|+.|+|.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            36899999999999999999999999999999998764      999999999999999999999999999999999998


Q ss_pred             CCC
Q 029166          137 NPA  139 (198)
Q Consensus       137 ~~~  139 (198)
                      +..
T Consensus        81 ~~~   83 (167)
T 1fxl_A           81 PSS   83 (167)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            654

>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=99.70  E-value=6e-16  Score=124.49  Aligned_cols=80  Identities=24%  Similarity=0.506  Sum_probs=73.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHH----HHhccCCceEEEEEeC---CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLR----QPFSQYGEIASVKIPV---GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~----~~F~~~G~i~~v~i~~---~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      +..+.++|||+|||+++++++|+    ++|++||.|.+|++++   ++|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   84 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   84 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEE
Confidence            44568899999999999999977    8999999999999876   5799999999999999999999999999999999


Q ss_pred             EeccCCC
Q 029166          133 SWGRNPA  139 (198)
Q Consensus       133 ~~a~~~~  139 (198)
                      +|++...
T Consensus        85 ~~a~~~~   91 (282)
T 3pgw_A           85 QYAKTDS   91 (282)
T ss_pred             EEeccCc
Confidence            9997654

>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=99.70  E-value=3.7e-17  Score=117.02  Aligned_cols=77  Identities=31%  Similarity=0.432  Sum_probs=68.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceE--EEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIA--SVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~--~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      ......++|||+|||++++|++|+++|++| .|.  +|+|+.+     +|||||+|.+.++|++||+ +++..|+|+.|+
T Consensus        37 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~  114 (126)
T 2hgm_A           37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIE  114 (126)
T ss_dssp             TCSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEE
Confidence            344567899999999999999999999999 677  8988864     7999999999999999998 477999999999


Q ss_pred             EEeccC
Q 029166          132 LSWGRN  137 (198)
Q Consensus       132 v~~a~~  137 (198)
                      |..+.+
T Consensus       115 V~~a~~  120 (126)
T 2hgm_A          115 VFKSSQ  120 (126)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            998854

>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=99.70  E-value=1.4e-16  Score=127.41  Aligned_cols=80  Identities=30%  Similarity=0.598  Sum_probs=75.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      .......++|||+|||+++|+++|+++|++||.|.+|.|.+++|||||+|.+.++|++|+..|++..|.|+.|+|.++.+
T Consensus        16 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~   95 (261)
T 3sde_A           16 EKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH   95 (261)
T ss_dssp             CCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc
Confidence            44455678999999999999999999999999999999999999999999999999999999999999999999999875

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.70  E-value=1.7e-16  Score=120.86  Aligned_cols=80  Identities=20%  Similarity=0.483  Sum_probs=74.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ....++|||+|||..+++++|+++|++||.|.+|++..+      ++||||+|.+.++|++|++.||+..|+|+.|+|+|
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            356789999999999999999999999999999999875      68999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 029166          135 GRNPAN  140 (198)
Q Consensus       135 a~~~~~  140 (198)
                      ++++..
T Consensus       191 a~~~~~  196 (198)
T 2yh0_A          191 ASVGAK  196 (198)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            987643

>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=99.69  E-value=5e-16  Score=108.82  Aligned_cols=82  Identities=18%  Similarity=0.297  Sum_probs=70.5

Q ss_pred             CCCCCCCeEEEcCCCCCCC-----------HHHHHHHhccCCceEEEEEeC--CCcEEEEEeCCHHHHHHHHHHhCCcee
Q 029166           59 EGDSSNTTIFVGGLDPNVT-----------DEDLRQPFSQYGEIASVKIPV--GKGCGFVQFANRENAEEALHKLNGTVI  125 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~-----------e~~l~~~F~~~G~i~~v~i~~--~kg~afV~f~~~~~a~~a~~~l~~~~~  125 (198)
                      ....+.++|+|.||....+           +++|+++|++||.|.+|.|..  ++|||||+|.+.++|++|++.||+..+
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   89 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWF   89 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEE
Confidence            3445688999999954432           589999999999999997753  479999999999999999999999999


Q ss_pred             CCeEeEEEeccCCCC
Q 029166          126 GKQSVRLSWGRNPAN  140 (198)
Q Consensus       126 ~g~~l~v~~a~~~~~  140 (198)
                      +|+.|+|+++.++..
T Consensus        90 ~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           90 GGRQITAQAWDGTTD  104 (112)
T ss_dssp             TTEECEEEECCSCCC
T ss_pred             CCcEEEEEEeCCCCC
Confidence            999999999987543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.69  E-value=1.1e-16  Score=123.50  Aligned_cols=78  Identities=23%  Similarity=0.538  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ...++|||+|||..+++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|.+|++.||+..|+|+.|+|+|+
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            34589999999999999999999999999999999875      689999999999999999999999999999999999


Q ss_pred             cCCC
Q 029166          136 RNPA  139 (198)
Q Consensus       136 ~~~~  139 (198)
                      +++.
T Consensus       203 ~~~~  206 (216)
T 2qfj_A          203 VTPP  206 (216)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8764

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.69  E-value=1e-16  Score=121.90  Aligned_cols=80  Identities=21%  Similarity=0.455  Sum_probs=68.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ....++|||+|||+++++++|+++|++||.|..|+|+.+      +|||||+|.+.++|++|++. ++..|+|+.|.|.|
T Consensus       101 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~  179 (196)
T 1l3k_A          101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRK  179 (196)
T ss_dssp             --CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEE
T ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEe
Confidence            345689999999999999999999999999999999864      68999999999999999985 89999999999999


Q ss_pred             ccCCCCC
Q 029166          135 GRNPANK  141 (198)
Q Consensus       135 a~~~~~~  141 (198)
                      +.++...
T Consensus       180 a~~k~~~  186 (196)
T 1l3k_A          180 ALSKQEM  186 (196)
T ss_dssp             CC-----
T ss_pred             cCChhHh
Confidence            9886554

>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=99.69  E-value=1.4e-16  Score=118.26  Aligned_cols=77  Identities=29%  Similarity=0.499  Sum_probs=71.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      +.++|||+|||+++++++|+++|++||.|.+|+++++      +|||||+|.+.++|++|++.|++..++|+.|+|.|+.
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            4689999999999999999999999999999998764      4899999999999999999999999999999999998


Q ss_pred             CCC
Q 029166          137 NPA  139 (198)
Q Consensus       137 ~~~  139 (198)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            654

>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=99.68  E-value=2.8e-16  Score=126.45  Aligned_cols=77  Identities=23%  Similarity=0.427  Sum_probs=72.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCC-cEEEEEeCCHHHHHHHHHHhCCceeC-CeEeEEEecc
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-GCGFVQFANRENAEEALHKLNGTVIG-KQSVRLSWGR  136 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~k-g~afV~f~~~~~a~~a~~~l~~~~~~-g~~l~v~~a~  136 (198)
                      .....++|||+|||..+++++|+++|++||.|.+|+|+.++ +||||+|.+.++|++|++.||+..|+ |+.|+|+|++
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            34457899999999999999999999999999999999876 99999999999999999999999999 9999999997

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.67  E-value=3.3e-16  Score=115.78  Aligned_cols=75  Identities=32%  Similarity=0.579  Sum_probs=70.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      ++|||+|||.++++++|+++|++||.|.+|+++.+     ++||||+|.+.++|++|++.|++..+.|+.|+|.++.+..
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            58999999999999999999999999999999764     5899999999999999999999999999999999997654

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.67  E-value=1.7e-16  Score=124.40  Aligned_cols=80  Identities=29%  Similarity=0.508  Sum_probs=74.3

Q ss_pred             CCCCCCeEEEcCCCC-CCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           60 GDSSNTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~-~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      ...+.++|||+|||+ ++++++|+++|++||.|.+|+|+++ ++||||+|.+.++|++|++.|++..+.|+.|.|++++.
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  109 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH  109 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            345678999999999 9999999999999999999999987 59999999999999999999999999999999999986


Q ss_pred             CC
Q 029166          138 PA  139 (198)
Q Consensus       138 ~~  139 (198)
                      ..
T Consensus       110 ~~  111 (229)
T 2adc_A          110 QN  111 (229)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=5e-17  Score=115.94  Aligned_cols=76  Identities=26%  Similarity=0.328  Sum_probs=67.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCce----EEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI----ASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i----~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      ..+..+|||+|||+++++++|+++|++||.|    ..|+|+.+     +|||||+|.+.++|++||+. |+..|+++.|+
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            3457899999999999999999999999875    67888753     69999999999999999995 99999999999


Q ss_pred             EEeccC
Q 029166          132 LSWGRN  137 (198)
Q Consensus       132 v~~a~~  137 (198)
                      |..+.+
T Consensus        99 V~~a~~  104 (123)
T 2dha_A           99 LFRSTA  104 (123)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            998854

>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=99.67  E-value=2.5e-16  Score=117.36  Aligned_cols=75  Identities=19%  Similarity=0.513  Sum_probs=70.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ...++|||+|||..+++++|+++|++||.|.+++++.+      +|||||+|.+.++|++|++.||+..++|+.|+|+||
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            44789999999999999999999999999999999875      589999999999999999999999999999999997


Q ss_pred             c
Q 029166          136 R  136 (198)
Q Consensus       136 ~  136 (198)
                      .
T Consensus       172 s  172 (172)
T 2g4b_A          172 S  172 (172)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=3e-16  Score=110.29  Aligned_cols=74  Identities=20%  Similarity=0.420  Sum_probs=63.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC---------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV---------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~---------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ...++|||+|||+++++++|+++|++||.|. +.++.         ++|||||+|.+.++|++||+.|+  .++|+.|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4578999999999999999999999999999 77754         37999999999999999999884  477887777


Q ss_pred             EeccCC
Q 029166          133 SWGRNP  138 (198)
Q Consensus       133 ~~a~~~  138 (198)
                      ..+...
T Consensus        83 ~~~~~~   88 (114)
T 2dnl_A           83 VSSPTI   88 (114)
T ss_dssp             ECCSSS
T ss_pred             ccCCCc
Confidence            765543

>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=99.66  E-value=3.1e-16  Score=119.24  Aligned_cols=81  Identities=25%  Similarity=0.447  Sum_probs=71.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      +......++|||+|||+++++++|+++|++||.|.+|.|+.+      +|||||+|.+.++|++|++. ++..++|+.|.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~   85 (196)
T 1l3k_A            7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVE   85 (196)
T ss_dssp             -CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEee
Confidence            344556789999999999999999999999999999999864      58999999999999999985 99999999999


Q ss_pred             EEeccCCC
Q 029166          132 LSWGRNPA  139 (198)
Q Consensus       132 v~~a~~~~  139 (198)
                      |.++....
T Consensus        86 v~~~~~~~   93 (196)
T 1l3k_A           86 PKRAVSRE   93 (196)
T ss_dssp             EEECCC--
T ss_pred             eecccCcc
Confidence            99997653

>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=99.65  E-value=7.1e-16  Score=120.89  Aligned_cols=77  Identities=25%  Similarity=0.467  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCC-ceEEEEEeC-CCcEEEEEeCCHHHHHHHHHHhCCceeC-CeEeEEEeccCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYG-EIASVKIPV-GKGCGFVQFANRENAEEALHKLNGTVIG-KQSVRLSWGRNP  138 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G-~i~~v~i~~-~kg~afV~f~~~~~a~~a~~~l~~~~~~-g~~l~v~~a~~~  138 (198)
                      .+.++|||+|||..+++++|+++|++|| .|..|+++. +++||||+|.+.++|++|++.|++..++ |+.|+|+|++++
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            4478999999999999999999999999 999999955 7899999999999999999999999999 999999999874

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.65  E-value=6.3e-16  Score=118.13  Aligned_cols=77  Identities=25%  Similarity=0.467  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCC-ceEEEEEeC-CCcEEEEEeCCHHHHHHHHHHhCCceeC-CeEeEEEeccCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYG-EIASVKIPV-GKGCGFVQFANRENAEEALHKLNGTVIG-KQSVRLSWGRNP  138 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G-~i~~v~i~~-~kg~afV~f~~~~~a~~a~~~l~~~~~~-g~~l~v~~a~~~  138 (198)
                      .+.++|||+|||..+++++|+++|++|| .|.+|+++. ++++|||+|.+.++|++|++.||+..++ |+.|+|+|++++
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            4578999999999999999999999999 999999965 7899999999999999999999999999 999999999874

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.64  E-value=7.4e-16  Score=114.83  Aligned_cols=75  Identities=21%  Similarity=0.447  Sum_probs=70.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccC----C-------ceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQY----G-------EIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~----G-------~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      +.++|||+|||+++++++|+++|++|    |       .|.++++.++++||||+|.+.++|++|+ .|++..+.|+.|+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~   81 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCceee
Confidence            46899999999999999999999999    7       8999999999999999999999999999 7999999999999


Q ss_pred             EEeccCC
Q 029166          132 LSWGRNP  138 (198)
Q Consensus       132 v~~a~~~  138 (198)
                      |.++...
T Consensus        82 v~~~~~~   88 (172)
T 2g4b_A           82 IRRPHDY   88 (172)
T ss_dssp             EECCSSC
T ss_pred             ecCCccc
Confidence            9998754

>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=99.64  E-value=7.2e-16  Score=115.41  Aligned_cols=79  Identities=25%  Similarity=0.393  Sum_probs=70.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEE-eCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI-PVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i-~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      .....++|||+|||..+++++|+++|++||.|..+.. ..++|||||+|.+.++|.+|++.||+..|+|+.|+|+||+++
T Consensus        95 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B           95 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            3446789999999999999999999999999887711 125799999999999999999999999999999999999875

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.64  E-value=3.9e-16  Score=119.25  Aligned_cols=77  Identities=30%  Similarity=0.520  Sum_probs=72.4

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           63 SNTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        63 ~~~~lfV~~l~~-~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      +.++|||+|||+ ++++++|+++|++||.|.+|+++.+ ++||||+|.+.++|++|++.|++..+.|+.|+|.+++...
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~   80 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   80 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCS
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCC
Confidence            368999999999 9999999999999999999999887 5999999999999999999999999999999999998654

>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=99.64  E-value=1.4e-15  Score=112.85  Aligned_cols=75  Identities=29%  Similarity=0.538  Sum_probs=69.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCC--eEeEE
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGK--QSVRL  132 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g--~~l~v  132 (198)
                      ....++|||+|||..+++++|+++|++||.|..+.++++      ++||||+|.+.++|.+|++.||+..++|  +.|+|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            445789999999999999999999999999999999875      4899999999999999999999999987  99999


Q ss_pred             Eec
Q 029166          133 SWG  135 (198)
Q Consensus       133 ~~a  135 (198)
                      +||
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.64  E-value=6.9e-16  Score=115.07  Aligned_cols=76  Identities=25%  Similarity=0.556  Sum_probs=69.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeC---CeEeEE
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIG---KQSVRL  132 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~---g~~l~v  132 (198)
                      ....++|||+|||..+++++|+++|++||.|.+++++++     +|||||+|.+.++|++|++.||+..+.   ++.|+|
T Consensus        92 ~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V  171 (175)
T 3nmr_A           92 AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV  171 (175)
T ss_dssp             CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEE
T ss_pred             cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEE
Confidence            346789999999999999999999999999999999875     689999999999999999999998776   489999


Q ss_pred             Eecc
Q 029166          133 SWGR  136 (198)
Q Consensus       133 ~~a~  136 (198)
                      +||.
T Consensus       172 ~~ad  175 (175)
T 3nmr_A          172 KFAD  175 (175)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9984

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.63  E-value=1e-15  Score=118.11  Aligned_cols=78  Identities=24%  Similarity=0.524  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .+.++|||+|||.++++++|+++|++||.|.+|+|+++      ++||||+|.+.++|++|++.|++..|+|+.|+|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            34689999999999999999999999999999999763      699999999999999999999999999999999988


Q ss_pred             cCCC
Q 029166          136 RNPA  139 (198)
Q Consensus       136 ~~~~  139 (198)
                      ....
T Consensus       106 ~~~~  109 (216)
T 2qfj_A          106 SNIG  109 (216)
T ss_dssp             SCCG
T ss_pred             CCcc
Confidence            7543

>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=99.63  E-value=4e-16  Score=115.75  Aligned_cols=75  Identities=21%  Similarity=0.480  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ..++|||+|||.++++++|+++|++||.|.+++++.+      +|||||+|.+.++|++|++ +++..++|+.|+|+||.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            4679999999999999999999999999999999864      5899999999999999998 89999999999999998


Q ss_pred             CC
Q 029166          137 NP  138 (198)
Q Consensus       137 ~~  138 (198)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=1.3e-15  Score=115.92  Aligned_cols=76  Identities=20%  Similarity=0.425  Sum_probs=70.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccC----C-------ceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQY----G-------EIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~----G-------~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      ..++|||+|||+++++++|+++|++|    |       .|.++.+.+++|||||+|.+.++|++|+ .|++..|.|+.|+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~   81 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEE
Confidence            46899999999999999999999999    6       7899999999999999999999999999 7999999999999


Q ss_pred             EEeccCCC
Q 029166          132 LSWGRNPA  139 (198)
Q Consensus       132 v~~a~~~~  139 (198)
                      |.++....
T Consensus        82 v~~~~~~~   89 (198)
T 2yh0_A           82 IRRPHDYQ   89 (198)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99987653

>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=99.62  E-value=1.3e-15  Score=116.69  Aligned_cols=74  Identities=18%  Similarity=0.351  Sum_probs=67.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      .++|||+|||+++++++|+++|++||.|..|+|++     .+|||||+|.+.++|++|++.+ +..++|+.|+|.|++.-
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence            58999999999999999999999999999999986     3699999999999999999855 46999999999998753

>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=99.62  E-value=1.2e-15  Score=113.79  Aligned_cols=77  Identities=27%  Similarity=0.500  Sum_probs=68.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC--------CCcEEEEEeCCHHHHHHHHHHhCCceeC---CeEeE
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV--------GKGCGFVQFANRENAEEALHKLNGTVIG---KQSVR  131 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~--------~kg~afV~f~~~~~a~~a~~~l~~~~~~---g~~l~  131 (198)
                      +.++|||+|||+++++++|+++|++||.|.+|+|++        +++||||+|.+.++|++|++.|++..+.   ++.+.
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            568999999999999999999999999999999974        4689999999999999999999998775   67888


Q ss_pred             EEeccCCC
Q 029166          132 LSWGRNPA  139 (198)
Q Consensus       132 v~~a~~~~  139 (198)
                      +.++....
T Consensus        82 ~~~~~~~~   89 (175)
T 3nmr_A           82 MKPADSEK   89 (175)
T ss_dssp             EEECGGGC
T ss_pred             Eccccccc
Confidence            88877543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.62  E-value=3.7e-15  Score=103.36  Aligned_cols=76  Identities=17%  Similarity=0.265  Sum_probs=67.2

Q ss_pred             CCCCeEEEcCCCC-----CCCHHHHHHHhccCCceEEEEEeC-------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 029166           62 SSNTTIFVGGLDP-----NVTDEDLRQPFSQYGEIASVKIPV-------GKGCGFVQFANRENAEEALHKLNGTVIGKQS  129 (198)
Q Consensus        62 ~~~~~lfV~~l~~-----~~~e~~l~~~F~~~G~i~~v~i~~-------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~  129 (198)
                      .++++|+|.||..     +-++++|+++|++||.|.+|.|++       ++||+||+|.+.++|++|++.|||..++|+.
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            3578999999963     236899999999999999999975       3699999999999999999999999999999


Q ss_pred             eEEEeccC
Q 029166          130 VRLSWGRN  137 (198)
Q Consensus       130 l~v~~a~~  137 (198)
                      |.|.++..
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

>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=99.61  E-value=1.9e-15  Score=111.69  Aligned_cols=75  Identities=35%  Similarity=0.654  Sum_probs=68.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeE--eEE
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQS--VRL  132 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~--l~v  132 (198)
                      ....++|||+|||..+++++|+++|++||.|.+++++.+      ++||||+|.+.++|++|++.||+..++|+.  |+|
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v  164 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV  164 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEE
Confidence            345689999999999999999999999999999998764      599999999999999999999999999964  888


Q ss_pred             Eec
Q 029166          133 SWG  135 (198)
Q Consensus       133 ~~a  135 (198)
                      +||
T Consensus       165 ~~A  167 (167)
T 1fxl_A          165 KFA  167 (167)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            886

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.60  E-value=1.2e-15  Score=108.32  Aligned_cols=73  Identities=19%  Similarity=0.265  Sum_probs=64.8

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCC----HHH----HHHHHH--HhCCce
Q 029166           65 TTIFVGGL----DPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFAN----REN----AEEALH--KLNGTV  124 (198)
Q Consensus        65 ~~lfV~~l----~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~----~~~----a~~a~~--~l~~~~  124 (198)
                      ++|||+||    |+.++|++|+++|++||+|.++.++.|      +|||||+|.+    +++    |.+|+.  .|++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    999999999999999999999999875      6999999996    333    788888  789999


Q ss_pred             eCCeEeEEEeccC
Q 029166          125 IGKQSVRLSWGRN  137 (198)
Q Consensus       125 ~~g~~l~v~~a~~  137 (198)
                      |+|+.|+|.+-+.
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999998764

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.60  E-value=3.7e-15  Score=119.94  Aligned_cols=81  Identities=21%  Similarity=0.315  Sum_probs=74.5

Q ss_pred             CCCCCCeEEEcCCCCCC-CHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           60 GDSSNTTIFVGGLDPNV-TDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~-~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      .....++|||+|||+.+ ++++|+++|++||.|.+++|+.+     +|+|||+|.+.++|.+|++.||+..++|+.|+|.
T Consensus       180 ~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  259 (284)
T 3smz_A          180 ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS  259 (284)
T ss_dssp             TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Confidence            34567899999999995 99999999999999999999875     7999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 029166          134 WGRNPAN  140 (198)
Q Consensus       134 ~a~~~~~  140 (198)
                      |++++..
T Consensus       260 ~a~~~~~  266 (284)
T 3smz_A          260 FCAPGPP  266 (284)
T ss_dssp             ECCSSSC
T ss_pred             EecCCCc
Confidence            9987654

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=1.6e-14  Score=99.13  Aligned_cols=76  Identities=17%  Similarity=0.268  Sum_probs=62.9

Q ss_pred             CCeEEEcCCC-------CCCCHHHHHHHhccCCceEEEEEe-CCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           64 NTTIFVGGLD-------PNVTDEDLRQPFSQYGEIASVKIP-VGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        64 ~~~lfV~~l~-------~~~~e~~l~~~F~~~G~i~~v~i~-~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ..+|-|.-..       ..+++++|+++|++||.|.+|.|+ +++|||||+|.+.++|+.|++.++  .+.++.|+|+|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V~~a   87 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKISWL   87 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEEECS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEEEEc
Confidence            4456565433       468999999999999999999997 468999999999999999999754  467999999999


Q ss_pred             cCCCCC
Q 029166          136 RNPANK  141 (198)
Q Consensus       136 ~~~~~~  141 (198)
                      +++...
T Consensus        88 ~~~~~~   93 (100)
T 2d9o_A           88 EGQPQD   93 (100)
T ss_dssp             SCCCCC
T ss_pred             cCCCCC
Confidence            876543

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.60  E-value=7.7e-15  Score=118.10  Aligned_cols=74  Identities=22%  Similarity=0.394  Sum_probs=70.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      +.++|||+|||.++++++|+++|++|| |.++.+.+++|||||+|.+.++|++|++.|++..+.|+.|.|.++..
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~~   94 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT   94 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEEecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecCC
Confidence            468999999999999999999999999 99999999999999999999999999999999999999999999753

>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=99.58  E-value=5.4e-15  Score=122.26  Aligned_cols=76  Identities=20%  Similarity=0.360  Sum_probs=67.6

Q ss_pred             CCCCCeEEEcC--CCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeC---Ce--EeEEE
Q 029166           61 DSSNTTIFVGG--LDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG---KQ--SVRLS  133 (198)
Q Consensus        61 ~~~~~~lfV~~--l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~---g~--~l~v~  133 (198)
                      +.++.+|||+|  |+..++|++|+++|++||+|.+|.+..+|+||||+|.+.++|++|++.|||.++.   |+  .|.|.
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~   94 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN   94 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEE
Confidence            45678999999  5788999999999999999999999999999999999999999999999999882   34  57777


Q ss_pred             ecc
Q 029166          134 WGR  136 (198)
Q Consensus       134 ~a~  136 (198)
                      ++.
T Consensus        95 ~~~   97 (345)
T 3tht_A           95 FVE   97 (345)
T ss_dssp             ECS
T ss_pred             Eee
Confidence            764

>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=99.58  E-value=9.8e-15  Score=109.15  Aligned_cols=81  Identities=22%  Similarity=0.409  Sum_probs=69.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCce-----EEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEI-----ASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i-----~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ....+.++|||+|||.++++++|+++|.+||.|     .+.....++|||||+|.+.++|++|++ |++..+.|+.|+|.
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            345568899999999999999999999998754     444555678999999999999999995 99999999999999


Q ss_pred             eccCCCC
Q 029166          134 WGRNPAN  140 (198)
Q Consensus       134 ~a~~~~~  140 (198)
                      ++.+...
T Consensus        87 ~~~~~~~   93 (175)
T 1fje_B           87 KPKGRDS   93 (175)
T ss_dssp             CCCCSSC
T ss_pred             cCCCccc
Confidence            9986543

>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=99.58  E-value=4.8e-15  Score=109.84  Aligned_cols=74  Identities=23%  Similarity=0.542  Sum_probs=67.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      +.++|||+|||+++++++|+++|++||.|.+|+++++      +|||||+|.+.++|++|++.  +..++|+.|.|.++.
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            4689999999999999999999999999999999874      58999999999999999984  678999999999886


Q ss_pred             CC
Q 029166          137 NP  138 (198)
Q Consensus       137 ~~  138 (198)
                      +.
T Consensus        80 ~~   81 (167)
T 2cjk_A           80 PR   81 (167)
T ss_dssp             CH
T ss_pred             ch
Confidence            53

>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=99.57  E-value=7.6e-15  Score=118.60  Aligned_cols=78  Identities=27%  Similarity=0.623  Sum_probs=71.8

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHhccCCceEEEEEeCC-------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           60 GDSSNTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVG-------KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~-~~e~~l~~~F~~~G~i~~v~i~~~-------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .....++|||+|||.. +++++|+++|++||.|..|+|+.+       +|||||+|.+.++|.+|+ .||+..|+|+.|+
T Consensus       206 ~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~  284 (292)
T 2ghp_A          206 ATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREIS  284 (292)
T ss_dssp             -CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEE
T ss_pred             cCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEE
Confidence            3456789999999999 999999999999999999999653       689999999999999999 9999999999999


Q ss_pred             EEeccCC
Q 029166          132 LSWGRNP  138 (198)
Q Consensus       132 v~~a~~~  138 (198)
                      |.||+++
T Consensus       285 V~~a~~k  291 (292)
T 2ghp_A          285 VSLADKK  291 (292)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            9999875

>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=99.56  E-value=4.5e-15  Score=114.74  Aligned_cols=74  Identities=20%  Similarity=0.261  Sum_probs=66.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCce--EEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCe----EeE
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEI--ASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQ----SVR  131 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i--~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~----~l~  131 (198)
                      .+.++|||+|||+++++++|+++|++||.|  .+++++.+    ++||||+|.+.++|.+||..||+..|++.    .+.
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~  200 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYT  200 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEE
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceE
Confidence            346789999999999999999999999999  89998875    48999999999999999999999999876    577


Q ss_pred             EEec
Q 029166          132 LSWG  135 (198)
Q Consensus       132 v~~a  135 (198)
                      |+||
T Consensus       201 vk~~  204 (205)
T 3tyt_A          201 LKLC  204 (205)
T ss_dssp             CEEE
T ss_pred             EEec
Confidence            7765

>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=99.53  E-value=3.5e-14  Score=114.65  Aligned_cols=78  Identities=17%  Similarity=0.358  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCC-ceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYG-EIASVKIPV-----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G-~i~~v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ..++|||+|||+.+++++|+++|++|| .|..|.++.     +++||||+|.+.++|++|++.|++..|+|+.|.|.|+.
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  195 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN  195 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            578999999999999999999999999 999999976     46999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      +...
T Consensus       196 ~~~~  199 (292)
T 2ghp_A          196 PLEK  199 (292)
T ss_dssp             CC--
T ss_pred             CCcc
Confidence            7543

>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=99.51  E-value=7.1e-14  Score=96.82  Aligned_cols=75  Identities=23%  Similarity=0.364  Sum_probs=65.3

Q ss_pred             CCCeEEEcCCC--CCCC--------HHHHHHHhccCCceEEEEEeCC--------CcEEEEEeCCHHHHHHHHHHhCCce
Q 029166           63 SNTTIFVGGLD--PNVT--------DEDLRQPFSQYGEIASVKIPVG--------KGCGFVQFANRENAEEALHKLNGTV  124 (198)
Q Consensus        63 ~~~~lfV~~l~--~~~~--------e~~l~~~F~~~G~i~~v~i~~~--------kg~afV~f~~~~~a~~a~~~l~~~~  124 (198)
                      +++.|.+.|+-  ..+.        +++|++.|++||.|.+|.|+++        +||+||+|.+.++|++|++.|||..
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            57789999973  3332        3689999999999999999763        6999999999999999999999999


Q ss_pred             eCCeEeEEEeccC
Q 029166          125 IGKQSVRLSWGRN  137 (198)
Q Consensus       125 ~~g~~l~v~~a~~  137 (198)
                      ++|+.|+|.++..
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            9999999999753

>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=99.50  E-value=8.7e-15  Score=101.28  Aligned_cols=67  Identities=25%  Similarity=0.486  Sum_probs=59.7

Q ss_pred             EcCCCCCCCHHHHHHHh------------ccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           69 VGGLDPNVTDEDLRQPF------------SQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        69 V~~l~~~~~e~~l~~~F------------~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      +.+|++.+++++|+++|            ++||.|.+|.|+++     +|||||+|.+.++|++|++.|||..++|+.|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56777777888777666            99999999999874     79999999999999999999999999999999


Q ss_pred             EEec
Q 029166          132 LSWG  135 (198)
Q Consensus       132 v~~a  135 (198)
                      |+|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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=99.48  E-value=8.3e-14  Score=111.16  Aligned_cols=77  Identities=30%  Similarity=0.451  Sum_probs=69.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHh-CCceeC---CeEeEEE
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKL-NGTVIG---KQSVRLS  133 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l-~~~~~~---g~~l~v~  133 (198)
                      +.++|||+|||..+++++|+++|++||.|.+|.|+.+     +|||||+|.+.++|.+|++.| ++..+.   ++.|.|+
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~  174 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE  174 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEe
Confidence            4679999999999999999999999999999999865     799999999999999999999 455554   9999999


Q ss_pred             eccCCC
Q 029166          134 WGRNPA  139 (198)
Q Consensus       134 ~a~~~~  139 (198)
                      ++.+..
T Consensus       175 ~~~~~~  180 (261)
T 3sde_A          175 PMEQFD  180 (261)
T ss_dssp             ECCCEE
T ss_pred             eccccC
Confidence            998654

>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=99.45  E-value=3.7e-13  Score=95.11  Aligned_cols=75  Identities=16%  Similarity=0.230  Sum_probs=65.4

Q ss_pred             CCCeEEEcCCCCC--C---CHHHHHHHhccCCceEEEEEeCC----------CcEEEEEeCCHHHHHHHHHHhCCceeCC
Q 029166           63 SNTTIFVGGLDPN--V---TDEDLRQPFSQYGEIASVKIPVG----------KGCGFVQFANRENAEEALHKLNGTVIGK  127 (198)
Q Consensus        63 ~~~~lfV~~l~~~--~---~e~~l~~~F~~~G~i~~v~i~~~----------kg~afV~f~~~~~a~~a~~~l~~~~~~g  127 (198)
                      ++++|++.|+-..  +   -+++|++.|++||.|.+|.|+++          +||+||+|.+.++|.+|++.|||..++|
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            4788999998421  2   36899999999999999999763          3899999999999999999999999999


Q ss_pred             eEeEEEeccC
Q 029166          128 QSVRLSWGRN  137 (198)
Q Consensus       128 ~~l~v~~a~~  137 (198)
                      +.|+|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999853

>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=99.42  E-value=1.5e-12  Score=91.32  Aligned_cols=75  Identities=11%  Similarity=0.175  Sum_probs=64.2

Q ss_pred             CCCeEEEcCCCCCC----------CHHHHHHHhccCCceEEEEEeCC--CcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           63 SNTTIFVGGLDPNV----------TDEDLRQPFSQYGEIASVKIPVG--KGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        63 ~~~~lfV~~l~~~~----------~e~~l~~~F~~~G~i~~v~i~~~--kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      +++.|.+.|+=..-          -+++|++.|++||.|.+|.|.++  +||+||+|.+.++|++|++.|||..++|+.|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i   85 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMI   85 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            46678888764322          13588999999999999999875  6999999999999999999999999999999


Q ss_pred             EEEeccC
Q 029166          131 RLSWGRN  137 (198)
Q Consensus       131 ~v~~a~~  137 (198)
                      +|+++..
T Consensus        86 ~v~~~~~   92 (114)
T 3s6e_A           86 TAAYVPL   92 (114)
T ss_dssp             EEEEECH
T ss_pred             EEEEEcH
Confidence            9999853

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=4.9e-12  Score=89.26  Aligned_cols=78  Identities=21%  Similarity=0.190  Sum_probs=70.4

Q ss_pred             CCCCCCCCeEEEcCCCCC-CCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCC-HHHHHHHHHHhC--CceeCCeEeEEE
Q 029166           58 SEGDSSNTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN-RENAEEALHKLN--GTVIGKQSVRLS  133 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~-~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~-~~~a~~a~~~l~--~~~~~g~~l~v~  133 (198)
                      +-.....+.|||+||++. +++++|+++|++||+|..|.+..+...|||+|.+ .++|..|++.|+  +..|.+..++++
T Consensus        12 ~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~e   91 (121)
T 1owx_A           12 SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   91 (121)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             cccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEE
Confidence            445667899999999999 9999999999999999999999998999999999 899999999994  678889888887


Q ss_pred             ec
Q 029166          134 WG  135 (198)
Q Consensus       134 ~a  135 (198)
                      ..
T Consensus        92 vL   93 (121)
T 1owx_A           92 VL   93 (121)
T ss_dssp             EC
T ss_pred             EC
Confidence            64

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.36  E-value=2.8e-12  Score=85.42  Aligned_cols=74  Identities=26%  Similarity=0.404  Sum_probs=62.6

Q ss_pred             CCCCeEEEcCCCC----CCCH----HHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           62 SSNTTIFVGGLDP----NVTD----EDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        62 ~~~~~lfV~~l~~----~~~e----~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ++..||+|.-.+.    ++-.    .+|.+.|++||+|..++++.++  +||+|.+.++|.+|++ |||..++|+.|+|+
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~   81 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--MWVTFLEGSSALNVLS-LNGKELLNRTITIA   81 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--EEEEESSHHHHHHGGG-GTTCEETTEEEEEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--EEEEECChHHHHHHHh-cCCeEeCCeEEEEE
Confidence            3466788876652    2322    5789999999999999999876  8999999999999998 99999999999999


Q ss_pred             eccCC
Q 029166          134 WGRNP  138 (198)
Q Consensus       134 ~a~~~  138 (198)
                      ++++.
T Consensus        82 lkt~d   86 (91)
T 2dnr_A           82 LKSPS   86 (91)
T ss_dssp             ECCCS
T ss_pred             eCCCC
Confidence            99863

>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=99.16  E-value=6.1e-11  Score=79.37  Aligned_cols=72  Identities=26%  Similarity=0.439  Sum_probs=61.9

Q ss_pred             CCCCeEEEcCCCCC------CCH---HHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           62 SSNTTIFVGGLDPN------VTD---EDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        62 ~~~~~lfV~~l~~~------~~e---~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ++..||+|.-++..      ..+   .+|.+.|.+||+|..++++.++  +||+|.+.++|.+||+ |++..++|+.|+|
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V   89 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--MLVTFADSHSALSVLD-VDGMKVKGRAVKI   89 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--EEEECSCSHHHHHHHH-GGGSEETTEEEEE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--EEEEEcChHHHHHHHh-cCCeeeCCeEEEE
Confidence            45678999887643      222   4688999999999999999887  9999999999999998 9999999999999


Q ss_pred             Eecc
Q 029166          133 SWGR  136 (198)
Q Consensus       133 ~~a~  136 (198)
                      ++..
T Consensus        90 ~~k~   93 (95)
T 1ufw_A           90 SGPS   93 (95)
T ss_dssp             ECCC
T ss_pred             eccC
Confidence            9754

>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=98.91  E-value=2.3e-09  Score=83.24  Aligned_cols=60  Identities=18%  Similarity=0.212  Sum_probs=55.5

Q ss_pred             CHHHHHHHhccCCceEEEEEe----------CCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           77 TDEDLRQPFSQYGEIASVKIP----------VGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        77 ~e~~l~~~F~~~G~i~~v~i~----------~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      .+++|++.|++||.|.++.|+          +.+|++||+|.+.++|.+|++.|||..++|+.|.+.+..
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            467899999999999999997          346999999999999999999999999999999999975

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.81  E-value=3.9e-08  Score=67.19  Aligned_cols=73  Identities=18%  Similarity=0.138  Sum_probs=68.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccC-----CceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQY-----GEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~-----G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      +.++|-+-+||+.++...|+.+.+++     |.|+.|.+..+.+-|+|+|.|...|-+|.-.|+|.+|+|+.|++.-.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv   97 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTI   97 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEECH
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCeEEEecCH
Confidence            46789999999999999999999999     99999999999999999999999999998889999999999998743

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.30  E-value=1.3e-05  Score=54.14  Aligned_cols=74  Identities=24%  Similarity=0.258  Sum_probs=63.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhcc-C----CceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQ-Y----GEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~-~----G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ....+|.|.|||+.++++.|+-+|++ -    |+|..++...  +-|+|+|.+.+.|++.|+. ..+.|++..|.|....
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~   82 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAP   82 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCC
Confidence            34679999999999999999999987 2    6899998876  7899999999999999873 4788999999998765


Q ss_pred             CC
Q 029166          137 NP  138 (198)
Q Consensus       137 ~~  138 (198)
                      +.
T Consensus        83 ~~   84 (104)
T 2dhx_A           83 PR   84 (104)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=98.23  E-value=6.3e-06  Score=55.92  Aligned_cols=75  Identities=13%  Similarity=0.161  Sum_probs=66.5

Q ss_pred             CCeEEEcCCCCCC-C----HHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           64 NTTIFVGGLDPNV-T----DEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        64 ~~~lfV~~l~~~~-~----e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      .++|+|.||+.++ .    .+.++++|..|+++......++-.-..|.|.+.++|.+|...||+..+.|++|+|-++.+.
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~   84 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCCC
Confidence            5679999998864 2    2578999999999999999998778899999999999999999999999999999999843

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.87  E-value=8.5e-05  Score=51.69  Aligned_cols=76  Identities=18%  Similarity=0.246  Sum_probs=62.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCC-eEeEEEecc
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGK-QSVRLSWGR  136 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g-~~l~v~~a~  136 (198)
                      +...+.+.|-|-++|+.. .+.|.++|++||.|.+........+-.|.|+++.+|++||. .|+..|++ ..|-|....
T Consensus        19 ~~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           19 EDHLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             --CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             CCCCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECC
Confidence            445557889999999985 56788899999999998886567999999999999999998 59999985 667777743

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.62  E-value=0.00051  Score=45.57  Aligned_cols=73  Identities=16%  Similarity=0.259  Sum_probs=57.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC--------CcEEEEEeCCHHHHHHHHHHhCCceeC---Ce--EeE
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG--------KGCGFVQFANRENAEEALHKLNGTVIG---KQ--SVR  131 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~--------kg~afV~f~~~~~a~~a~~~l~~~~~~---g~--~l~  131 (198)
                      ++|-|++||+.+||+++.+.++...++........        -.-|+|.|.+.+++..-.+.++|+.+-   |.  .-.
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            57999999999999999999998877666555331        267999999999999999999999873   22  335


Q ss_pred             EEeccC
Q 029166          132 LSWGRN  137 (198)
Q Consensus       132 v~~a~~  137 (198)
                      |++|--
T Consensus        82 VE~AP~   87 (91)
T 1uw4_A           82 VEFAPF   87 (91)
T ss_dssp             EEECSS
T ss_pred             EEEcCC
Confidence            666643

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.57  E-value=0.00037  Score=46.54  Aligned_cols=55  Identities=22%  Similarity=0.334  Sum_probs=45.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHh
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL  120 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l  120 (198)
                      ..+.++| ++|.++...||.++|+.||.| .|+++.+ .-|||.|.+++.|..|+..+
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidD-TsAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD-TSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEET-TEEEEECSCHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcC-CeEEEEecCHHHHHHHHHhc
Confidence            4556666 999999999999999999843 3555544 68999999999999999865

>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=97.26  E-value=0.00038  Score=46.61  Aligned_cols=55  Identities=20%  Similarity=0.308  Sum_probs=45.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN  121 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~  121 (198)
                      .+.++| ++|.++...||.++|+.||. ..|+++.+ .-|||.|.+++.|..|+..+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidD-TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD-TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEET-TEEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcC-CeEEEEecCHHHHHHHHHhcc
Confidence            345566 99999999999999999993 45666655 689999999999999998764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.23  E-value=0.00048  Score=48.58  Aligned_cols=72  Identities=19%  Similarity=0.261  Sum_probs=55.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEE-EEEeC-------------------CCcEEEEEeCCHHHHHHHHHHhCC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS-VKIPV-------------------GKGCGFVQFANRENAEEALHKLNG  122 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~-v~i~~-------------------~kg~afV~f~~~~~a~~a~~~l~~  122 (198)
                      ....|.|-+.|+..+ ..+-+.|++||.|.+ +.+.+                   ...+--|+|+++.+|++||. .||
T Consensus         6 ~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENG   83 (132)
T ss_dssp             --CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTT
T ss_pred             CceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCC
Confidence            356788889987755 567778999999877 22211                   25788999999999999998 599


Q ss_pred             ceeCCeEeEEEecc
Q 029166          123 TVIGKQSVRLSWGR  136 (198)
Q Consensus       123 ~~~~g~~l~v~~a~  136 (198)
                      ..|+|..|-|.+.+
T Consensus        84 ~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           84 AVFNGVLLGVIPYT   97 (132)
T ss_dssp             CEETTEECEEEECC
T ss_pred             eEeCcEEEEEEECC
Confidence            99999988888764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=97.07  E-value=0.00032  Score=59.93  Aligned_cols=53  Identities=17%  Similarity=0.308  Sum_probs=42.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCc-EEEEEeCCHHHHHHHHH
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG-CGFVQFANRENAEEALH  118 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg-~afV~f~~~~~a~~a~~  118 (198)
                      ++|||. .+..+++++|.++|++||.|.++.+-.++| |+.|||.+.+++.+++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            789997 789999999999999999999999988765 89999999999987764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.98  E-value=0.0026  Score=42.48  Aligned_cols=73  Identities=11%  Similarity=0.224  Sum_probs=53.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC--------CcEEEEEeCCHHHHHHHHHHhCCceeCC---e--Ee
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG--------KGCGFVQFANRENAEEALHKLNGTVIGK---Q--SV  130 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~--------kg~afV~f~~~~~a~~a~~~l~~~~~~g---~--~l  130 (198)
                      +-+|-|+.||+.+||+++.+.++..=++........        -.-|+|.|.+.+++..-.+..+|+.+-+   .  .-
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            457999999999999998888876544322222111        2678999999999999999999998732   2  34


Q ss_pred             EEEecc
Q 029166          131 RLSWGR  136 (198)
Q Consensus       131 ~v~~a~  136 (198)
                      .|++|-
T Consensus        89 ~VE~AP   94 (97)
T 2l08_A           89 VVEFAP   94 (97)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            566664

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

Probab=95.52  E-value=0.0043  Score=44.46  Aligned_cols=38  Identities=13%  Similarity=0.122  Sum_probs=35.2

Q ss_pred             CcEEEEEeCCHHHHHHHHHHh-CCceeCCeEeEEEeccCC
Q 029166          100 KGCGFVQFANRENAEEALHKL-NGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus       100 kg~afV~f~~~~~a~~a~~~l-~~~~~~g~~l~v~~a~~~  138 (198)
                      +|+++|+|.+.++|++|++.+ |+..++| .|.+.++...
T Consensus        13 ~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A           13 KGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             CEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            699999999999999999999 9999999 9999988753

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=94.46  E-value=0.021  Score=41.02  Aligned_cols=25  Identities=16%  Similarity=0.165  Sum_probs=22.1

Q ss_pred             CCcEEEEEeCCHHHHHHHHHHhCCc
Q 029166           99 GKGCGFVQFANRENAEEALHKLNGT  123 (198)
Q Consensus        99 ~kg~afV~f~~~~~a~~a~~~l~~~  123 (198)
                      .+||+||+|.+.++|++|++.+++.
T Consensus        12 ~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A           12 LKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             CEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             ccchhHHHHHHHHhHHHHHHhhccc
Confidence            4799999999999999999887653

>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=93.26  E-value=0.34  Score=41.84  Aligned_cols=55  Identities=22%  Similarity=0.361  Sum_probs=45.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN  121 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~  121 (198)
                      ...++|+ +|..+...+|.++|+.||.| +|+++ +...|||.|.+.+.|..++..+.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~wi-ddt~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWI-DDTSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEEC-SSSEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEE-cCCeEEEEECCHHHHHHHHHHHH
Confidence            4566666 88899999999999999954 55555 44689999999999999998874

---

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	198
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-24
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-23
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-21
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-20
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-19
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	6e-19
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-18
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-18
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-18
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-18
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-17
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-17
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-17
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	6e-17
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-17
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	9e-17
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-16
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-16
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-16
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-16
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-16
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-16
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-16
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-16
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-15
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-15
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-15
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	4e-15
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-15
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	9e-15
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	9e-15
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	9e-15
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-14
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-14
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-14
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-14
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-14
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	5e-14
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-14
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-14
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	6e-14
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	8e-14
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	9e-14
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	9e-14
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-13
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-13
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-13
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-13
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-13
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-13
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	8e-13
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	8e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-12
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-11
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-11
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-11
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	6e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-11
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	8e-11
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	9e-11
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-10
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-10
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-10
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-10
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-10
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-10
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-09
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-09
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	6e-09
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:) 1e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-08
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	6e-08
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	1e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	1e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	6e-06
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	0.002

>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 = 90.0 bits (223), Expect = 2e-24
 Identities = 27/83 (32%), Positives = 48/83 (57%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL 117
           ++    N T++ GG+   +TD+ +RQ FS +G+I  +++   KG  FV+F+  E+A  A+
Sbjct: 12  NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAI 71

Query: 118 HKLNGTVIGKQSVRLSWGRNPAN 140
             +NGT I    V+  WG+   +
Sbjct: 72  VSVNGTTIEGHVVKCYWGKESPD 94

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 86.5 bits (214), Expect = 4e-23
 Identities = 27/94 (28%), Positives = 48/94 (51%), Gaps = 3/94 (3%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDE-DLRQPFSQYGEIASVKIPVGKGCGFVQFA 108
           G+ G   +++  S N+ +F+G L+  V  + D+   FS+YG+I    +   KG  FVQ+ 
Sbjct: 1   GSSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--KGFAFVQYV 58

Query: 109 NRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           N  NA  A+   +G +I  Q + ++    P   +
Sbjct: 59  NERNARAAVAGEDGRMIAGQVLDINLAAEPKVNR 92

>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 = 80.9 bits (199), Expect = 5e-21
 Identities = 27/88 (30%), Positives = 44/88 (50%), Gaps = 4/88 (4%)

Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG----CGFVQFANRENAE 114
           E D    T++VG L  +VT+  + Q FSQ G   S K+           FV+F    +A 
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 62

Query: 115 EALHKLNGTVIGKQSVRLSWGRNPANKQ 142
            AL  +NG  I  + V+++W   P++++
Sbjct: 63  AALAAMNGRKILGKEVKVNWATTPSSQK 90

>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 = 78.0 bits (192), Expect = 5e-20
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHK 119
           +++VG L P+VT+  L + FS  G I S+++          G  +V F    +AE AL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 120 LNGTVIGKQSVRLSW 134
           +N  VI  + VR+ W
Sbjct: 62  MNFDVIKGKPVRIMW 76

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 76.9 bits (189), Expect = 2e-19
 Identities = 24/79 (30%), Positives = 46/79 (58%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
           +  + +FVG L P++T+E++R+ F +YG+   V I   KG GF++   R  AE A  +L+
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELD 65

Query: 122 GTVIGKQSVRLSWGRNPAN 140
              +  + +R+ +  + A+
Sbjct: 66  NMPLRGKQLRVRFACHSAS 84

>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 = 75.4 bits (185), Expect = 6e-19
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 6/80 (7%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------FVQFANRENAEEA 116
           SNT + V  L  ++TD +L   F   G I + +I      G      FV F +  +++ A
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 117 LHKLNGTVIGKQSVRLSWGR 136
           +  LNG  +  + +++S+ R
Sbjct: 61  IKVLNGITVRNKRLKVSYAR 80

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 75.0 bits (184), Expect = 1e-18
 Identities = 22/94 (23%), Positives = 44/94 (46%), Gaps = 8/94 (8%)

Query: 57  QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK-------GCGFVQFAN 109
           Q     + + I V  +       ++R+ FS +GE+ +V++P          G GFV F  
Sbjct: 1   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 60

Query: 110 RENAEEALHKL-NGTVIGKQSVRLSWGRNPANKQ 142
           +++A++A + L + T +  + + L W  +    Q
Sbjct: 61  KQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 75.4 bits (185), Expect = 1e-18
 Identities = 16/83 (19%), Positives = 35/83 (42%), Gaps = 3/83 (3%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS---VKIPVGKGCGFVQFANRENAEEALHK 119
            N  +++  L   +T E++   F +YG I        P  +G  +V + +  +A+ A   
Sbjct: 6   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 120 LNGTVIGKQSVRLSWGRNPANKQ 142
           L+G  +  + + + +       Q
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQ 88

>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 = 73.8 bits (181), Expect = 2e-18
 Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 9/84 (10%)

Query: 60  GDS-SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANREN 112
           G+S  +T ++V  L   +TD+ L   F +YG I    I         +G  FV++  RE 
Sbjct: 1   GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 60

Query: 113 AEEALHKLNGTVI--GKQSVRLSW 134
           A+EA+  LN  +   G Q + +  
Sbjct: 61  AQEAISALNNVIPEGGSQPLSVRL 84

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.5 bits (180), Expect = 5e-18
 Identities = 24/86 (27%), Positives = 47/86 (54%), Gaps = 7/86 (8%)

Query: 55  GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG------CGFVQFA 108
           GP SE +  + T++VGGLD  V++  L + F Q G + +  +P  +        GFV+F 
Sbjct: 1   GPISERNQ-DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFL 59

Query: 109 NRENAEEALHKLNGTVIGKQSVRLSW 134
           + E+A+ A+  ++   +  + +R++ 
Sbjct: 60  SEEDADYAIKIMDMIKLYGKPIRVNK 85

>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 = 72.0 bits (176), Expect = 1e-17
 Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 1/81 (1%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
           SS   ++V  L  + ++E + + F+     A  ++   +   FV F+NRE+A EA+  LN
Sbjct: 6   SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALN 65

Query: 122 GTVIGKQSVRLSWGRNPANKQ 142
           G V+    + ++  + P +K 
Sbjct: 66  GKVLDGSPIEVTLAK-PVDKD 85

>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 = 72.3 bits (177), Expect = 1e-17
 Identities = 23/87 (26%), Positives = 45/87 (51%), Gaps = 7/87 (8%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC------GFVQFANRENAEEAL 117
           + T++VG L    T+E + + FS+ G+I  + + + K         FV++ +R +AE A+
Sbjct: 7   SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 66

Query: 118 HKLNGTVIGKQSVRLSWGRNPA-NKQF 143
             +NGT +  + +R  W       +Q+
Sbjct: 67  RYINGTRLDDRIIRTDWDAGFKEGRQY 93

>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 = 71.6 bits (175), Expect = 2e-17
 Identities = 22/87 (25%), Positives = 46/87 (52%), Gaps = 6/87 (6%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEE 115
           ++   ++VGGL   V D+ L   F  +G+I  ++IP+       +G  FV+F   E+A  
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 116 ALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           A+  +N + +  +++R++  +    K+
Sbjct: 63  AIDNMNESELFGRTIRVNLAKPMRIKE 89

>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 = 70.5 bits (172), Expect = 6e-17
 Identities = 18/84 (21%), Positives = 41/84 (48%), Gaps = 7/84 (8%)

Query: 64  NTTIFVGGLDPNVTDEDLRQP----FSQYGEIASVKIPV---GKGCGFVQFANRENAEEA 116
           N TI++  L+  +  ++L++     FS++G+I  + +      +G  FV F    +A  A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 117 LHKLNGTVIGKQSVRLSWGRNPAN 140
           L  + G     + +R+ + +  ++
Sbjct: 63  LRSMQGFPFYDKPMRIQYAKTDSD 86

>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 = 70.1 bits (171), Expect = 7e-17
 Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 117
           +  ++V GL   +T ++L Q FSQYG I + +I V +      G GF++F  R  AEEA+
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 118 HKLNGTVIGKQSVRL 132
             LNG      +  +
Sbjct: 66  KGLNGQKPSGATEPI 80

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.1 bits (171), Expect = 9e-17
 Identities = 24/94 (25%), Positives = 47/94 (50%), Gaps = 6/94 (6%)

Query: 48  SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP---VGKGCGF 104
           S G   +GP     +++  I+VG L P++  +D+   F +YG I  + +     G    F
Sbjct: 1   SGGGVIRGP---AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAF 57

Query: 105 VQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP 138
           V+F +  +AE+A++  +G       +R+ + R+ 
Sbjct: 58  VEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG 91

>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 = 69.8 bits (170), Expect = 2e-16
 Identities = 21/98 (21%), Positives = 36/98 (36%), Gaps = 14/98 (14%)

Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC--------------GF 104
           + DS N+ I+V GL+ +VT +DL   F Q G +   K                       
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 105 VQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           V + +   A+ A+   +G       +++S  R      
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 100

>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 = 69.3 bits (169), Expect = 2e-16
 Identities = 29/84 (34%), Positives = 43/84 (51%), Gaps = 4/84 (4%)

Query: 57  QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKI----PVGKGCGFVQFANREN 112
            SE  S+   + V  +     D DLRQ F Q+G+I  V+I       KG GFV F N  +
Sbjct: 4   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD 63

Query: 113 AEEALHKLNGTVIGKQSVRLSWGR 136
           A+ A  KL+GTV+  + + ++   
Sbjct: 64  ADRAREKLHGTVVEGRKIEVNNAT 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 = 68.9 bits (168), Expect = 2e-16
 Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 7/91 (7%)

Query: 56  PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG------CGFVQFAN 109
           P    D + T I V  L  +  + DL++ F  +G I+ + +   K         F+ F  
Sbjct: 1   PNRRADDNAT-IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 59

Query: 110 RENAEEALHKLNGTVIGKQSVRLSWGRNPAN 140
           RE+A  A+  ++G       + + W +   N
Sbjct: 60  REDAARAIAGVSGFGYDHLILNVEWAKPSTN 90

>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 = 69.3 bits (169), Expect = 2e-16
 Identities = 23/99 (23%), Positives = 39/99 (39%), Gaps = 9/99 (9%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV--GKGCGFVQFANRENAEEAL 117
           G S    I V  L   VT + L Q FS++G +  +       +    +Q+A+  +A+ A 
Sbjct: 3   GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAK 62

Query: 118 HKLNGTVIGKQS--VRLSWGRN-----PANKQFRADYGN 149
             L+G  I      +R+ + +        N     DY  
Sbjct: 63  LSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTR 101

>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 = 68.0 bits (166), Expect = 3e-16
 Identities = 15/73 (20%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENAEEALHKLN 121
           + V  LD  V+D D+++ F+++G +    +         G   V F  + +A +A+ + N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 122 GTVIGKQSVRLSW 134
           G  +  + + +  
Sbjct: 63  GVPLDGRPMNIQL 75

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.5 bits (167), Expect = 3e-16
 Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 4/83 (4%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV----GKGCGFVQFANRENA 113
           S   S    IF+  LD ++ ++ L   FS +G I S K+       KG GFV F  +E A
Sbjct: 2   SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAA 61

Query: 114 EEALHKLNGTVIGKQSVRLSWGR 136
           E A+ K+NG ++  + V +   +
Sbjct: 62  ERAIEKMNGMLLNDRKVFVGRFK 84

>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 = 67.8 bits (165), Expect = 4e-16
 Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEA 116
           S T + V  L  N+T E+ R  F   GEI S K+          G GFV + + ++AE+A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 117 LHKLNGTVIGKQSVRLSWGR 136
           ++ LNG  +  +++++S+ R
Sbjct: 61  INTLNGLRLQTKTIKVSYAR 80

>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 = 67.4 bits (164), Expect = 6e-16
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 9/81 (11%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC---------GFVQFANRENAEEAL 117
           +F+  L+ + T+E L+  FS+ G I S  I   K           GFV++   E A++AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 118 HKLNGTVIGKQSVRLSWGRNP 138
            +L G  +    + +      
Sbjct: 61  KQLQGHTVDGHKLEVRISERA 81

>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 = 67.0 bits (163), Expect = 1e-15
 Identities = 25/90 (27%), Positives = 42/90 (46%), Gaps = 3/90 (3%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVK-IPVGKGCGFVQFANRENAEEALH 118
           G S ++ +FVG    ++T+++LR+ FSQYG++  V      +   FV FA+ + A+    
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 119 KLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
                +I   SV +S      N       G
Sbjct: 61  --EDLIIKGISVHISNAEPKHNSNSGPSSG 88

>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 = 66.2 bits (161), Expect = 2e-15
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
              T++V G D  +T   LR  FS +G I  + +   + C FV +   E+A++A+ +LNG
Sbjct: 4   KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNG 61

Query: 123 TVIGKQSVRLSWGR 136
           T +    ++++  R
Sbjct: 62  TQVESVQLKVNIAR 75

>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 = 66.3 bits (161), Expect = 3e-15
 Identities = 25/94 (26%), Positives = 41/94 (43%), Gaps = 7/94 (7%)

Query: 49  NGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG----- 103
                 G Q EG      +F+  L     D+DL Q F  +G + S K+ + K        
Sbjct: 4   QSIGAAGSQKEGPE-GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCF 62

Query: 104 -FVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
            FV + N  +A+ A+  +NG  IG + +++   R
Sbjct: 63  GFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR 96

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 65.8 bits (160), Expect = 4e-15
 Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 56  PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-VGKGCGFVQFANRENAE 114
             S+   +  T+    L  N+T+++L++ F    EI  V      KG  +++F +  +AE
Sbjct: 8   CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAE 67

Query: 115 EALHKLNGTVIGKQSVRLSWGR 136
           + L +  G  I  +SV L +  
Sbjct: 68  KNLEEKQGAEIDGRSVSLYYTG 89

>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 = 65.0 bits (158), Expect = 5e-15
 Identities = 14/74 (18%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKL 120
           +F+GGL   + D+ +++  + +G + +  +         KG  F ++ +    ++A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 121 NGTVIGKQSVRLSW 134
           NG  +G + + +  
Sbjct: 64  NGMQLGDKKLLVQR 77

>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 = 65.2 bits (158), Expect = 9e-15
 Identities = 13/84 (15%), Positives = 32/84 (38%), Gaps = 5/84 (5%)

Query: 60  GDSSNTTIFVGGLDPNVTDE-----DLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 114
           G S ++ +     + +V  E          F  Y +  + +         + F+N  +A 
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAA 60

Query: 115 EALHKLNGTVIGKQSVRLSWGRNP 138
           +A  +L+ T    + ++L + +  
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTL 84

>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 = 64.3 bits (156), Expect = 9e-15
 Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 7/83 (8%)

Query: 55  GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS------VKIPVGKGCGFVQFA 108
           G ++  D  N  + V GL    T+ DLR+ FS+YG IA        +    +G  FV F 
Sbjct: 1   GNRANPDP-NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 59

Query: 109 NRENAEEALHKLNGTVIGKQSVR 131
           N ++A+EA  + NG  +  + +R
Sbjct: 60  NVDDAKEAKERANGMELDGRRIR 82

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.7 bits (157), Expect = 9e-15
 Identities = 15/81 (18%), Positives = 30/81 (37%), Gaps = 10/81 (12%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV--------GKGCGFVQFANRENAEE 115
           N  +F+GG+      E++ +  ++  E     I           +G  FV++ +   A  
Sbjct: 1   NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 60

Query: 116 ALHKLNG--TVIGKQSVRLSW 134
           A  KL      +    + + W
Sbjct: 61  ARRKLMPGRIQLWGHQIAVDW 81

>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 = 64.7 bits (157), Expect = 1e-14
 Identities = 20/100 (20%), Positives = 37/100 (37%), Gaps = 10/100 (10%)

Query: 51  APGQGPQ---SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKG 101
           +P + P    S  +    T+F   L   +   DL   FS  G++  V+I         KG
Sbjct: 2   SPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 61

Query: 102 CGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANK 141
             +V+F   ++       L G  +    + +   +   N+
Sbjct: 62  IAYVEFCEIQSV-PLAIGLTGQRLLGVPIIVQASQAEKNR 100

>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 = 64.4 bits (156), Expect = 1e-14
 Identities = 26/95 (27%), Positives = 46/95 (48%), Gaps = 6/95 (6%)

Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAE 114
           D S  ++FVG +    T+E L+  FS+ G + S ++         KG GF ++ ++E A 
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 115 EALHKLNGTVIGKQSVRLSWGRNPANKQFRADYGN 149
            A+  LNG     +++R+    +  NK+     G 
Sbjct: 65  SAMRNLNGREFSGRALRVDNAASEKNKEELKSLGT 99

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.3 bits (156), Expect = 1e-14
 Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 6/94 (6%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRE 111
           S G S +  +FV  L    ++EDL + FS YG ++ +  P+        G  FV F   E
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 112 NAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRA 145
           +A +A  +++G V   + + +             
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSG 95

>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 = 64.1 bits (155), Expect = 2e-14
 Identities = 19/90 (21%), Positives = 30/90 (33%), Gaps = 1/90 (1%)

Query: 54  QGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANR-EN 112
                E        F G LD     EDL   FS +GEI  +    G   G + F  + + 
Sbjct: 1   HHGSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKE 60

Query: 113 AEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           A       N   +  ++  ++W       +
Sbjct: 61  ALGKAKDANNGNLQLRNKEVTWEVLEGEVE 90

>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 = 63.2 bits (153), Expect = 3e-14
 Identities = 22/84 (26%), Positives = 32/84 (38%), Gaps = 6/84 (7%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRE 111
           S G    T I V  +   V+ +++   F  Y  I               G   V F +R+
Sbjct: 3   SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 62

Query: 112 NAEEALHKLNGTVIGKQSVRLSWG 135
            A  A+  LN   IG + V+L  G
Sbjct: 63  EATAAVIDLNDRPIGSRKVKLVLG 86

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.2 bits (153), Expect = 5e-14
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN 121
           + +  +  GGL   V+   L     + G + ++ +P  K   F ++   E ++ A   LN
Sbjct: 18  TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLN 77

Query: 122 GTVIG-----KQSVRLSW 134
           G  +      K ++ L++
Sbjct: 78  GKEVVDDLGQKITLYLNF 95

>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 = 62.8 bits (152), Expect = 5e-14
 Identities = 25/87 (28%), Positives = 47/87 (54%), Gaps = 6/87 (6%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEE 115
           S    +FVGGL  +  ++ L Q FS+YG+I+ V +         +G GFV F N ++A++
Sbjct: 3   SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 62

Query: 116 ALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           A+  +NG  +  + +R+      ++ +
Sbjct: 63  AMMAMNGKSVDGRQIRVDQAGKSSDNR 89

>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 = 62.7 bits (152), Expect = 5e-14
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 9/76 (11%)

Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANREN 112
                 + + V GL    T++DL++ FS +GE+  V++          G GFV+F   E 
Sbjct: 3   RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 62

Query: 113 AEEAL---HKLNGTVI 125
             + +   H ++G   
Sbjct: 63  QVKVMSQRHMIDGRWC 78

>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 = 62.3 bits (151), Expect = 6e-14
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 6/68 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALHKL 120
           IFVGGL P+  +E +R+ F  +GE+ S+++P+        G  F+ F   E  ++ + K 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 121 NGTVIGKQ 128
              V   +
Sbjct: 62  YHNVGLSK 69

>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 = 61.9 bits (150), Expect = 8e-14
 Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 1/76 (1%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT 123
           +T + V G         L Q F+QYG I    +        +++ ++  A +AL K    
Sbjct: 4   DTWVTVFGFPQASASYILLQ-FAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRI 62

Query: 124 VIGKQSVRLSWGRNPA 139
                 + +    +  
Sbjct: 63  FGESIMIGVKPCIDKN 78

>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 = 61.7 bits (149), Expect = 9e-14
 Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 7/82 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKI-------PVGKGCGFVQFANRENAEEALHK 119
           IF+G LDP + ++ L   FS +G I               KG  F+ FA+ + ++ A+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 120 LNGTVIGKQSVRLSWGRNPANK 141
           +NG  +  + + +S+     +K
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 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 = 62.7 bits (151), Expect = 9e-14
 Identities = 18/83 (21%), Positives = 30/83 (36%)

Query: 55  GPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAE 114
           G       S T I    L       ++++ FS++G +  V +P G     V+F     A 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEAR 60

Query: 115 EALHKLNGTVIGKQSVRLSWGRN 137
           +A   L  +      + L W   
Sbjct: 61  KAFRHLAYSKFHHVPLYLEWAPI 83

>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 = 61.5 bits (149), Expect = 1e-13
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 7/74 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALHKL 120
           +F+GGL    T E LR+ F Q+GE+    +          G GFV F ++   ++ L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 121 NGTVIGKQSVRLSW 134
           +   +  +++    
Sbjct: 62  SRHELDSKTIDPKV 75

>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 = 62.1 bits (150), Expect = 1e-13
 Identities = 32/93 (34%), Positives = 49/93 (52%), Gaps = 8/93 (8%)

Query: 58  SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRE 111
           S+ D++ T IFVGGL  + TD  LR+ F  +G+I    +   +      G GFV  A+R 
Sbjct: 4   SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRA 63

Query: 112 NAEEALHKLNGTVIGKQ-SVRLSW-GRNPANKQ 142
            AE A    N  + G++ +V L++ G  P + Q
Sbjct: 64  AAERACKDPNPIIDGRKANVNLAYLGAKPRSLQ 96

>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 = 60.9 bits (147), Expect = 2e-13
 Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTV- 124
            +++G L P VT +DLRQ F       + ++ +  G  FV + ++  A  A+  L+G V 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 62

Query: 125 IGKQSVRLSWGRNPANK 141
           +  + + + +  +   +
Sbjct: 63  LHGKIMEVDYSVSKKLR 79

>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 = 60.8 bits (147), Expect = 3e-13
 Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 8/90 (8%)

Query: 51  APGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGF 104
            P +  + E +     +F+GGL    T+E LR  + Q+G++    +         +G GF
Sbjct: 8   VPLERKKREKEQF-RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 66

Query: 105 VQFANRENAEEALHKLNGTVIGKQSVRLSW 134
           V F++    + A+       I  + V    
Sbjct: 67  VTFSSMAEVDAAM-AARPHSIDGRVVEPKR 95

>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 = 60.1 bits (145), Expect = 5e-13
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 8/85 (9%)

Query: 56  PQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC------GFVQFAN 109
           PQ   +     +FV  +     ++++++ F  YGEI ++ + + +          V++  
Sbjct: 1   PQRSVE--GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 58

Query: 110 RENAEEALHKLNGTVIGKQSVRLSW 134
            + A  A   LNG  I  Q++++ W
Sbjct: 59  HKQALAAKEALNGAEIMGQTIQVDW 83

>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 = 60.6 bits (146), Expect = 5e-13
 Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 2/90 (2%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 109
           G+ G        S +  + V GL  +V + DL +   ++G I  V +   K    V+F N
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFEN 60

Query: 110 RENAEEALHKL--NGTVIGKQSVRLSWGRN 137
            ++A+E +         I  Q    ++  +
Sbjct: 61  IDSAKECVTFAADVPVYIAGQQAFFNYSTS 90

>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 = 59.7 bits (144), Expect = 8e-13
 Identities = 21/93 (22%), Positives = 48/93 (51%), Gaps = 3/93 (3%)

Query: 47  ASNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQ 106
            S+G+ G+    + + +   ++VGGL PN +   L + F ++G I ++    G    ++Q
Sbjct: 1   GSSGSSGKIGYGKANPTTR-LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQ 59

Query: 107 FANRENAEEALHKLNGTVIGKQS--VRLSWGRN 137
           + + + A+ A  K+ G  +G     +R+ + ++
Sbjct: 60  YESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS 92

>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 = 59.3 bits (143), Expect = 8e-13
 Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 6/69 (8%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHK 119
            +F+GGL    TDE LR  F Q+G +    +         +G GFV +A  E  + A++ 
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 120 LNGTVIGKQ 128
               V G+ 
Sbjct: 68  RPHKVDGRV 76

>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 = 58.5 bits (141), Expect = 1e-12
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 10/69 (14%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG------CGFVQFANRENAEEAL--- 117
           +F+GGL  + T +DL+  FS++GE+    + +          GFV F   E+ ++ +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 118 -HKLNGTVI 125
            HKLNG VI
Sbjct: 62  EHKLNGKVI 70

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 57.5 bits (138), Expect = 3e-12
 Identities = 12/79 (15%), Positives = 28/79 (35%), Gaps = 6/79 (7%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEAL 117
             T+++    P+ T  ++R        +A             +   ++   ++E+A   +
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 118 HKLNGTVIGKQSVRLSWGR 136
            KLNG  I   ++      
Sbjct: 61  EKLNGLKIEGYTLVTKVSN 79

>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 = 56.7 bits (136), Expect = 1e-11
 Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 6/84 (7%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEAL 117
           N  +++  L P VT+ DL   F+++ E     I          G  F+ F N+E A +AL
Sbjct: 18  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 118 HKLNGTVIGKQSVRLSWGRNPANK 141
           H +NG  +  + + + +G+N   +
Sbjct: 78  HLVNGYKLYGKILVIEFGKNKKQR 101

>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 = 55.9 bits (134), Expect = 1e-11
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 7/74 (9%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG------CGFVQFANRENAEEALHKL 120
           IFVGGL  N T ED++  F Q+G++    +   K        GFV F + +  E+   ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 121 NGTVIGKQSVRLSW 134
           +   I  + V    
Sbjct: 61  HFHEINNKMVECKK 74

>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 = 56.7 bits (136), Expect = 2e-11
 Identities = 27/97 (27%), Positives = 45/97 (46%), Gaps = 2/97 (2%)

Query: 64  NTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVGKG-CGFVQFANRENAEEALHKLN 121
           N+ + V  L+P  VT + L   F  YG++  VKI   K     VQ A+   A+ A+  LN
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 122 GTVIGKQSVRLSWGRNPANKQFRADYGNQWSGAYYGG 158
           G  +  + +R++  ++   +  R    +Q     YG 
Sbjct: 62  GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGN 98

>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 = 55.1 bits (132), Expect = 4e-11
 Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 1/80 (1%)

Query: 60  GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHK 119
           G S ++ I V  L  +   +++      Y       +   K   FV   N E A+ A+  
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLK-YCYVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 120 LNGTVIGKQSVRLSWGRNPA 139
            +      + + +      A
Sbjct: 60  FHQYSFRGKDLIVQLQPTDA 79

>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 = 54.4 bits (130), Expect = 6e-11
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 3/78 (3%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVK--IPVGKGCGFVQFANRENAEEALHKLN 121
           + T+ +  + P+V++EDL+  FS  G +          +    +Q  + E A +AL  L+
Sbjct: 10  SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLH 69

Query: 122 GTVIGK-QSVRLSWGRNP 138
              +G+   +R+S+ ++ 
Sbjct: 70  NHDLGENHHLRVSFSKST 87

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.4 bits (130), Expect = 7e-11
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 12/82 (14%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----------KGCGFVQFANRENAE 114
            ++VG +   +T+E +   F+    +  +    G           K   F++F + +   
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 115 EALHKLNGTVIGKQSVRLSWGR 136
           +A+   +G +   QS+++    
Sbjct: 63  QAMA-FDGIIFQGQSLKIRRPH 83

>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 = 54.0 bits (129), Expect = 8e-11
 Identities = 14/81 (17%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 59  EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGCGFVQFANRENA 113
           + D  N ++++ G   + T +D+++     G++ ++++        KG  FV F + E+A
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 60

Query: 114 EEALHKLNGTVIGKQSVRLSW 134
           ++ + +  G    +  + + +
Sbjct: 61  KKFV-ETPGQKYKETDLLILF 80

>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 = 53.6 bits (128), Expect = 9e-11
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 6/71 (8%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKG------CGFVQFANRENAEEALHKL 120
           +++ GL P  TD+DL +    YG+I S K  + K        GFV F +   A++A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 121 NGTVIGKQSVR 131
             + +  Q  +
Sbjct: 61  KASGVQAQMAK 71

>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 = 53.6 bits (128), Expect = 2e-10
 Identities = 23/99 (23%), Positives = 40/99 (40%), Gaps = 7/99 (7%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCG 103
           G+ G        S   T F+G L  +VT+E +++ F      A             KG G
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 104 FVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           + +F + ++   AL  LN   +G + +R+       +K 
Sbjct: 61  YAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKD 98

>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 = 53.3 bits (127), Expect = 2e-10
 Identities = 16/94 (17%), Positives = 38/94 (40%), Gaps = 6/94 (6%)

Query: 48  SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-----GKGC 102
           ++G   Q  + + +   T +++  L  ++ +++L      +G++ S +I        +G 
Sbjct: 3   ASGVQAQMAKQQ-EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGV 61

Query: 103 GFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR 136
           GF +  + E  E  +   NG  I       +   
Sbjct: 62  GFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 95

>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 = 53.3 bits (127), Expect = 3e-10
 Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 12/88 (13%)

Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAE 114
            +   T+F+  L  +  +E L +   Q+G++  V++ +        GC F QF  +E A+
Sbjct: 5   VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ 64

Query: 115 EALHKLN------GTVIGKQSVRLSWGR 136
           + L   +      G  +  + +++    
Sbjct: 65  KCLAAASLEAEGGGLKLDGRQLKVDLAV 92

>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 = 53.0 bits (127), Expect = 3e-10
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 2/58 (3%)

Query: 79  EDLRQPFSQYGEIASVKIPVG--KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW 134
           EDLR   S++G+I  + +      G   V F + E A+  +  L+G   G + +    
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 91

>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 = 52.5 bits (125), Expect = 4e-10
 Identities = 15/94 (15%), Positives = 34/94 (36%), Gaps = 9/94 (9%)

Query: 59  EGD--SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANR 110
           EGD  S+     +  +  ++T  D+ Q         +    +      G G   VQF N 
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 60

Query: 111 ENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFR 144
           ++A ++  +L+   +  +   +        ++  
Sbjct: 61  DDARKSE-RLHRKKLNGREAFVHVVTLEDMREIE 93

>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 = 52.5 bits (125), Expect = 4e-10
 Identities = 23/99 (23%), Positives = 40/99 (40%), Gaps = 1/99 (1%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFAN 109
           G+ G         S+  + V GL P+ + +DL+    + G++         G G V++  
Sbjct: 1   GSSGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDV-CYADVQKDGMGMVEYLR 59

Query: 110 RENAEEALHKLNGTVIGKQSVRLSWGRNPANKQFRADYG 148
           +E+ E AL KL+ T         S+ R    +      G
Sbjct: 60  KEDMEYALRKLDDTKFRSHEGETSYIRVYPERSSGPSSG 98

>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 = 53.9 bits (128), Expect = 6e-10
 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 6/63 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP------VGKGCGFVQFANRENAEEALHK 119
            +F+GGL    TDE LR  F Q+G +    +         +G GFV +A  E  + A++ 
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 120 LNG 122
              
Sbjct: 68  RPH 70

>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 = 50.0 bits (118), Expect = 1e-08
 Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 63  SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEA 116
           +   IFVGG+  +  +  LR  F QYG+I  ++I         +G  FV F + ++ ++ 
Sbjct: 96  TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155

Query: 117 LHKLNGTVIGKQSVRLSW 134
           +       +   +  +  
Sbjct: 156 V-IQKYHTVNGHNCEVRK 172

>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 = 51.7 bits (123), Expect = 9e-10
 Identities = 18/97 (18%), Positives = 32/97 (32%), Gaps = 5/97 (5%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC----GFV 105
           G+ G    S   ++   + + GL    T+ D+   FS    +         G       V
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADV 60

Query: 106 QFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
           +FA  E+A  A+   +   +  + V L          
Sbjct: 61  EFATHEDAVAAM-AKDKANMQHRYVELFLNSTAGTSG 96

>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 = 50.9 bits (121), Expect = 2e-09
 Identities = 12/80 (15%), Positives = 29/80 (36%), Gaps = 3/80 (3%)

Query: 66  TIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEAL--HKLNG 122
            + +            L Q    +G I++  I       F++ A  E+A+ A+  +    
Sbjct: 10  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTP 69

Query: 123 TVIGKQSVRLSWGRNPANKQ 142
            ++  + VR+   +     +
Sbjct: 70  ALVFGKPVRVHLSQKYKRIK 89

>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 = 50.6 bits (120), Expect = 2e-09
 Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 2/75 (2%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEI-ASVKIPVGKGCGFVQFANRENAEEALHKLNG 122
           N  +F+  L     +  L   F+Q+        +P      FV+F     +  A   L G
Sbjct: 8   NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQG 67

Query: 123 TVIGK-QSVRLSWGR 136
             I    ++++++ +
Sbjct: 68  FKITPTHAMKITFAK 82

>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 = 51.8 bits (123), Expect = 2e-09
 Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 6/87 (6%)

Query: 61  DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGC------GFVQFANRENAE 114
                 + V  +   V +  LRQ F +YG I SVKI   +        GFV+F +  +A+
Sbjct: 39  PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQ 98

Query: 115 EALHKLNGTVIGKQSVRLSWGRNPANK 141
           +A+  LNG  I  + ++++   +   +
Sbjct: 99  QAIAGLNGFNILNKRLKVALAASGHQR 125

>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 = 50.2 bits (119), Expect = 2e-09
 Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 12/80 (15%)

Query: 66  TIFVGGLDPNVTDEDLRQPF---SQYGEIASVKIPVGK---------GCGFVQFANRENA 113
            +FV GL   + D ++ +      ++G+I  V I                +V +   E+A
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 114 EEALHKLNGTVIGKQSVRLS 133
             A+  +N  V+  ++++ S
Sbjct: 70  LRAIQCVNNVVVDGRTLKAS 89

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.0 bits (116), Expect = 6e-09
 Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 9/81 (11%)

Query: 64  NTTIFVGGLDPNVTDED-LRQPFSQYGEIASVKIPV-------GKGCGFVQFANRENAEE 115
              I +  L   + DE+ LR+ F  +G I  + IP           C F+ F N+++AE 
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 116 ALHKLNGTVIGKQSVRLSWGR 136
           AL ++N +++G + + +S   
Sbjct: 64  AL-QMNRSLLGNREISVSLAD 83

>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 = 48.9 bits (116), Expect = 1e-08
 Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 6/85 (7%)

Query: 56  PQSEGDSSNTT-IFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFAN 109
             ++G  S  + + +        +E   +   +YGE+  + +         G  +V+F  
Sbjct: 18  QSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRR 77

Query: 110 RENAEEALHKLNGTVIGKQSVRLSW 134
            E+AE+A+  LN      Q +    
Sbjct: 78  EEDAEKAVIDLNNRWFNGQPIHAEL 102

>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 = 47.8 bits (113), Expect = 1e-08
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 66  TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGK------GCGFVQFANRENAEEALHK 119
            IFVGG+  +  +  LR  F QYG+I  ++I   +      G  FV F + + + + +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD-SVDKIVI 62

Query: 120 LNGTVIGKQSVR 131
                +   +  
Sbjct: 63  QKYHTVNGHNCE 74

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.2 bits (111), Expect = 2e-08
 Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 4/68 (5%)

Query: 65  TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP----VGKGCGFVQFANRENAEEALHKL 120
           TT+ V  L  +     + + F   G I  V +            ++FA  + A  A+ K 
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 60

Query: 121 NGTVIGKQ 128
           +  V   +
Sbjct: 61  HKVVGQNE 68

>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 = 46.4 bits (109), Expect = 6e-08
 Identities = 19/86 (22%), Positives = 33/86 (38%), Gaps = 1/86 (1%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           + V GL P+ + +DL+    +             G G V+F  +E+   A+ KL+ T   
Sbjct: 3   VVVSGLPPSGSWQDLKD-HMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFR 61

Query: 127 KQSVRLSWGRNPANKQFRADYGNQWS 152
                 ++ R   +      YG   S
Sbjct: 62  SHEGETAYIRVKVDGPRSPSYGRSRS 87

>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 = 1e-07
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 8/71 (11%)

Query: 72  LDPNVTDEDLRQPFSQYGEIASVKIP--------VGKGCGFVQFANRENAEEALHKLNGT 123
            +     ED+R   S+YG + S++IP         G G  FV+F +  + ++A+  L G 
Sbjct: 22  EEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR 81

Query: 124 VIGKQSVRLSW 134
               + V   +
Sbjct: 82  KFANRVVVTKY 92

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (104), Expect = 5e-07
 Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 6/85 (7%)

Query: 50  GAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCG------ 103
           G+ G    S   +++  + + GL    + E++ Q FS    + +         G      
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 104 FVQFANRENAEEALHKLNGTVIGKQ 128
           FVQFA++E AE+AL K    +  + 
Sbjct: 61  FVQFASQEIAEKALKKHKERIGHRY 85

>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 = 43.3 bits (101), Expect = 1e-06
 Identities = 11/76 (14%), Positives = 32/76 (42%), Gaps = 2/76 (2%)

Query: 64  NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHK--LN 121
           +  + +  L   VT+ ++      +G++ ++ +  GK   F++ A  E A   ++     
Sbjct: 8   SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAV 67

Query: 122 GTVIGKQSVRLSWGRN 137
              +  Q + + +  +
Sbjct: 68  TPHLRNQPIYIQYSNH 83

>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 = 42.6 bits (99), Expect = 1e-06
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 67  IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIG 126
           I + GL  +VT++++    S Y       +   KG  FV   N E AE A++  + + + 
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELK-YCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLR 59

Query: 127 KQSVRLSWGRNPA 139
           ++ + +      A
Sbjct: 60  ERELSVQLQPTDA 72

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 41.1 bits (95), Expect = 6e-06
 Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 6/80 (7%)

Query: 62  SSNTTIFVGGLDPNVTDEDLRQPFSQYGEI-----ASVKIPVGKGCGFVQFANRENAEEA 116
           ++   +F+G L+PN +  +L+   S+           V+    +  G+V F + E+ E+A
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA 70

Query: 117 LHKLNGTVIGKQSVRLSWGR 136
           L  L G  +    ++L   +
Sbjct: 71  LE-LTGLKVFGNEIKLEKPK 89

>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 = 34.5 bits (78), Expect = 0.002
 Identities = 15/101 (14%), Positives = 36/101 (35%), Gaps = 11/101 (10%)

Query: 48  SNGAPGQGPQSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKG 101
           S     +        +   +++ GL     ++ +   F +   +               G
Sbjct: 2   SPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATG 61

Query: 102 CGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPANKQ 142
            GFV+F N  + + AL   +   +G + +++    +P  K+
Sbjct: 62  EGFVEFRNEADYKAAL-CRHKQYMGNRFIQV----HPITKK 97

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	198
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.88
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.87
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.87
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.87
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.87
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.87
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.86
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.86
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.86
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.86
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.86
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.86
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.86
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.85
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.85
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.85
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.85
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.85
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.85
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.84
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.84
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.84
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.84
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.84
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.84
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.84
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.83
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.83
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.83
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.83
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.83
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.82
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.82
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.82
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.82
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.82
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.82
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.82
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.82
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.82
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.81
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.81
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.81
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.81
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.8
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.8
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.8
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.8
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.79
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.79
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.79
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.78
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.78
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.78
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.78
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.78
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.77
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.77
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.74
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.73
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.7
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.67
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.66
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.66
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.65
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.62
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	99.56
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.55
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.45
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.36
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.84
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.6
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.51
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.12

>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=99.88  E-value=2.5e-22  Score=135.93  Aligned_cols=77  Identities=35%  Similarity=0.702  Sum_probs=73.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      ..++|||+|||..+++++|+++|++||.|.+|+|+++||||||+|.+.++|++|+..|++..|+|+.|+|+|+++..
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999998643

>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=99.87  E-value=4.1e-22  Score=135.37  Aligned_cols=80  Identities=31%  Similarity=0.574  Sum_probs=71.6

Q ss_pred             CCCCCCCCeEEEcCCC-CCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           58 SEGDSSNTTIFVGGLD-PNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~-~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      .+.....++|||+||+ ..+++++|+++|++||.|.+|+|.  |+||||+|.+.++|++||+.||+..|.|+.|+|+|++
T Consensus         9 ~~~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   86 (98)
T d1wf2a_           9 TDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAA   86 (98)
T ss_dssp             CCCSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETT
T ss_pred             CCCCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            3444556789999997 568899999999999999999994  7999999999999999999999999999999999998


Q ss_pred             CCC
Q 029166          137 NPA  139 (198)
Q Consensus       137 ~~~  139 (198)
                      ++.
T Consensus        87 ~~~   89 (98)
T d1wf2a_          87 EPK   89 (98)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            653

>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=99.87  E-value=6.2e-22  Score=132.42  Aligned_cols=82  Identities=32%  Similarity=0.514  Sum_probs=74.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ++.+.++|||+|||.++++++|+++|++||.|.+|+|+.+    ++||||+|.+.++|+.|++.|++..|.|+.|+|.||
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            3455789999999999999999999999999999999864    689999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 029166          136 RNPANK  141 (198)
Q Consensus       136 ~~~~~~  141 (198)
                      +++..+
T Consensus        84 ~~~~~~   89 (90)
T d2cqia1          84 TTPSSQ   89 (90)
T ss_dssp             CCTTCC
T ss_pred             CCCCCC
Confidence            876543

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.87  E-value=1.1e-21  Score=133.40  Aligned_cols=79  Identities=28%  Similarity=0.466  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ...++|||+|||+++++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|++||+.||+..|+|+.|+|+++
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            34678999999999999999999999999999999764      689999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      +++..
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            97643

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.9e-21  Score=130.78  Aligned_cols=82  Identities=35%  Similarity=0.553  Sum_probs=75.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      .......++|||+|||+++++++|+++|++||.|.+|+++.+    ++||||+|.+.++|++|++.||+..|+|+.|+|+
T Consensus         5 ~~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           5 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            344556778999999999999999999999999999999875    6899999999999999999999999999999999


Q ss_pred             eccCCC
Q 029166          134 WGRNPA  139 (198)
Q Consensus       134 ~a~~~~  139 (198)
                      ||+++.
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ecCcCC
Confidence            998754

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.87  E-value=4.5e-22  Score=130.75  Aligned_cols=74  Identities=28%  Similarity=0.514  Sum_probs=70.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      +++|||+|||.++++++|+++|++||.|.+++|+++      ++||||+|.+.++|++|++.||+..++|+.|+|+||+|
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            578999999999999999999999999999998753      68999999999999999999999999999999999986

>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=99.87  E-value=6.7e-22  Score=132.24  Aligned_cols=79  Identities=25%  Similarity=0.508  Sum_probs=73.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ..+.++|||+|||.++++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|++|++.|++..|+|+.|+|+|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345678999999999999999999999999999999864      57999999999999999999999999999999999


Q ss_pred             ccCCC
Q 029166          135 GRNPA  139 (198)
Q Consensus       135 a~~~~  139 (198)
                      |+++.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            99764

>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=99.86  E-value=5.5e-22  Score=132.39  Aligned_cols=79  Identities=27%  Similarity=0.575  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .+.++|||+|||+++++++|+++|++||+|.+|+|+.+      +|||||+|.+.++|++|++.||+..|+|+.|+|+||
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35679999999999999999999999999999999763      699999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      +++..
T Consensus        83 ~p~~~   87 (89)
T d2cqba1          83 KPMRI   87 (89)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87643

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=7.9e-22  Score=129.54  Aligned_cols=74  Identities=34%  Similarity=0.606  Sum_probs=69.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      .++|||+|||.+++|++|+++|++||.|.+|+++++      +|||||+|.++++|++|++.||+..|+|+.|+|+||+|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            467999999999999999999999999999999763      58999999999999999999999999999999999986

>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=99.86  E-value=7.9e-22  Score=130.80  Aligned_cols=77  Identities=31%  Similarity=0.592  Sum_probs=73.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      ..++|||+|||.++++++|+++|++||.|.+|++.++++||||+|.+.++|++|++.||+..|+|+.|+|+||.+..
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999998653

>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=99.86  E-value=1.3e-21  Score=129.65  Aligned_cols=82  Identities=24%  Similarity=0.382  Sum_probs=75.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      +.....++|||+|||+++++++|+++|++||.|..+++.++++||||+|.+.++|..|+..||+..|+|+.|+|+||+|+
T Consensus         3 d~~~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~   82 (86)
T d2cpda1           3 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   82 (86)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             ccccCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCC
Confidence            33445689999999999999999999999999999999889999999999999999999999999999999999999976


Q ss_pred             CC
Q 029166          139 AN  140 (198)
Q Consensus       139 ~~  140 (198)
                      ..
T Consensus        83 ~~   84 (86)
T d2cpda1          83 DK   84 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.5e-21  Score=131.35  Aligned_cols=79  Identities=28%  Similarity=0.509  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ...+++|||+|||+++++++|+++|++||+|.+|.|+++      +|||||+|.+.++|+.|++.||+..|+|+.|+|+|
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            346789999999999999999999999999999999764      57999999999999999999999999999999999


Q ss_pred             ccCCC
Q 029166          135 GRNPA  139 (198)
Q Consensus       135 a~~~~  139 (198)
                      +....
T Consensus        84 a~~~~   88 (93)
T d1h2vz_          84 DAGFK   88 (93)
T ss_dssp             ESCCC
T ss_pred             cCCCC
Confidence            97543

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.3e-21  Score=133.73  Aligned_cols=79  Identities=28%  Similarity=0.513  Sum_probs=72.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ++.++|||+|||+++++++|+++|++||.|.+++++.+      ||||||+|.+.++|+.||+.||+..|+|+.|+|+||
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            34678999999999999999999999999999988753      589999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      +++.+
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            98754

>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=99.86  E-value=9.4e-22  Score=130.98  Aligned_cols=79  Identities=23%  Similarity=0.496  Sum_probs=72.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ...+.++|||+|||.++++++|+++|++||.|.+|+|+++      +|||||+|.+.++|++|++.||+..|+|+.|+|+
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~   82 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999999764      5899999999999999999999999999999999


Q ss_pred             eccCC
Q 029166          134 WGRNP  138 (198)
Q Consensus       134 ~a~~~  138 (198)
                      ||.++
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            99864

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=9.8e-22  Score=132.23  Aligned_cols=78  Identities=27%  Similarity=0.512  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ...++|||+|||.++++++|+++|++||.|.+++|+++      +|||||+|.+.++|++|++.||+..|+|+.|+|+||
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34579999999999999999999999999999999763      689999999999999999999999999999999999


Q ss_pred             cCCC
Q 029166          136 RNPA  139 (198)
Q Consensus       136 ~~~~  139 (198)
                      +++.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8754

>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=99.86  E-value=3.7e-21  Score=129.82  Aligned_cols=78  Identities=26%  Similarity=0.535  Sum_probs=72.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC---CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV---GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~---~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+..   .++||||+|.+.++|+.||+.||++.|+|+.|+|+||++
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            44567899999999999999999999999999999865   379999999999999999999999999999999999986


Q ss_pred             C
Q 029166          138 P  138 (198)
Q Consensus       138 ~  138 (198)
                      .
T Consensus        91 ~   91 (95)
T d1x4aa1          91 G   91 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.85  E-value=3.7e-21  Score=138.56  Aligned_cols=81  Identities=30%  Similarity=0.492  Sum_probs=73.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ....++|||+|||+++++++|+++|++||.|.+|+|+++      ||||||+|.+.++|++||+.||+..|+|+.|+|+|
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            334578999999999999999999999999999999753      68999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 029166          135 GRNPANK  141 (198)
Q Consensus       135 a~~~~~~  141 (198)
                      |++...+
T Consensus       119 a~~~~~~  125 (139)
T d1u6fa1         119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             cCCCCCC
Confidence            9875443

>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=1.6e-21  Score=127.29  Aligned_cols=75  Identities=29%  Similarity=0.558  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      ...++|||+||+  +||++|+++|++||.|.++++.++++||||+|.+.++|.+|++.||+..++|+.|+|+||+++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            346799999985  899999999999999999999999999999999999999999999999999999999999864

>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=99.85  E-value=4.1e-22  Score=130.46  Aligned_cols=76  Identities=22%  Similarity=0.421  Sum_probs=71.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCc-eeCCeEeEEEeccCCCC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGT-VIGKQSVRLSWGRNPAN  140 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~-~~~g~~l~v~~a~~~~~  140 (198)
                      .+|||+|||+++++++|+++|++||.|.+++++++|+||||+|.+.++|++|++.||+. .++|+.|+|+||.++..
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            47999999999999999999999999999888889999999999999999999999985 69999999999998654

>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=99.85  E-value=1.9e-21  Score=129.77  Aligned_cols=77  Identities=32%  Similarity=0.579  Sum_probs=72.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      ..+|||+|||+++++++|+++|++||.|.+++|+.+    +|||||+|.+.++|++|++.||+..|+|+.|+|++|+++.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            457999999999999999999999999999999874    6999999999999999999999999999999999998764


Q ss_pred             C
Q 029166          140 N  140 (198)
Q Consensus       140 ~  140 (198)
                      +
T Consensus        88 ~   88 (89)
T d1cvja2          88 E   88 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=3.4e-21  Score=129.75  Aligned_cols=79  Identities=25%  Similarity=0.589  Sum_probs=72.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-------CcEEEEEeCCHHHHHHHHHHh-CCceeCCeEeEE
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-------KGCGFVQFANRENAEEALHKL-NGTVIGKQSVRL  132 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-------kg~afV~f~~~~~a~~a~~~l-~~~~~~g~~l~v  132 (198)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+|+++       +|||||+|.+.++|++|++.| |+..|+|+.|+|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            345678999999999999999999999999999999653       689999999999999999998 899999999999


Q ss_pred             EeccCCC
Q 029166          133 SWGRNPA  139 (198)
Q Consensus       133 ~~a~~~~  139 (198)
                      +||++..
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9998754

>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=99.85  E-value=1.3e-21  Score=135.55  Aligned_cols=78  Identities=22%  Similarity=0.387  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      ...++|||+|||+.+++++|+++|++||+|.+|.|.++++||||+|.+.++|++|++.||+..|.|+.|.|+|+....
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            346799999999999999999999999999999999999999999999999999999999999999999999997543

>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=99.85  E-value=4.5e-21  Score=130.12  Aligned_cols=80  Identities=25%  Similarity=0.404  Sum_probs=73.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      ...+..+|||+|||+++++++|+++|++||+|++++|.+ ++||||+|.+.++|++||+.||+..|+|+.|+|.+++.+.
T Consensus        11 ~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             CCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            344677899999999999999999999999999999875 5999999999999999999999999999999999998654


Q ss_pred             C
Q 029166          140 N  140 (198)
Q Consensus       140 ~  140 (198)
                      .
T Consensus        90 ~   90 (98)
T d1wg4a_          90 E   90 (98)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.85  E-value=2.7e-21  Score=129.22  Aligned_cols=79  Identities=32%  Similarity=0.644  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.      ++|||||+|.++++|+.|++.|++..|+|+.|+|+||
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            4578899999999999999999999999999998876      3699999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      .++..
T Consensus        83 ~~~~~   87 (90)
T d1x5sa1          83 GKSSD   87 (90)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87644

>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=99.85  E-value=1e-20  Score=128.17  Aligned_cols=78  Identities=24%  Similarity=0.554  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCC--eEeEEEeccCC
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGK--QSVRLSWGRNP  138 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g--~~l~v~~a~~~  138 (198)
                      ..+.++|||+|||+++++++|+++|++||+|..+++.++++||||+|.+.++|+.|++.||+..|++  ++|+|+||++.
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            3457899999999999999999999999999999999999999999999999999999999999976  58999999864

>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=6.1e-21  Score=126.99  Aligned_cols=76  Identities=16%  Similarity=0.261  Sum_probs=69.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      ..++|||+|||+++++++|+++|++|| +..+.+.+.++||||+|.+.++|++|++.||+..|+|+.|+|+|+++..
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            357899999999999999999999999 4556677789999999999999999999999999999999999997653

>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=99.84  E-value=8.5e-21  Score=124.90  Aligned_cols=77  Identities=18%  Similarity=0.372  Sum_probs=70.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCcee-CCeEeEEEecc
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVI-GKQSVRLSWGR  136 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~~-~g~~l~v~~a~  136 (198)
                      ..+++++|||+|||.++++++|+++|++||.|.+|+++++ ++||||+|.+.++|+.|++.|++..| +++.|+|+||+
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            3445789999999999999999999999999999999875 58999999999999999999999988 47899999997

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1.1e-20  Score=129.31  Aligned_cols=80  Identities=34%  Similarity=0.529  Sum_probs=71.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ..+.+.++|||+|||++++|++|+++|++||+|.+|+|+.+      +|||||+|.+.++|++||+.+++ .|+|+.|+|
T Consensus         5 ~~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V   83 (103)
T d2cqda1           5 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   83 (103)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEE
Confidence            44455688999999999999999999999999999999763      69999999999999999998875 799999999


Q ss_pred             EeccCCC
Q 029166          133 SWGRNPA  139 (198)
Q Consensus       133 ~~a~~~~  139 (198)
                      ++|....
T Consensus        84 ~~a~~~~   90 (103)
T d2cqda1          84 NLAYLGA   90 (103)
T ss_dssp             EESTTTC
T ss_pred             EEcCCCC
Confidence            9998643

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=3.2e-21  Score=127.54  Aligned_cols=75  Identities=20%  Similarity=0.504  Sum_probs=70.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      .+|||+|||++++|++|+++|++||+|.+++|+++      ++||||+|.++++|+.|++.||+..|+|+.|+|+||.+.
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            57999999999999999999999999999999864      699999999999999999999999999999999999864


Q ss_pred             C
Q 029166          139 A  139 (198)
Q Consensus       139 ~  139 (198)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=3.5e-21  Score=128.14  Aligned_cols=78  Identities=32%  Similarity=0.488  Sum_probs=70.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPAN  140 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~~  140 (198)
                      ...++|||+|||++++|++|+++|++||.|.+|++.. +++||||+|.+.++|++|+.  +++.|+|+.|+|++|+++..
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCC
Confidence            3478999999999999999999999999999998876 47999999999999999985  78899999999999987654


Q ss_pred             C
Q 029166          141 K  141 (198)
Q Consensus       141 ~  141 (198)
                      .
T Consensus        81 ~   81 (88)
T d1wf0a_          81 S   81 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.84  E-value=5.5e-21  Score=125.19  Aligned_cols=74  Identities=16%  Similarity=0.280  Sum_probs=68.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      +++|||+|||+++++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|++.||+..++|+.|+|++++|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            47999999999999999999999999998877754      379999999999999999999999999999999999986

>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=99.84  E-value=8.6e-21  Score=123.43  Aligned_cols=72  Identities=21%  Similarity=0.445  Sum_probs=68.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      +|||+|||+++++++|+++|++||.|.+++|..+     +|||||+|.+.++|++|++.||+..++|+.|+|++|.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            6999999999999999999999999999999864     68999999999999999999999999999999999863

>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=99.84  E-value=4.5e-20  Score=126.43  Aligned_cols=83  Identities=22%  Similarity=0.266  Sum_probs=74.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHh--CCceeCCeEeEEEec
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL--NGTVIGKQSVRLSWG  135 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l--~~~~~~g~~l~v~~a  135 (198)
                      .....++++|||+|||..++|++|+++|++||.|.++.+.++|++|||+|++.++|+.|++.|  +...++|+.|+|.|+
T Consensus         9 ~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s   88 (104)
T d1wexa_           9 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEc
Confidence            344456889999999999999999999999999999999999999999999999999999977  566789999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      +.+..
T Consensus        89 ~~~~~   93 (104)
T d1wexa_          89 TSKRI   93 (104)
T ss_dssp             SSSSC
T ss_pred             CCCcc
Confidence            86543

>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=99.83  E-value=6.6e-21  Score=125.94  Aligned_cols=72  Identities=29%  Similarity=0.535  Sum_probs=67.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC---------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        67 lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~---------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      |||+|||+++++++|+++|++||.|.+++|+++         ||||||+|.+.++|++|++.||+..|+|+.|+|+||+.
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            799999999999999999999999999998752         68999999999999999999999999999999999965


Q ss_pred             C
Q 029166          138 P  138 (198)
Q Consensus       138 ~  138 (198)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.83  E-value=7.1e-21  Score=124.40  Aligned_cols=71  Identities=35%  Similarity=0.631  Sum_probs=68.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      +|||+|||++++|++|+++|++||+|.+|+|+++      +|||||+|.++++|+.|++.|++..++|+.|+|.||+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            6999999999999999999999999999999864      5899999999999999999999999999999999996

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=3.3e-20  Score=127.05  Aligned_cols=78  Identities=29%  Similarity=0.535  Sum_probs=68.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC-------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV-------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~-------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .+.++|||+|||++++|++|+++|++|| |.++.++.       .+|||||+|.+.++|++|++ ||+..|+|+.|+|++
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            3568999999999999999999999999 77777654       25899999999999987775 999999999999999


Q ss_pred             ccCCCCC
Q 029166          135 GRNPANK  141 (198)
Q Consensus       135 a~~~~~~  141 (198)
                      |.++..+
T Consensus        91 a~~~~~~   97 (104)
T d1wi8a_          91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876543

>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=2.2e-21  Score=128.93  Aligned_cols=74  Identities=23%  Similarity=0.397  Sum_probs=68.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      .+|||+|||+++++++|+++|++||.|.++++.++ |||||+|.+.++|++||+.||+..|+|+.|+|.+++.+.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            36999999999999999999999999999998764 899999999999999999999999999999999887544

>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=99.83  E-value=1.6e-20  Score=128.40  Aligned_cols=76  Identities=24%  Similarity=0.439  Sum_probs=70.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      .++|||+|||+++++++|+++|++||.|.++.|+++      +|||||+|.+.++|++|++ ++++.|+|+.|.|++|++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            479999999999999999999999999999999763      6999999999999999996 799999999999999987


Q ss_pred             CCC
Q 029166          138 PAN  140 (198)
Q Consensus       138 ~~~  140 (198)
                      +.+
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>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=99.83  E-value=1.3e-20  Score=124.48  Aligned_cols=74  Identities=30%  Similarity=0.543  Sum_probs=68.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCC--eEeEEE
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGK--QSVRLS  133 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g--~~l~v~  133 (198)
                      ...++|||+|||++++|++|+++|++||.|.+++|+++      +|||||+|.+.++|++|++.||+..+.|  ++|+|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            45678999999999999999999999999999999864      5899999999999999999999999976  789999


Q ss_pred             ec
Q 029166          134 WG  135 (198)
Q Consensus       134 ~a  135 (198)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            97

>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=99.83  E-value=2.8e-20  Score=129.43  Aligned_cols=75  Identities=19%  Similarity=0.396  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC---CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG---KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~---kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      .+++|||+|||..+++++|+++|++||.|.+|++..+   +|||||+|.+.++|..|++.||+..|+|+.|+|.++..
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4679999999999999999999999999999999864   79999999999999999999999999999999999864

>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=6.2e-20  Score=122.00  Aligned_cols=80  Identities=14%  Similarity=0.267  Sum_probs=73.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHh--CCceeCCeEeEEEeccC
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL--NGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l--~~~~~~g~~l~v~~a~~  137 (198)
                      +..++++|||+|||..+++++|+++|++||.|.++++.++++||||+|.+.++|++|++.+  ++..++|+.|+|.|++.
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~   83 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   83 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCC
Confidence            4557889999999999999999999999999999999999999999999999999999865  67789999999999986


Q ss_pred             CC
Q 029166          138 PA  139 (198)
Q Consensus       138 ~~  139 (198)
                      +.
T Consensus        84 ~~   85 (88)
T d2cq1a1          84 KE   85 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.83  E-value=1.3e-20  Score=124.50  Aligned_cols=73  Identities=36%  Similarity=0.682  Sum_probs=67.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCC--eEeEEEe
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGK--QSVRLSW  134 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g--~~l~v~~  134 (198)
                      .+++|||+|||+++++++|+++|++||+|.+++|+++      ++||||+|.+.++|++|++.||+..+.|  ++|+|+|
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            3578999999999999999999999999999999763      5899999999999999999999999987  4699998


Q ss_pred             c
Q 029166          135 G  135 (198)
Q Consensus       135 a  135 (198)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            7

>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=99.82  E-value=1.4e-20  Score=127.18  Aligned_cols=83  Identities=25%  Similarity=0.395  Sum_probs=73.6

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEe-CCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-VGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~-~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      .....+.++|||+|||.++++++|+++|++||.|..+... .+++||||+|.+.++|++|++.||+..|+|+.|+|+|+.
T Consensus        10 ~~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~   89 (96)
T d1fjca_          10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             TSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             cCcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            3444557899999999999999999999999998877653 357999999999999999999999999999999999999


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      ++..
T Consensus        90 ~k~~   93 (96)
T d1fjca_          90 EKGG   93 (96)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            8654

>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=99.82  E-value=4.5e-20  Score=123.16  Aligned_cols=77  Identities=25%  Similarity=0.429  Sum_probs=69.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|+.+      ||||||+|.+.++|++||+.  .+.|+|+.|.|++|
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            35678999999999999999999999999999999864      58999999999999999984  45899999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      .++..
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            87643

>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=99.82  E-value=2.3e-20  Score=122.73  Aligned_cols=70  Identities=39%  Similarity=0.586  Sum_probs=65.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      +.++|||+|||+.+++++|+++|++||.|.+|+|+.+      ++||||+|.+.++|++|++.||+..|+|+.|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4678999999999999999999999999999998764      589999999999999999999999999999987

>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=99.82  E-value=2.2e-20  Score=127.21  Aligned_cols=82  Identities=28%  Similarity=0.428  Sum_probs=71.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEE--------EEeC------CCcEEEEEeCCHHHHHHHHHHhCCc
Q 029166           58 SEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASV--------KIPV------GKGCGFVQFANRENAEEALHKLNGT  123 (198)
Q Consensus        58 ~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v--------~i~~------~kg~afV~f~~~~~a~~a~~~l~~~  123 (198)
                      ++.+...++|||+|||.++++++|+++|++||.|..+        .+..      .++||||+|.++++|++|++.||+.
T Consensus         2 p~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~   81 (101)
T d2cpea1           2 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   81 (101)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCC
Confidence            4456678899999999999999999999999988543        3222      2589999999999999999999999


Q ss_pred             eeCCeEeEEEeccCCC
Q 029166          124 VIGKQSVRLSWGRNPA  139 (198)
Q Consensus       124 ~~~g~~l~v~~a~~~~  139 (198)
                      .|+|+.|+|+||+++.
T Consensus        82 ~~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          82 DFQGSKLKVSLARKKP   97 (101)
T ss_dssp             EETTEECEEECSSCCC
T ss_pred             EECCEEEEEEEcCCCC
Confidence            9999999999998754

>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=99.82  E-value=4.2e-20  Score=125.09  Aligned_cols=80  Identities=23%  Similarity=0.481  Sum_probs=71.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhC------CceeCC
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLN------GTVIGK  127 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~------~~~~~g  127 (198)
                      +..+.++|||+|||++++|++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++.|+      +..++|
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            3445789999999999999999999999999999988663      6999999999999999999886      677899


Q ss_pred             eEeEEEeccCCC
Q 029166          128 QSVRLSWGRNPA  139 (198)
Q Consensus       128 ~~l~v~~a~~~~  139 (198)
                      +.|+|+||+++.
T Consensus        84 r~l~v~~a~~k~   95 (98)
T d1x4ha1          84 RQLKVDLAVTRD   95 (98)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCC
Confidence            999999998754

>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=99.82  E-value=1.8e-20  Score=123.26  Aligned_cols=75  Identities=31%  Similarity=0.607  Sum_probs=67.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCceEEE-EEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           67 IFVGGLDPNVTDEDLRQPFSQYGEIASV-KIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        67 lfV~~l~~~~~e~~l~~~F~~~G~i~~v-~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      |||+|||++++|++|+++|++||.|.++ ++++      ++|||||+|.+.++|++|++.|++..++|+.|+|+||.++.
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            7999999999999999999999998764 6654      36999999999999999999999999999999999998765


Q ss_pred             CC
Q 029166          140 NK  141 (198)
Q Consensus       140 ~~  141 (198)
                      .+
T Consensus        81 ~k   82 (83)
T d1x5ta1          81 SK   82 (83)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=99.82  E-value=5.8e-20  Score=118.55  Aligned_cols=71  Identities=23%  Similarity=0.404  Sum_probs=67.7

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCC
Q 029166           67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNP  138 (198)
Q Consensus        67 lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~  138 (198)
                      |||+|||+++++++|+++|++|| +..+++.++++||||+|.+.++|++|++.||+..++|+.|+|+|++..
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-LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 778888999999999999999999999999999999999999999754

>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=99.82  E-value=3.1e-20  Score=128.18  Aligned_cols=76  Identities=30%  Similarity=0.525  Sum_probs=70.3

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHhccCCceEEEEEeCC-CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccCCC
Q 029166           64 NTTIFVGGLDP-NVTDEDLRQPFSQYGEIASVKIPVG-KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRNPA  139 (198)
Q Consensus        64 ~~~lfV~~l~~-~~~e~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~~~  139 (198)
                      +++|||+||++ .+++++|+++|++||.|.+|+|+++ +|||||+|++.++|++|++.|++..|.|+.|+|+|++...
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~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            57899999965 5999999999999999999999886 5899999999999999999999999999999999997543

>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=99.82  E-value=4.1e-20  Score=121.86  Aligned_cols=73  Identities=27%  Similarity=0.490  Sum_probs=67.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ..++|||+|||+++++++|+++|++||.|.+++|+.+      +|||||+|.+.++|++|++ ++++.|+|+.|+|+.|.
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            3579999999999999999999999999999999764      6999999999999999997 69999999999999885

>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=99.82  E-value=5.3e-21  Score=131.13  Aligned_cols=79  Identities=29%  Similarity=0.538  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .+.++|||+|||+++++++|+++|++||+|.+|+|+.+      +|||||+|.+.++|++|++.||+..|+|+.|+|+||
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a   85 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34578999999999999999999999999999998763      589999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      .++..
T Consensus        86 ~~~~~   90 (104)
T d1p1ta_          86 ASEKN   90 (104)
T ss_dssp             TCTTH
T ss_pred             CCCCC
Confidence            87543

>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=99.82  E-value=6.6e-21  Score=129.98  Aligned_cols=75  Identities=23%  Similarity=0.360  Sum_probs=69.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      +.++|||+|||+++++++|+++|+.||+|.+|+|+++      ||||||+|.+.++|++|++ ||+..|+|+.|+|++++
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            4578999999999999999999999999999999873      6899999999999999996 99999999999999987


Q ss_pred             CC
Q 029166          137 NP  138 (198)
Q Consensus       137 ~~  138 (198)
                      ++
T Consensus        96 ~~   97 (101)
T d2cq4a1          96 AE   97 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            53

>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=99.81  E-value=5.7e-20  Score=122.15  Aligned_cols=77  Identities=22%  Similarity=0.391  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC--CCcEEEEEeCCHHHHHHHHHHhCCcee-CCeEeEEEeccCC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV--GKGCGFVQFANRENAEEALHKLNGTVI-GKQSVRLSWGRNP  138 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~--~kg~afV~f~~~~~a~~a~~~l~~~~~-~g~~l~v~~a~~~  138 (198)
                      +++++|||+|||+++++++|+++|++||.|.++.+..  +++||||+|++.++|.+|+..|++..| +|+.|+|+|+++.
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            3478999999999999999999999999998887664  579999999999999999999999988 5899999999864

>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=99.81  E-value=5.2e-20  Score=121.88  Aligned_cols=75  Identities=27%  Similarity=0.620  Sum_probs=67.9

Q ss_pred             CCCeEEEcCCCCCCC-HHHHHHHhccCCceEEEEEeC-------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           63 SNTTIFVGGLDPNVT-DEDLRQPFSQYGEIASVKIPV-------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~-e~~l~~~F~~~G~i~~v~i~~-------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ..++|||+|||++++ |++|+++|++||.|.+|+|..       ++|||||+|.+.++|++|++ ||+..|+|+.|+|++
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            468999999999865 677999999999999999865       36899999999999999996 999999999999999


Q ss_pred             ccCC
Q 029166          135 GRNP  138 (198)
Q Consensus       135 a~~~  138 (198)
                      |+++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9864

>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=99.81  E-value=1e-20  Score=122.71  Aligned_cols=70  Identities=26%  Similarity=0.519  Sum_probs=66.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ++|||+|||++++|++|+++|++||.|.+++|+++      ||||||+|.+.++|++|++ ++++.|+|+.|+|+.|
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            68999999999999999999999999999999773      6999999999999999997 7999999999999987

>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=99.81  E-value=7.7e-20  Score=124.16  Aligned_cols=79  Identities=15%  Similarity=0.208  Sum_probs=72.2

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHH--HhCCceeCCeEeEEEecc
Q 029166           60 GDSSNTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALH--KLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~-~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~--~l~~~~~~g~~l~v~~a~  136 (198)
                      ....+++|||+|||.+ +|+++|+++|++||.|.++.+++++++|||+|.+.++|.+|++  .+++..++|+.|+|.||+
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~   93 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSE   93 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEEC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcC
Confidence            3455789999999985 8999999999999999999999999999999999999999997  568889999999999997


Q ss_pred             CC
Q 029166          137 NP  138 (198)
Q Consensus       137 ~~  138 (198)
                      ..
T Consensus        94 ~~   95 (99)
T d1x4fa1          94 KY   95 (99)
T ss_dssp             SC
T ss_pred             Cc
Confidence            54

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=6.7e-20  Score=122.58  Aligned_cols=78  Identities=23%  Similarity=0.535  Sum_probs=70.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----HhccCCceEEEEEeC---CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQ----PFSQYGEIASVKIPV---GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~----~F~~~G~i~~v~i~~---~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ++++|||+|||+++++++|++    +|++||+|.+|++.+   .++||||+|.+.++|.+|++.||+..++|+.|+|+||
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            468999999999999998864    589999999999865   3799999999999999999999999999999999999


Q ss_pred             cCCCC
Q 029166          136 RNPAN  140 (198)
Q Consensus       136 ~~~~~  140 (198)
                      +++.+
T Consensus        82 k~~~~   86 (91)
T d1nu4a_          82 KTDSD   86 (91)
T ss_dssp             SSCCT
T ss_pred             CCCch
Confidence            87653

>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=99.80  E-value=1.2e-19  Score=118.15  Aligned_cols=71  Identities=24%  Similarity=0.511  Sum_probs=66.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      .++|||+|||+++|+++|+++|++||.|..+.++.+      +|||||+|.+.++|++|++ +++..|+|+.|+|+.|
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            579999999999999999999999999999998763      5999999999999999996 8999999999999876

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.80  E-value=1.5e-20  Score=125.78  Aligned_cols=78  Identities=22%  Similarity=0.415  Sum_probs=69.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEe-----CCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----VGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~-----~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      ......+|||+|||+++++++|+++|++||.|..++|+     +++|||||+|.+.++|++||+ ||+..|+|+.|+|++
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            34456799999999999999999999999988777664     358999999999999999996 999999999999999


Q ss_pred             ccCC
Q 029166          135 GRNP  138 (198)
Q Consensus       135 a~~~  138 (198)
                      |+.+
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            9863

>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=99.80  E-value=6.3e-20  Score=118.36  Aligned_cols=69  Identities=25%  Similarity=0.563  Sum_probs=64.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      +|||+|||++++|++|+++|++||+|.+++|+.+      +|||||+|.+.++|++||+ +++..|+|+.|+|+.|
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            5999999999999999999999999999999873      6999999999999999997 7999999999999754

>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=99.80  E-value=9.2e-20  Score=124.21  Aligned_cols=78  Identities=18%  Similarity=0.395  Sum_probs=70.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           60 GDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        60 ~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .+.+.++|||+|||.++++++|+++|++||.|..+.+..+     +|||||+|.+.++|++|++.|||..|.|+.|.|.+
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            3445689999999999999999999999999999988753     58999999999999999999999999999998888


Q ss_pred             ccC
Q 029166          135 GRN  137 (198)
Q Consensus       135 a~~  137 (198)
                      ++|
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            765

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.8e-19  Score=122.97  Aligned_cols=81  Identities=23%  Similarity=0.315  Sum_probs=69.7

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           57 QSEGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        57 ~~~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      .........+|||+|||+++||++|+++|..||. ..|.++.+     +|||||+|.+.++|++|++ +|+..|+|+.|+
T Consensus         8 ~~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~   85 (102)
T d1weza_           8 SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVE   85 (102)
T ss_dssp             SSCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCE
T ss_pred             CCCcCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEE
Confidence            3445566789999999999999999999999984 45666553     6899999999999999987 899999999999


Q ss_pred             EEeccCCC
Q 029166          132 LSWGRNPA  139 (198)
Q Consensus       132 v~~a~~~~  139 (198)
                      |.|+....
T Consensus        86 V~~s~~~~   93 (102)
T d1weza_          86 LFLNSTAG   93 (102)
T ss_dssp             EEEECCCC
T ss_pred             EEEcCCCC
Confidence            99998654

>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=99.79  E-value=4.6e-20  Score=118.98  Aligned_cols=69  Identities=28%  Similarity=0.637  Sum_probs=64.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      +|||+|||+++|+++|+++|++||.|.+|+|+.+      ||||||+|.+.++|++||+ .+++.|+|+.|+|+.|
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            6999999999999999999999999999999874      6999999999999999997 5778999999999875

>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=99.79  E-value=1e-19  Score=117.25  Aligned_cols=69  Identities=30%  Similarity=0.527  Sum_probs=64.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           66 TIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        66 ~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      +|||+|||++++|++|+++|++||.|..+.++.+      ++||||+|.+.++|++|++ +|++.|+|+.|+|++|
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            5999999999999999999999999999988663      6999999999999999997 9999999999999986

>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=99.79  E-value=4.5e-20  Score=125.91  Aligned_cols=78  Identities=29%  Similarity=0.513  Sum_probs=71.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ++++|||+|||.++++++|+++|++||.|..+.++.      .++||||+|.+.++|+.|++.||+..|.|+.|+|+||+
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            468999999999999999999999999988776653      47999999999999999999999999999999999999


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      ++.+
T Consensus        97 ~k~~  100 (102)
T d2cpxa1          97 NKKQ  100 (102)
T ss_dssp             CCSC
T ss_pred             Cccc
Confidence            8654

>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=99.78  E-value=3.1e-19  Score=122.16  Aligned_cols=79  Identities=14%  Similarity=0.161  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCC-CH----HHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           62 SSNTTIFVGGLDPNV-TD----EDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~-~e----~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ...++|||+||+..+ ++    ++|+++|++||.|.++++++++++|||+|.+.++|++|++.||+..|+|+.|+|.||+
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   82 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecc
Confidence            346789999999875 43    5699999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029166          137 NPAN  140 (198)
Q Consensus       137 ~~~~  140 (198)
                      ++..
T Consensus        83 ~~~~   86 (104)
T d1weya_          83 TLHI   86 (104)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            6543

>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=99.78  E-value=6.8e-19  Score=117.11  Aligned_cols=78  Identities=15%  Similarity=0.189  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHh--CCceeCCeEeEEEeccC
Q 029166           61 DSSNTTIFVGGLDPN-VTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKL--NGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~-~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l--~~~~~~g~~l~v~~a~~  137 (198)
                      ...+++|||+|||.. +|+++|.++|++||.|.++.+++++++|||+|++.++|+.|++.|  ++..++|++|+|+||++
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~   84 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCC
Confidence            345788999999986 789999999999999999999999999999999999999999965  78889999999999985


Q ss_pred             C
Q 029166          138 P  138 (198)
Q Consensus       138 ~  138 (198)
                      .
T Consensus        85 ~   85 (89)
T d1x4da1          85 Y   85 (89)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.78  E-value=1.6e-18  Score=118.56  Aligned_cols=80  Identities=24%  Similarity=0.282  Sum_probs=69.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ....+..+|||+|||++++|++|+++|..+|.|..+.++.      .+|||||+|.++++|++|++ +|+..|+++.|+|
T Consensus        10 ~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V   88 (104)
T d1wg5a_          10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEI   88 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEE
Confidence            3444566899999999999999999999999887754433      36999999999999999996 8999999999999


Q ss_pred             EeccCCC
Q 029166          133 SWGRNPA  139 (198)
Q Consensus       133 ~~a~~~~  139 (198)
                      .++.+..
T Consensus        89 ~~~~~~~   95 (104)
T d1wg5a_          89 FKSSRAE   95 (104)
T ss_dssp             EEECTTT
T ss_pred             EECCHHH
Confidence            9998653

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=3.1e-19  Score=123.01  Aligned_cols=79  Identities=24%  Similarity=0.275  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeC--CCcEEEEEeCCHHHHHHHHHHhCCcee--CCeEeEEEeccC
Q 029166           62 SSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV--GKGCGFVQFANRENAEEALHKLNGTVI--GKQSVRLSWGRN  137 (198)
Q Consensus        62 ~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~--~kg~afV~f~~~~~a~~a~~~l~~~~~--~g~~l~v~~a~~  137 (198)
                      .+..+|||+|||+.+||++|+++|++||.|.+|.|..  ++++|||+|.++++|+.|++.||+..|  .++.|+|.|+++
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~   84 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL   84 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSS
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCC
Confidence            4567899999999999999999999999999998875  468999999999999999999999998  578999999986


Q ss_pred             CCC
Q 029166          138 PAN  140 (198)
Q Consensus       138 ~~~  140 (198)
                      +..
T Consensus        85 ~~~   87 (108)
T d2adba1          85 TSL   87 (108)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            543

>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=99.78  E-value=3.5e-19  Score=120.19  Aligned_cols=77  Identities=19%  Similarity=0.405  Sum_probs=68.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCc-eEEEEEeC-------CCcEEEEEeCCHHHHHHHHHHhCC--ceeCCeEeEEE
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGE-IASVKIPV-------GKGCGFVQFANRENAEEALHKLNG--TVIGKQSVRLS  133 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~-i~~v~i~~-------~kg~afV~f~~~~~a~~a~~~l~~--~~~~g~~l~v~  133 (198)
                      +++|||+|||.++++++|+++|++||+ |.++.|++       ++|||||+|.+.++|..|++.|++  ..++|+.|+|+
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999996 89999865       368999999999999999999864  45679999999


Q ss_pred             eccCCCC
Q 029166          134 WGRNPAN  140 (198)
Q Consensus       134 ~a~~~~~  140 (198)
                      ||+++..
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9987544

>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=99.77  E-value=7.4e-19  Score=115.95  Aligned_cols=73  Identities=18%  Similarity=0.379  Sum_probs=67.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      ..++|||+|||.++++++|+++|+.||.|..|+|..+     ||||||+|.+.++|++||+ +++..+.|+.|.|.|++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            3578999999999999999999999999999999763     5899999999999999996 79999999999999975

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.77  E-value=5.3e-19  Score=113.92  Aligned_cols=70  Identities=21%  Similarity=0.301  Sum_probs=65.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ++|||+|||+++++++|+++|+.||.|..|++..+    ++||||+|.++++|++|+. +++..|+|+.|.|+.+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            58999999999999999999999999999999774    4799999999999999996 8999999999999865

>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=99.77  E-value=4.7e-19  Score=117.92  Aligned_cols=71  Identities=24%  Similarity=0.480  Sum_probs=65.1

Q ss_pred             CCCeEEEcCCCCCCCHHHH---HHHhccCCceEEEEEeCC---------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEe
Q 029166           63 SNTTIFVGGLDPNVTDEDL---RQPFSQYGEIASVKIPVG---------KGCGFVQFANRENAEEALHKLNGTVIGKQSV  130 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l---~~~F~~~G~i~~v~i~~~---------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l  130 (198)
                      ..++|||+|||+++++++|   +++|++||+|.+|.|+++         ++||||+|.+.++|++|++.||+..++|+.|
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            3567999999999999999   678999999999999874         2899999999999999999999999999999


Q ss_pred             EEE
Q 029166          131 RLS  133 (198)
Q Consensus       131 ~v~  133 (198)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            984

>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=99.74  E-value=3.2e-18  Score=112.98  Aligned_cols=73  Identities=29%  Similarity=0.389  Sum_probs=65.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEE-EEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS-VKIPV-----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~-v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ..++|||+|||+++++++|+++|+.||.|.. +.+..     ++|+|||+|.+.++|++|++.||+..|+|+.|+|+++
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            4568999999999999999999999998855 34433     3699999999999999999999999999999999985

>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=99.73  E-value=1.2e-18  Score=111.29  Aligned_cols=65  Identities=34%  Similarity=0.600  Sum_probs=61.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCceEEEEEeC------CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeE
Q 029166           67 IFVGGLDPNVTDEDLRQPFSQYGEIASVKIPV------GKGCGFVQFANRENAEEALHKLNGTVIGKQSVR  131 (198)
Q Consensus        67 lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~  131 (198)
                      |||+|||.++++++|+++|++||.|..+++..      +++||||+|.+.++|++|++.||+..|+|+.|+
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            79999999999999999999999999998876      369999999999999999999999999998764

>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=99.70  E-value=1.9e-17  Score=112.84  Aligned_cols=76  Identities=18%  Similarity=0.212  Sum_probs=66.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEE-EEEeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIAS-VKIPV-----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~-v~i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      +....+|||+|||+++++++|+++|..||.|.. +.+..     .+|||||+|.+.++|++||+ ||+..|+|+.|.|.+
T Consensus         5 ~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           5 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHV   83 (103)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEE
Confidence            344568999999999999999999999998876 44433     37999999999999999996 899999999999999


Q ss_pred             ccC
Q 029166          135 GRN  137 (198)
Q Consensus       135 a~~  137 (198)
                      +..
T Consensus        84 ~~~   86 (103)
T d2cpya1          84 VTL   86 (103)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            754

>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=7e-17  Score=109.64  Aligned_cols=64  Identities=23%  Similarity=0.460  Sum_probs=59.7

Q ss_pred             CCCCeEEE--cCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCcee
Q 029166           62 SSNTTIFV--GGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVI  125 (198)
Q Consensus        62 ~~~~~lfV--~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~  125 (198)
                      .+..+|||  +|||..+|+++|+++|++||.|..|.+.++++||||+|.+.++|++|++.|||..|
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            34678888  55999999999999999999999999999999999999999999999999999887

>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=99.66  E-value=1e-16  Score=110.98  Aligned_cols=74  Identities=24%  Similarity=0.343  Sum_probs=65.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCH-HHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANR-ENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~-~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      ...+||+|||+.+|+++|+++|++||+|.+|+|+++++||||+|.++ ++|..|+..|++..+.++.+.|.|+..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            34569999999999999999999999999999999999999999985 789999999999988877777777653

>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=99.66  E-value=4.9e-17  Score=112.46  Aligned_cols=76  Identities=17%  Similarity=0.299  Sum_probs=65.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEE-EeC-----CCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEe
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVK-IPV-----GKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSW  134 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~-i~~-----~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  134 (198)
                      .....+|||+|||+++|+++|+++|+.||.|..+. +..     .+|||||+|.+.++|++|++ ||+..|+|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            44567999999999999999999999999886532 222     25999999999999999996 999999999999998


Q ss_pred             ccC
Q 029166          135 GRN  137 (198)
Q Consensus       135 a~~  137 (198)
                      +.+
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            753

>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=99.65  E-value=1.1e-18  Score=116.29  Aligned_cols=71  Identities=17%  Similarity=0.390  Sum_probs=62.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEe-----------CCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEE
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIP-----------VGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLS  133 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~-----------~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~  133 (198)
                      ++|||+|||.+++|++|+++|++||.|..+.+.           ++++||||+|.+.++|++|++ ||+..+.|+.|+|+
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            689999999999999999999999877655442           358999999999999999985 99999999999997


Q ss_pred             ecc
Q 029166          134 WGR  136 (198)
Q Consensus       134 ~a~  136 (198)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.62  E-value=8.2e-16  Score=114.47  Aligned_cols=79  Identities=22%  Similarity=0.450  Sum_probs=71.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEE
Q 029166           59 EGDSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRL  132 (198)
Q Consensus        59 ~~~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v  132 (198)
                      ......++|||+|||+.+++++|+++|+.||.|..+.|+.+      +|||||+|.+.++|++|++ +++..++|+.|+|
T Consensus        92 ~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V  170 (183)
T d1u1qa_          92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEV  170 (183)
T ss_dssp             TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEE
T ss_pred             ccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEE
Confidence            34556789999999999999999999999999999988763      5899999999999999997 7889999999999


Q ss_pred             EeccCC
Q 029166          133 SWGRNP  138 (198)
Q Consensus       133 ~~a~~~  138 (198)
                      .+|.++
T Consensus       171 ~~A~~k  176 (183)
T d1u1qa_         171 RKALSK  176 (183)
T ss_dssp             EECCCH
T ss_pred             EecCCc
Confidence            999764

>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=99.62  E-value=3.6e-16  Score=101.73  Aligned_cols=73  Identities=19%  Similarity=0.270  Sum_probs=64.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCe-EeEEEeccC
Q 029166           63 SNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQ-SVRLSWGRN  137 (198)
Q Consensus        63 ~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~-~l~v~~a~~  137 (198)
                      +.+.|+|+++|++++++.| ++|++||+|.++++.++++|+||+|.++++|++||+ +||..|+|+ .|.|..+..
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            4578999999999887655 579999999999999999999999999999999996 999999997 467887654

>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=99.56  E-value=2.4e-16  Score=107.49  Aligned_cols=71  Identities=20%  Similarity=0.288  Sum_probs=66.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG-----KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      +.++|.++..+++|++|+++|++||+|.+|+|+++     +|||||+|.+.++|.+|++.|||..++|+.|+|++.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            45888888889999999999999999999999763     699999999999999999999999999999999985

>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=99.55  E-value=1.3e-14  Score=97.78  Aligned_cols=81  Identities=19%  Similarity=0.311  Sum_probs=69.3

Q ss_pred             CCCCCCCeEEEcCC--CCCCC---------HHHHHHHhccCCceEEEEEeCC--CcEEEEEeCCHHHHHHHHHHhCCcee
Q 029166           59 EGDSSNTTIFVGGL--DPNVT---------DEDLRQPFSQYGEIASVKIPVG--KGCGFVQFANRENAEEALHKLNGTVI  125 (198)
Q Consensus        59 ~~~~~~~~lfV~~l--~~~~~---------e~~l~~~F~~~G~i~~v~i~~~--kg~afV~f~~~~~a~~a~~~l~~~~~  125 (198)
                      .....+++|+|.||  |.++.         +++|++.|++||.|..|.+..+  +||+||+|.+.++|.+|+..||+..+
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            34456789999998  54321         3688999999999999998875  69999999999999999999999999


Q ss_pred             CCeEeEEEeccCCC
Q 029166          126 GKQSVRLSWGRNPA  139 (198)
Q Consensus       126 ~g~~l~v~~a~~~~  139 (198)
                      +|+.|+|+++.++.
T Consensus        83 ~gr~i~v~~~~g~~   96 (99)
T d2dita1          83 GGRQITAQAWDGTT   96 (99)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCEEEEEEEeCCcC
Confidence            99999999987653

>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=99.45  E-value=2.3e-13  Score=100.91  Aligned_cols=75  Identities=27%  Similarity=0.477  Sum_probs=66.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC------CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEeccC
Q 029166           64 NTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG------KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGRN  137 (198)
Q Consensus        64 ~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~~  137 (198)
                      .++|||+|||+++++++|+++|++||.|.++.++++      +|||||+|.+.++|++|+. +++..+..+.+.+.+..+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            379999999999999999999999999999998753      6899999999999999998 567788888888887765


Q ss_pred             CC
Q 029166          138 PA  139 (198)
Q Consensus       138 ~~  139 (198)
                      ..
T Consensus        85 ~~   86 (183)
T d1u1qa_          85 RE   86 (183)
T ss_dssp             TT
T ss_pred             cc
Confidence            43

>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=99.36  E-value=4.8e-13  Score=90.80  Aligned_cols=75  Identities=23%  Similarity=0.373  Sum_probs=64.7

Q ss_pred             CCCeEEEcCC--CCCCC--------HHHHHHHhccCCceEEEEEeCC--------CcEEEEEeCCHHHHHHHHHHhCCce
Q 029166           63 SNTTIFVGGL--DPNVT--------DEDLRQPFSQYGEIASVKIPVG--------KGCGFVQFANRENAEEALHKLNGTV  124 (198)
Q Consensus        63 ~~~~lfV~~l--~~~~~--------e~~l~~~F~~~G~i~~v~i~~~--------kg~afV~f~~~~~a~~a~~~l~~~~  124 (198)
                      +++.|.|.|+  +..+.        .++|++.|++||.|++|.|.++        .|++||+|.+.++|.+|+..|||..
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            4778999998  44432        3578999999999999999762        4899999999999999999999999


Q ss_pred             eCCeEeEEEeccC
Q 029166          125 IGKQSVRLSWGRN  137 (198)
Q Consensus       125 ~~g~~l~v~~a~~  137 (198)
                      ++|+.|.|.+...
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            9999999999853

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.84  E-value=5.7e-05  Score=45.69  Aligned_cols=57  Identities=25%  Similarity=0.341  Sum_probs=50.0

Q ss_pred             HHHHHhccCCceEEEEEeCC---CcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEecc
Q 029166           80 DLRQPFSQYGEIASVKIPVG---KGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWGR  136 (198)
Q Consensus        80 ~l~~~F~~~G~i~~v~i~~~---kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a~  136 (198)
                      .|...|.+++.|.++.|...   .-.|-|...+..+|..|+..|+...|++++|.|.++.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            44567889999999999663   2569999999999999999999999999999999985

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.60  E-value=0.00013  Score=46.77  Aligned_cols=72  Identities=17%  Similarity=0.284  Sum_probs=58.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCC--------CcEEEEEeCCHHHHHHHHHHhCCceeCC---e--EeE
Q 029166           65 TTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVG--------KGCGFVQFANRENAEEALHKLNGTVIGK---Q--SVR  131 (198)
Q Consensus        65 ~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~--------kg~afV~f~~~~~a~~a~~~l~~~~~~g---~--~l~  131 (198)
                      ++|-|+.||+.+||+++.+.+...+++........        -.-|+|.|.+.+++..-.+..+|+.+-+   .  .-.
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            68999999999999999999998888877665431        2679999999999999999999998732   1  335


Q ss_pred             EEecc
Q 029166          132 LSWGR  136 (198)
Q Consensus       132 v~~a~  136 (198)
                      |++|-
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66664

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.51  E-value=0.00014  Score=46.23  Aligned_cols=54  Identities=30%  Similarity=0.462  Sum_probs=47.5

Q ss_pred             HHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhCCceeCCeEeEEEec
Q 029166           79 EDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLNGTVIGKQSVRLSWG  135 (198)
Q Consensus        79 ~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~~~~~~g~~l~v~~a  135 (198)
                      ++|.+.|..||+|.-|+++.  +--.|+|.+-++|.+|++ +++.++.|+.|+|...
T Consensus        39 ~~Llq~l~~~GeViLvRFv~--d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQ--GQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEET--TEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeC--CeEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            46778889999999998875  478999999999999998 8999999999999854

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.12  E-value=0.021  Score=36.38  Aligned_cols=59  Identities=19%  Similarity=0.268  Sum_probs=46.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhccCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhC
Q 029166           61 DSSNTTIFVGGLDPNVTDEDLRQPFSQYGEIASVKIPVGKGCGFVQFANRENAEEALHKLN  121 (198)
Q Consensus        61 ~~~~~~lfV~~l~~~~~e~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~a~~a~~~l~  121 (198)
                      .+...-||.-.+|..+...+|.++|+.||.|.- ..+ +---|||...+.+.|+.++..+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~V-swI-ddTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQI-SWI-DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCC-EEE-ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceEE-EEe-cCceEEEEecCHHHHHHHHHHhc
Confidence            334456888899999999999999999998643 333 33589999999999999887543