Citrus Sinensis ID: 023954

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-----
Protein Sequence
MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKHTYASILRVAKGQSTPSVTPQPSVSKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMWH
Secondary Structure (PSIPRED)
cccccccEEEEEEEEcccccccEEEEEEEEEEEccccccccEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccEEEEcccccccHHHHHHHHHccccEEEccEEEEccccccccEEEEEEccHHHHHHHHHcccEEEc
Secondary Structure Prediction (SSPRO)
ccccccEEEEEEEccHHHccccEEEEEEEEEEcccccccEEEEEEEEEccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHccccccccEEEEcccccccEEEEEEEccHHHHHHHHHcccEEEc
Coil and Loop (DISEMBL)
mslnysgieiktahsleswnGGVLVMVSGSVQVKDFSARRKFVQTFFlapqekvpnhlmggeiqareyvspvdvkqngliddysfpeqrlqqvpeseniledspaeelnGSLQNAVNAAqdylpasveepvgepqkhTYASILRVakgqstpsvtpqpsvsknispvsdwnhvpqpttqqetVSSYAYEKswadtgeeisavedeeeiksvyvrnlppsvsesEIAEEFKKFGelssegvvirsrKDVGICYAFvefedmtgvRNAVEVCILMWH
Flexible Loop (DISEMBL)
MSLNYSGIEIKtahsleswnGGVLVMVSGSVQVKDFSARRKFVQTfflapqekvpnHLMGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKHTYASILRVAKGQSTPSVTPQPSVSKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADTGEEIsavedeeeiksvyvrnlppsvseSEIAEEFKkfgelssegvvirsrkDVGICYAfvefedmtgvRNAVEVCILMWH
Low Complexity Region (SEG)
MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKHTYASILRVAKGqstpsvtpqpsvsKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADTGeeisavedeeeIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMWH
Disordered region (IsUnstruct)
******GIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQAREYVSPVDVKQNGLIDDY****************************************************************************************************************************************************FGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW*
Disordered Region (DISOPRED)
****YSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQAREYVSPVD*************************************************************************************************************************************EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMWH
Disordered Region (DISEMBL)
MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKHTYASILRVA****************NISPVSDWNHVPQ*********SYAYEKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMWH
Disordered Region (DISPRO)
**LNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEI********************************************************************************RVAKG**********************************************************EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMWH
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKHTYASILRVAKGQSTPSVTPQPSVSKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMWH
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	275	2.2.26 [Sep-21-2011]
O64380	660	Polyadenylate-binding pro	no	no	0.221	0.092	0.403	4e-05
P04147	577	Polyadenylate-binding pro	yes	no	0.305	0.145	0.322	0.0001
Q6CDH3	629	Polyadenylate-binding pro	yes	no	0.36	0.157	0.306	0.0007

>sp|O64380|PABP3_ARATH Polyadenylate-binding protein 3 OS=Arabidopsis thaliana GN=PAB3 PE=2 SV=1

 Score = 48.9 bits (115), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNA 266
              +VYV+NLP  + E E+ + F KFG +SS  VV+R +     C+ FV FE      +A
Sbjct: 227 RFTNVYVKNLPKEIGEDELRKTFGKFGVISS-AVVMRDQSGNSRCFGFVNFECTEAAASA 285

Query: 267 VE 268
           VE
Sbjct: 286 VE 287

Binds the poly(A) tail of mRNA.
Arabidopsis thaliana (taxid: 3702)

>sp|P04147|PABP_YEAST Polyadenylate-binding protein, cytoplasmic and nuclear OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PAB1 PE=1 SV=4

 Score = 47.4 bits (111), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 12/96 (12%)

Query: 189 EKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV 248
           ++  A TG E  +VE+     S+YV +L PSVSE+ + + F   G +SS  V   +    
Sbjct: 20  DQKQAATGSESQSVENSS--ASLYVGDLEPSVSEAHLYDIFSPIGSVSSIRVCRDAITKT 77

Query: 249 GICYAFVEFEDMTGVRNAVE----------VCILMW 274
            + YA+V F D    R A+E          +C +MW
Sbjct: 78  SLGYAYVNFNDHEAGRKAIEQLNYTPIKGRLCRIMW 113

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, interacts with the nuclear cleavage factor IA (CFIA), which is required for both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. Regulates PAN activity via interaction with the stimulator PAN3 or the inhibitor PBP1. In the cytoplasm, affects both translation and mRNA decay. Stimulates translation by interaction with translation initiation factor eIF4G, a subunit of the cap-binding complex eIF4F, bringing the 5'- and 3'-ends of the mRNA in proximity. The formation of this circular mRNP structure appears to be critical for the synergistic effects of the cap and the poly(A) tail in facilitating translation initiation, recycling of ribosomes, and mRNA stability. Also regulates translation termination by recruiting eukaryotic release factor 3 (eRF3). Interaction with eRF3 is also required for regulation of normal mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN. Loss of PAB1 from the mRNP after deadenylation triggers mRNA degradation. Inhibits the major cytoplasmic mRNA deadenylase CCR4-NOT complex. Is also associated peripherally with COPI vesicles through its interaction with ARF1, and this is required for correct localization of the asymmetrically distributed ASH1 mRNA.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q6CDH3|PABP_YARLI Polyadenylate-binding protein, cytoplasmic and nuclear OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=PAB1 PE=3 SV=1

 Score = 44.7 bits (104), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 54/111 (48%), Gaps = 12/111 (10%)

Query: 176 PTTQQETVSSYAYEKSWADT--GEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFG 233
           P T++ET +  A  +  A T   EE  + ED+ +  S+YV  L PSV+E+ + E F   G
Sbjct: 11  PATKEETTTEAAPAEGEAKTESSEEKGSKEDQGDNASLYVGELDPSVTEAMLFEIFNPIG 70

Query: 234 ELSSEGVVIRSRKDVGICYAFVEFEDMT-GVRNAVEV---------CILMW 274
            ++S  V   +     + YA+V F +   G+R   E+         C +MW
Sbjct: 71  PVTSVRVCRDAITRRSLGYAYVNFHNQADGIRALEELNYSPIKERPCRIMW 121

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, involved in both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. In the cytoplasm, stimulates translation initiation and regulates mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

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	275
255574885	472	Ras-GTPase-activating protein-binding pr	0.970	0.565	0.592	2e-96
224107513	455	predicted protein [Populus trichocarpa]	0.963	0.582	0.589	4e-96
363807448	471	uncharacterized protein LOC100795457 [Gl	0.963	0.562	0.589	3e-92
296083732	475	unnamed protein product [Vitis vinifera]	0.989	0.572	0.582	3e-92
225433269	751	PREDICTED: uncharacterized protein LOC10	0.989	0.362	0.582	5e-92
356575200	472	PREDICTED: uncharacterized protein LOC10	0.967	0.563	0.573	2e-91
147859669	518	hypothetical protein VITISV_026572 [Viti	0.88	0.467	0.545	8e-80
356576442	468	PREDICTED: putative G3BP-like protein-li	0.949	0.557	0.527	3e-79
449432500	473	PREDICTED: putative G3BP-like protein-li	0.963	0.560	0.536	3e-79
168988195	565	nuclear transport family protein [Cucumi	0.963	0.469	0.536	6e-79

>gi|255574885|ref|XP_002528349.1| Ras-GTPase-activating protein-binding protein, putative [Ricinus communis] gi|223532217|gb|EEF34021.1| Ras-GTPase-activating protein-binding protein, putative [Ricinus communis]

 Score =  358 bits (918), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 185/312 (59%), Positives = 224/312 (71%), Gaps = 45/312 (14%)

Query: 1   MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK------- 53
           MSLNY+ IEI+TAHS+ESWNGGVLVMVSGSVQVKD + RRKFV+TFFLAPQEK       
Sbjct: 65  MSLNYTAIEIRTAHSVESWNGGVLVMVSGSVQVKDSTERRKFVETFFLAPQEKGYFVLND 124

Query: 54  ------------------------------------VPNHLMGGEIQAREYVSPVDVKQN 77
                                               V N+L+GGE QARE+V+P D K+N
Sbjct: 125 VFHFIDEAPIHHHPAVILTQNHLDSKVNVPTAIPEPVANYLLGGEFQAREFVAPADAKEN 184

Query: 78  GL-IDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQK 136
           GL +D+Y+F EQ+L Q PESEN+ E++ + E NG LQ   ++AQD L ASV+EP+GEPQK
Sbjct: 185 GLPVDNYTFQEQQLHQAPESENVREEN-SIEANGPLQKTGSSAQDQLLASVDEPIGEPQK 243

Query: 137 HTYASILRVAKGQSTPSVTPQPSVSKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADTG 196
           HTYASILRVAKGQS PSV  QPS++KN  P SDWNH  QP +Q ETV++ ++E+  ADT 
Sbjct: 244 HTYASILRVAKGQSAPSVASQPSLNKNSPPTSDWNHASQPISQTETVTANSFERFGADTV 303

Query: 197 EEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVE 256
           EE S  EDE+E+KSVYVRNLP ++SE+EIAEEFK FG +  +GVVIRSRKDVG+CYAFVE
Sbjct: 304 EENSTAEDEDEVKSVYVRNLPTTISEAEIAEEFKNFGSIVPDGVVIRSRKDVGVCYAFVE 363

Query: 257 FEDMTGVRNAVE 268
           FEDMT V NAV+
Sbjct: 364 FEDMTAVHNAVK 375

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224107513|ref|XP_002314507.1| predicted protein [Populus trichocarpa] gi|222863547|gb|EEF00678.1| predicted protein [Populus trichocarpa]

 Score =  357 bits (915), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 184/312 (58%), Positives = 219/312 (70%), Gaps = 47/312 (15%)

Query: 1   MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK------- 53
           MSL Y+GIEI+TAH+L+SWNGGVLVMVSG VQVK F  +RKFV+TFFLAPQEK       
Sbjct: 52  MSLKYTGIEIRTAHALDSWNGGVLVMVSGYVQVKGFDNKRKFVETFFLAPQEKGYFVLND 111

Query: 54  ------------------------------------VPNHLMGGEIQAREYVSPVDVKQN 77
                                               VP +LMGGE QARE+V+P D K+N
Sbjct: 112 VFHFIDEQPTHHHPAVFLAQIHLDSKLNSPNAIPEPVPTYLMGGETQAREFVAPADAKEN 171

Query: 78  GLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKH 137
           G +D Y+FPE+RLQQ  ESENILE++  E+ NGSL+N  + AQD  PASVEEP  EPQKH
Sbjct: 172 GPVDSYTFPEKRLQQASESENILEENSVEKPNGSLKNTASNAQDRQPASVEEPAREPQKH 231

Query: 138 TYASILRVAKGQSTPSVTPQPSVSKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADTGE 197
           TYASILRVAKGQS  SVTPQPSV+KN++P S+WNH  Q   QQ TV S ++E+  A+T E
Sbjct: 232 TYASILRVAKGQSATSVTPQPSVNKNVTPASEWNHTSQAPVQQSTVMSDSFERPEAETAE 291

Query: 198 EISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEF 257
           EI     E+EI+SVYVRNL P++SE+EI EEFK FGE+  +GVVIRSRKDVG+CYAFVEF
Sbjct: 292 EIH----EDEIRSVYVRNLLPTLSEAEIEEEFKNFGEIVPDGVVIRSRKDVGVCYAFVEF 347

Query: 258 EDMTGVRNAVEV 269
           EDM GV NAV+ 
Sbjct: 348 EDMAGVHNAVKA 359

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807448|ref|NP_001242133.1| uncharacterized protein LOC100795457 [Glycine max] gi|255640125|gb|ACU20353.1| unknown [Glycine max]

 Score =  344 bits (882), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 185/314 (58%), Positives = 225/314 (71%), Gaps = 49/314 (15%)

Query: 1   MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK------- 53
           MSL+Y+GIEIKTA SLESW+GGVLVMVSGSVQVKD+S RRKF+QTFFLAPQEK       
Sbjct: 65  MSLSYTGIEIKTAQSLESWSGGVLVMVSGSVQVKDYSRRRKFMQTFFLAPQEKGFFVLND 124

Query: 54  ------------------------------------VPNHLMGGEIQAREYVSPVDVKQN 77
                                               V N+L+G +IQAR+YV+  +VK+N
Sbjct: 125 IFHFVEEDPVHQQQAVLLPQSNLDPKLNASSAINKPVSNYLLGRDIQARDYVATNEVKEN 184

Query: 78  GLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKH 137
           G++D+Y F EQR+Q+ P+SE+I ED+  EE NGSLQ++VNA QD+ PAS +EP GEPQKH
Sbjct: 185 GVVDNYGFSEQRMQRAPDSEHIREDNAVEESNGSLQSSVNAVQDHAPASPDEPAGEPQKH 244

Query: 138 TYASILRVAKGQSTPSVTPQPSVSKNISPVSDWNHVPQPTTQQE--TVSSYAYEKSWADT 195
           TYASILRVAKGQSTPSV  Q    KN+SP S+W+H PQ ++QQ+  T S+ A+E+S  D 
Sbjct: 245 TYASILRVAKGQSTPSVASQ---HKNVSP-SEWDHAPQSSSQQQQMTASANAFERSETDA 300

Query: 196 GEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFV 255
            EE  A EDE+EIKSVYVRNL P+VS SEI +EFK FG +  +GVVIRSRKDVG+CYAFV
Sbjct: 301 AEEFPATEDEDEIKSVYVRNLSPTVSPSEIEDEFKNFGRIRPDGVVIRSRKDVGVCYAFV 360

Query: 256 EFEDMTGVRNAVEV 269
           EFEDMTGV NAV+ 
Sbjct: 361 EFEDMTGVYNAVKA 374

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296083732|emb|CBI23721.3| unnamed protein product [Vitis vinifera]

 Score =  343 bits (881), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 184/316 (58%), Positives = 227/316 (71%), Gaps = 44/316 (13%)

Query: 1   MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK------- 53
           MSLNY+GIEIKTAHSLESWNGGVLV+VSGSVQ+KDFS RRKFVQTFFLAPQEK       
Sbjct: 65  MSLNYTGIEIKTAHSLESWNGGVLVVVSGSVQIKDFSGRRKFVQTFFLAPQEKGFFVLND 124

Query: 54  ------------------------------------VPNHLMGGEIQAREYVSPVDVKQN 77
                                               V N+++GGEIQARE+V+PV+  +N
Sbjct: 125 ILHFIDEDLIQQHPAALLAQSSLDSRLNASNTIPEPVSNYMLGGEIQAREFVAPVNAMEN 184

Query: 78  GLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKH 137
           G +D Y FPEQRLQQV E++NI ED+  E+ NGSLQN +N  QD  PA V+EPVGEPQKH
Sbjct: 185 GPVDRYGFPEQRLQQVTETDNIPEDNSGEDSNGSLQNVMNTLQDLPPAPVDEPVGEPQKH 244

Query: 138 TYASILRVAKGQSTPSVTPQPSVSKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADTGE 197
           TYASILRVAKGQS PSV+PQ   +K++ P S+W+H+PQP+ +Q   SS  +EK  ++  E
Sbjct: 245 TYASILRVAKGQSVPSVSPQSYNNKSMPPASEWHHMPQPSNEQSVASSVMFEKPASEVAE 304

Query: 198 EISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVE 256
           E+S VEDE EIKSVYVRNLP +VS SEIA+EFK FG L  +GVVIR+RKD +G+CYAFVE
Sbjct: 305 EVSGVEDEGEIKSVYVRNLPSTVSASEIAKEFKNFGRLKPDGVVIRNRKDNIGVCYAFVE 364

Query: 257 FEDMTGVRNAVEVCIL 272
           +ED++GV+NA++   +
Sbjct: 365 YEDISGVQNAIKASTI 380

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  343 bits (880), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 184/316 (58%), Positives = 227/316 (71%), Gaps = 44/316 (13%)

Query: 1   MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK------- 53
           MSLNY+GIEIKTAHSLESWNGGVLV+VSGSVQ+KDFS RRKFVQTFFLAPQEK       
Sbjct: 326 MSLNYTGIEIKTAHSLESWNGGVLVVVSGSVQIKDFSGRRKFVQTFFLAPQEKGFFVLND 385

Query: 54  ------------------------------------VPNHLMGGEIQAREYVSPVDVKQN 77
                                               V N+++GGEIQARE+V+PV+  +N
Sbjct: 386 ILHFIDEDLIQQHPAALLAQSSLDSRLNASNTIPEPVSNYMLGGEIQAREFVAPVNAMEN 445

Query: 78  GLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKH 137
           G +D Y FPEQRLQQV E++NI ED+  E+ NGSLQN +N  QD  PA V+EPVGEPQKH
Sbjct: 446 GPVDRYGFPEQRLQQVTETDNIPEDNSGEDSNGSLQNVMNTLQDLPPAPVDEPVGEPQKH 505

Query: 138 TYASILRVAKGQSTPSVTPQPSVSKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADTGE 197
           TYASILRVAKGQS PSV+PQ   +K++ P S+W+H+PQP+ +Q   SS  +EK  ++  E
Sbjct: 506 TYASILRVAKGQSVPSVSPQSYNNKSMPPASEWHHMPQPSNEQSVASSVMFEKPASEVAE 565

Query: 198 EISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVE 256
           E+S VEDE EIKSVYVRNLP +VS SEIA+EFK FG L  +GVVIR+RKD +G+CYAFVE
Sbjct: 566 EVSGVEDEGEIKSVYVRNLPSTVSASEIAKEFKNFGRLKPDGVVIRNRKDNIGVCYAFVE 625

Query: 257 FEDMTGVRNAVEVCIL 272
           +ED++GV+NA++   +
Sbjct: 626 YEDISGVQNAIKASTI 641

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575200|ref|XP_003555730.1| PREDICTED: uncharacterized protein LOC100817177 [Glycine max]

 Score =  342 bits (876), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 180/314 (57%), Positives = 223/314 (71%), Gaps = 48/314 (15%)

Query: 1   MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK------- 53
           MSL+Y+ IEIKTA SLESW+GGVLVMVSGSVQVKD+S RRKF+QTFFLAPQEK       
Sbjct: 65  MSLSYARIEIKTAQSLESWSGGVLVMVSGSVQVKDYSRRRKFMQTFFLAPQEKGFFVLND 124

Query: 54  ------------------------------------VPNHLMGGEIQAREYVSPVDVKQN 77
                                               V N+L+GG+IQAR+YV+  +VK+N
Sbjct: 125 IFHFVEEDPVHQQQPVLLPQSNLDSKLNASSATNKPVSNYLLGGDIQARDYVATNEVKEN 184

Query: 78  GLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKH 137
           G++D+Y F EQR+Q+ P++E+I ED+  EE NGSLQ++VNA QD++P S +EP GEPQKH
Sbjct: 185 GVVDNYGFSEQRMQRAPDTEHIREDNTVEESNGSLQSSVNAVQDHVPVSPDEPAGEPQKH 244

Query: 138 TYASILRVAKGQSTPSVTPQPSVSKNISPVSDWNHVPQPTTQQE--TVSSYAYEKSWADT 195
           TYASILRVAKG STP V  QPS  KN+SP S+W+H P  ++QQ+    S+ A+E+S  D 
Sbjct: 245 TYASILRVAKGLSTP-VASQPS-HKNVSP-SEWDHAPHSSSQQQQTIASANAFERSETDA 301

Query: 196 GEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFV 255
            EE  A EDE+EIKSVYVRNL P+VS SEI +EFK FG +  +GVV+RSRKDVG+CYAFV
Sbjct: 302 VEEFPATEDEDEIKSVYVRNLSPAVSPSEIEDEFKNFGRIRPDGVVVRSRKDVGVCYAFV 361

Query: 256 EFEDMTGVRNAVEV 269
           EFEDMTGV NAV+ 
Sbjct: 362 EFEDMTGVHNAVKA 375

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147859669|emb|CAN83110.1| hypothetical protein VITISV_026572 [Vitis vinifera]

 Score =  303 bits (775), Expect = 8e-80,   Method: Compositional matrix adjust.
 Identities = 156/286 (54%), Positives = 197/286 (68%), Gaps = 44/286 (15%)

Query: 31  VQVKDFSARRKFVQTFFLAPQEK------------------------------------- 53
           VQ+KDFS RRKFVQTFFLAPQEK                                     
Sbjct: 79  VQIKDFSGRRKFVQTFFLAPQEKGFFVLNDILHFIDEDLIQQHPAALLAQSSLDSRLNAS 138

Query: 54  ------VPNHLMGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEE 107
                 V N+++GGEIQARE+V+PV+  +NG +D YSFPEQRLQQV E+E I ED+  E+
Sbjct: 139 NTIPEPVSNYMLGGEIQAREFVAPVNAMENGPVDRYSFPEQRLQQVTETEIIPEDNSGED 198

Query: 108 LNGSLQNAVNAAQDYLPASVEEPVGEPQKHTYASILRVAKGQSTPSVTPQPSVSKNISPV 167
            NGSLQN +N  QD  PA V+EPVGEPQKHTYASILRVAKGQS PSV+PQ   +K++ P 
Sbjct: 199 SNGSLQNVMNTLQDLPPAPVDEPVGEPQKHTYASILRVAKGQSVPSVSPQLYNNKSMPPA 258

Query: 168 SDWNHVPQPTTQQETVSSYAYEKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAE 227
           S+W+H+PQP+ +Q   SS  +EK  ++  EE+S VEDE EIKSVYVRNLP +VS SEIA+
Sbjct: 259 SEWHHMPQPSNEQSVASSVMFEKPASEVAEEVSGVEDEGEIKSVYVRNLPSTVSASEIAK 318

Query: 228 EFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVCIL 272
           EFK FG +  +GVVIR+RKD +G+CYAFVE+ED++GV+NA++   +
Sbjct: 319 EFKNFGRVKPDGVVIRNRKDNIGVCYAFVEYEDISGVQNAIKASTV 364

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576442|ref|XP_003556340.1| PREDICTED: putative G3BP-like protein-like [Glycine max]

 Score =  301 bits (770), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 164/311 (52%), Positives = 209/311 (67%), Gaps = 50/311 (16%)

Query: 1   MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK------- 53
           MSL++ GIEIKTA SLESW+GGVLVMVSGSVQ+K ++ RR+F+QTFFLAPQEK       
Sbjct: 65  MSLSFIGIEIKTAQSLESWSGGVLVMVSGSVQLKGYNVRRQFMQTFFLAPQEKGFFVLND 124

Query: 54  ------------------------------------VPNHLMGGEIQAREYVSPVDVKQN 77
                                               V NHL+GG+I AR++V+  +VK+N
Sbjct: 125 VFHFVEEEPVHHHQPVFLAQSNLDSKLNAPSTINKPVSNHLLGGDIHARDFVATNEVKEN 184

Query: 78  GLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKH 137
           G +++Y F  Q++ +V +SE+I ED  AEE +GS Q  V+A Q+++P++ E P  EPQKH
Sbjct: 185 GAVNNYGFSHQQMLRVHDSEHIQEDVVAEESHGSFQPTVDAVQEHVPSAEESPE-EPQKH 243

Query: 138 TYASILRVAKGQSTPSVTPQPSVSKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADTGE 197
           TYASILRVAKGQ+TPSV  QPS  KN++ + DW+H P   +QQ T    ++E+S     E
Sbjct: 244 TYASILRVAKGQATPSVASQPS-QKNLTSL-DWDHAPLTNSQQTT----SFERSETVVVE 297

Query: 198 EISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEF 257
           E    EDE+EIKSVYVRNL P+VS SEI EEFK FG +  +GVVIRSRKDVG+CYAFVEF
Sbjct: 298 EAPTTEDEDEIKSVYVRNLSPTVSASEIEEEFKNFGRIQPDGVVIRSRKDVGVCYAFVEF 357

Query: 258 EDMTGVRNAVE 268
           EDM GV NAV+
Sbjct: 358 EDMMGVHNAVK 368

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449432500|ref|XP_004134037.1| PREDICTED: putative G3BP-like protein-like [Cucumis sativus] gi|449487478|ref|XP_004157646.1| PREDICTED: putative G3BP-like protein-like [Cucumis sativus]

 Score =  301 bits (770), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 168/313 (53%), Positives = 204/313 (65%), Gaps = 48/313 (15%)

Query: 1   MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK------- 53
           MSL+Y+GIEIKTAHSLESWNGGVLVMVSGSVQ+K+ +  R FVQTFFLAPQEK       
Sbjct: 65  MSLSYTGIEIKTAHSLESWNGGVLVMVSGSVQLKNLNRMRNFVQTFFLAPQEKGYFVLND 124

Query: 54  ------------------------------------VPNHLMGGEIQAREYVSPVDVKQN 77
                                               V N+ + G +Q RE+  PV VK+N
Sbjct: 125 IFHFVDEDPVHHYPAVLLSQSNLDSTLNAPTAVPETVSNYSLNGAVQVREFAPPV-VKEN 183

Query: 78  GLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKH 137
           G ID++ F EQ++QQVPE++NI+E++ AE +N    NA   +QD+ P SVEE   EPQKH
Sbjct: 184 GHIDNHKFVEQQVQQVPEAKNIIEENTAE-VNSMHHNASAISQDHFPVSVEEHAEEPQKH 242

Query: 138 TYASILRVAKGQSTPS--VTPQPSVSKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADT 195
           TYASILRV KGQ  PS    PQ  VSK   P S+ N+ P PT+QQ   S+         T
Sbjct: 243 TYASILRVVKGQDVPSPVAAPQYPVSKGTPPASEQNYTPPPTSQQ-VPSASQNNSEMEQT 301

Query: 196 GEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFV 255
           G E  +++DE EIKSVYVRNLP +VS SE+ EEFK FG+LSS+GVVIRSRKDVG CYAFV
Sbjct: 302 GGEFPSIDDEGEIKSVYVRNLPSTVSASEVEEEFKHFGKLSSDGVVIRSRKDVGFCYAFV 361

Query: 256 EFEDMTGVRNAVE 268
           EFED+TGV+NAV+
Sbjct: 362 EFEDITGVQNAVK 374

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168988195|gb|ACA35266.1| nuclear transport family protein [Cucumis sativus]

 Score =  300 bits (767), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 168/313 (53%), Positives = 204/313 (65%), Gaps = 48/313 (15%)

Query: 1   MSLNYSGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK------- 53
           MSL+Y+GIEIKTAHSLESWNGGVLVMVSGSVQ+K+ +  R FVQTFFLAPQEK       
Sbjct: 149 MSLSYTGIEIKTAHSLESWNGGVLVMVSGSVQLKNLNRMRNFVQTFFLAPQEKGYFVLND 208

Query: 54  ------------------------------------VPNHLMGGEIQAREYVSPVDVKQN 77
                                               V N+ + G +Q RE+  PV VK+N
Sbjct: 209 IFHFVDEDPVHHYPAVLLSQSNLDSTLNAPTAVPETVSNYSLNGAVQVREFAPPV-VKEN 267

Query: 78  GLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKH 137
           G ID++ F EQ++QQVPE++NI+E++ AE +N    NA   +QD+ P SVEE   EPQKH
Sbjct: 268 GHIDNHKFVEQQVQQVPEAKNIIEENTAE-VNSMHHNASAISQDHFPVSVEEHAEEPQKH 326

Query: 138 TYASILRVAKGQSTPS--VTPQPSVSKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADT 195
           TYASILRV KGQ  PS    PQ  VSK   P S+ N+ P PT+QQ   S+         T
Sbjct: 327 TYASILRVVKGQDVPSPVAAPQYPVSKGTPPASEQNYTPPPTSQQ-VPSASQNNSEMEQT 385

Query: 196 GEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFV 255
           G E  +++DE EIKSVYVRNLP +VS SE+ EEFK FG+LSS+GVVIRSRKDVG CYAFV
Sbjct: 386 GGEFPSIDDEGEIKSVYVRNLPSTVSASEVEEEFKHFGKLSSDGVVIRSRKDVGFCYAFV 445

Query: 256 EFEDMTGVRNAVE 268
           EFED+TGV+NAV+
Sbjct: 446 EFEDITGVQNAVK 458

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	275
TAIR|locus:2172472	450	AT5G43960 [Arabidopsis thalian	0.76	0.464	0.387	6.9e-31
TAIR|locus:2173567	460	AT5G60980 [Arabidopsis thalian	0.214	0.128	0.457	1.8e-18
TAIR|locus:2152566	458	AT5G48650 [Arabidopsis thalian	0.734	0.441	0.242	5.2e-12
TAIR|locus:2023854	428	AT1G13730 [Arabidopsis thalian	0.905	0.581	0.241	5.2e-08
TAIR|locus:2026423	427	AT1G69250 [Arabidopsis thalian	0.901	0.580	0.240	2.1e-07
UNIPROTKB|I3LPH5	448	G3BP2 "Uncharacterized protein	0.505	0.310	0.288	1e-06
MGI|MGI:2442040	482	G3bp2 "GTPase activating prote	0.509	0.290	0.281	2.8e-06
RGD|1309571	449	G3bp2 "GTPase activating prote	0.509	0.311	0.281	3.1e-06
UNIPROTKB|Q2KJ17	449	G3BP2 "GTPase activating prote	0.509	0.311	0.281	4e-06
UNIPROTKB|Q9UN86	482	G3BP2 "Ras GTPase-activating p	0.509	0.290	0.281	4.9e-06

TAIR|locus:2172472 AT5G43960 [Arabidopsis thaliana (taxid:3702)]

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 90/232 (38%), Positives = 127/232 (54%)

Query:    50 PQEKVPNHLMGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEELN 109
             P  +V ++++  E +A +YV+ V +K + L+D YS  E + Q  P+ E+  ED  A E  
Sbjct:   155 PDPQVSDYVL--EEEASDYVNAVQIKDD-LVDKYSLQEDQHQ--PQHEDY-EDEVAIEET 208

Query:   110 GSLQNAVNAAQDYLPASVEEPVGEPQKHTYASILRVAKGXXXXXXXXXX-XXXKNISPVS 168
                + AV+   ++  A VEEPVGE  K +YASIL+VAK               K+   ++
Sbjct:   209 PREEVAVDVVHEHRAAPVEEPVGEKSKMSYASILKVAKEAATVPVAATQPSYNKSSQDIN 268

Query:   169 DWNH---VPQPTT-------QQETVSSYAYEK-SWADTGXXXXXXXXXXXIKSVYVRNLP 217
             +W+     P P         QQ   S+Y  +  + A+ G            KSVYVRNLP
Sbjct:   269 EWDQPMRTPSPQLAAPLAPIQQSNSSTYVSDYGAEAEDGSGFEDFE----FKSVYVRNLP 324

Query:   218 PSVSESEIAEEFKKFGELSSEGVVIRSRKDV-GICYAFVEFEDMTGVRNAVE 268
               +S SEI EEFK FG +  +GV +R+RKDV G+CYAFVEFEDMT V NA++
Sbjct:   325 SDISASEIEEEFKNFGTIKPDGVFLRTRKDVMGVCYAFVEFEDMTSVENAIK 376

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005622 "intracellular" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0006913 "nucleocytoplasmic transport" evidence=ISS

GO:0006499 "N-terminal protein myristoylation" evidence=RCA

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

TAIR|locus:2173567 AT5G60980 [Arabidopsis thaliana (taxid:3702)]

 Score = 150 (57.9 bits), Expect = 1.8e-18, Sum P(2) = 1.8e-18
 Identities = 27/59 (45%), Positives = 40/59 (67%)

Query:   210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
             S+YVRNLP   + +++ E FK FG +  EG+ +RS K  G C+ FVEFE  +G ++A+E
Sbjct:   294 SIYVRNLPFDSTPTQLEEVFKNFGAIKHEGIQVRSNKQQGFCFGFVEFETSSGKQSALE 352

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005622 "intracellular" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0006913 "nucleocytoplasmic transport" evidence=ISS

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

TAIR|locus:2152566 AT5G48650 [Arabidopsis thaliana (taxid:3702)]

 Score = 120 (47.3 bits), Expect = 5.2e-12, Sum P(2) = 5.2e-12
 Identities = 55/227 (24%), Positives = 100/227 (44%)

Query:    56 NHLMGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNA 115
             N + G E  A   V+PV  + +  +D+ +  +  L  VPE  N   +    E+    + A
Sbjct:   163 NGMKGSEQAACVSVNPVCKEVSKPLDNENAKDNVL--VPEIAN---EVARTEITCK-EVA 216

Query:   116 VNAAQDYLPASVEEPVGEPQKHTYASILRVAKGXXXXXXXXXXXXXKNISPVSDWNHVPQ 175
              ++ ++Y P   ++ + +  K +YAS+L+V K              K   P    +  P 
Sbjct:   217 DDSQKNYDP---DDGLADAPKKSYASVLKVTKDKFGVPAVSLPSPKK--IPKDQEHQAPS 271

Query:   176 -PTTQQ------ETVSSYAYEKSWADTGXXXXXXXXXXXIK-------SVYVRNLPPSVS 221
              P+T Q      +  SS   +   +DT             +       S+YVR+LP + +
Sbjct:   272 DPSTGQILKDQGQQASSDPSQVIESDTVSESVDASENGHNQEAVAEGTSIYVRHLPFNAN 331

Query:   222 ESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
                +  EFK+FG +++ G+ + +++ +G  Y FVEFE+      A+E
Sbjct:   332 IDMLEAEFKQFGAITNGGIQVINQRGLGYPYGFVEFEEADAAHRAIE 378

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0006810 "transport" evidence=IEA

GO:0006913 "nucleocytoplasmic transport" evidence=ISS

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2023854 AT1G13730 [Arabidopsis thaliana (taxid:3702)]

 Score = 148 (57.2 bits), Expect = 5.2e-08, P = 5.2e-08
 Identities = 68/281 (24%), Positives = 122/281 (43%)

Query:     1 MSLNY--SGIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK----- 53
             MS +Y  S I+I TA S  S+  GV+ +V+G + VK+   R +F Q+FFL P        
Sbjct:    67 MSFDYEISKIQILTADSQASYMNGVVTLVTGLLTVKE-GQRMRFSQSFFLVPLNGSYFVL 125

Query:    54 ------VPNHLMGGEIQAREY--VSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPA 105
                   V + ++  E   +E   V P  V+    +D+ + P     Q PE++   E++  
Sbjct:   126 NDVFRYVADEIVEPEANKKEVEEVIPQVVQPTEQVDEVAEPVTIPTQQPEAKQTTENTVK 185

Query:   106 EELNGSLQNAVNAAQDYLPASVEEPVGEPQKHTYASILR-VAKGXXXXXXXXXXXXXKNI 164
             +             +D +       V  P+K ++A I++ +A+              K+ 
Sbjct:   186 KPERAVANGHPKTQEDNVVNDKSNGVDAPKK-SFAHIVQDLAQNGATFNAKASPAKPKS- 243

Query:   165 SPVSDWNHVPQPTTQQETVS-SYAYEKSWADTGXXXXXXXXXXXIKSVYVRNLPPSVSES 223
              PV+      +P+  +E+ + +   E S A T              +++V NL    +  
Sbjct:   244 KPVT------KPSAARESKAPAPVSEHSSAATIDQQAEGY------TIFVANLLMDATPE 291

Query:   224 EIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVR 264
             ++ E FK FG ++ +G+ +RS +  G C+ FV F     V+
Sbjct:   292 QLNETFKGFGAITKDGIQVRSYRLKGNCFGFVTFASAEAVK 332

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0006810 "transport" evidence=IEA

GO:0006913 "nucleocytoplasmic transport" evidence=ISS

GO:0009165 "nucleotide biosynthetic process" evidence=RCA

TAIR|locus:2026423 AT1G69250 [Arabidopsis thaliana (taxid:3702)]

 Score = 143 (55.4 bits), Expect = 2.1e-07, P = 2.1e-07
 Identities = 67/279 (24%), Positives = 111/279 (39%)

Query:     9 EIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK--VPNHLMGGEIQAR 66
             E+ +  S  S   G+ +MV G +  KD + RRKF Q F+LA Q    V N ++    Q  
Sbjct:    75 EVLSVDSQNSLEDGIFIMVIGFMTGKD-NQRRKFSQMFYLARQNTLVVLNDMLRYVDQED 133

Query:    67 --------EYVSPVDVKQNGL--IDDYSFPEQRLQQVPESENILEDSPAEEL-NGSLQNA 115
                     E V+ +    +GL   +     ++ +  V +S N   +  A  L NG ++ +
Sbjct:   134 SSTTETPCEPVTEIVRPADGLKKAEKTELKQKNVASVEKSVNAAVEKNAAPLDNGKMKQS 193

Query:   116 VNAAQDYLPASVEEPVGEPQ----KHTYASILRVAKGXXXXXXXXXXXXXKNISPVSDWN 171
               A    +   V EP   PQ    K ++A I+    G                +PV    
Sbjct:   194 EKAV---ITQKVTEPDAAPQPDGAKRSFADIV----GSMAKNAAPFQVKSPVQAPVQKPK 246

Query:   172 HVPQPTTQQETVSSYAYEKSWADTGXXXXXXXXXXXIKSVYVRNLPPSVSESEIAEEFKK 231
             +V QP             KS                  S++V NLP +    ++ E FK 
Sbjct:   247 YVGQPRAAAAPQKPAYVSKSIKKNDQKVIEVPGT----SIFVANLPLNAMPPQLFELFKD 302

Query:   232 FGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVE 268
             FG +   G+ +RS +     +C+ F+ FE +  V++ ++
Sbjct:   303 FGPIKENGIQVRSSRGNANPVCFGFISFETVASVQSVLQ 341

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0006810 "transport" evidence=IEA

GO:0006913 "nucleocytoplasmic transport" evidence=ISS

GO:0006499 "N-terminal protein myristoylation" evidence=RCA

GO:0006888 "ER to Golgi vesicle-mediated transport" evidence=RCA

GO:0009165 "nucleotide biosynthetic process" evidence=RCA

GO:0043090 "amino acid import" evidence=RCA

UNIPROTKB|I3LPH5 G3BP2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 116 (45.9 bits), Expect = 1.0e-06, Sum P(2) = 1.0e-06
 Identities = 43/149 (28%), Positives = 63/149 (42%)

Query:     1 MSLNYSGIEIKTAH--SLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHL 58
             +SLN+S    K  H  +  + + GV+V V G +        RKF+QTF LAP+  VPN  
Sbjct:    66 LSLNFSECHTKIRHVDAHATLSDGVVVQVMGLLS-NSGQPERKFMQTFVLAPEGSVPNKF 124

Query:    59 MGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNA--- 115
                    R Y   V       +D+ S  E  +++  E      + P +E N     A   
Sbjct:   125 YVHNDMFR-YEDEVFGDSEPELDEES--EDEVEEEQEERQPTPE-PVQETNSGYYEAHPV 180

Query:   116 VNAAQDYLPASVEEPVGEPQKHTYASILR 144
              N  ++ L  S  EP  EP+  T    L+
Sbjct:   181 TNGIEEPLEESSHEPEPEPESETKTEELK 209

GO:0005737 "cytoplasm" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:2442040 G3bp2 "GTPase activating protein (SH3 domain) binding protein 2" [Mus musculus (taxid:10090)]

 Score = 113 (44.8 bits), Expect = 2.8e-06, Sum P(2) = 2.8e-06
 Identities = 42/149 (28%), Positives = 63/149 (42%)

Query:     1 MSLNYSGIEIKTAH--SLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHL 58
             +SLN+S    K  H  +  + + GV+V V G +        RKF+QTF LAP+  VPN  
Sbjct:    66 LSLNFSECHTKIRHVDAHATLSDGVVVQVMGLLS-NSGQPERKFMQTFVLAPEGSVPNKF 124

Query:    59 MGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNA--- 115
                    R Y   V       +D+ S  E  +++  E      +   E  N +  +A   
Sbjct:   125 YVHNDMFR-YEDEVFGDSEPELDEES--EDEVEEEQEDRQPSPEPVQENANSAYYDAHPV 181

Query:   116 VNAAQDYLPASVEEPVGEPQKHTYASILR 144
              N  ++ L  S  EP  EP+  T    L+
Sbjct:   182 TNGIEEPLEESSHEPEPEPESETKTEELK 210

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0007264 "small GTPase mediated signal transduction" evidence=ISO

GO:0051028 "mRNA transport" evidence=IEA

RGD|1309571 G3bp2 "GTPase activating protein (SH3 domain) binding protein 2" [Rattus norvegicus (taxid:10116)]

 Score = 112 (44.5 bits), Expect = 3.1e-06, Sum P(2) = 3.1e-06
 Identities = 42/149 (28%), Positives = 62/149 (41%)

Query:     1 MSLNYSGIEIKTAH--SLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHL 58
             +SLN+S    K  H  +  + + GV+V V G +        RKF+QTF LAP+  VPN  
Sbjct:    66 LSLNFSECHTKIRHVDAHATLSDGVVVQVMGLLS-NSGQPERKFMQTFVLAPEGSVPNKF 124

Query:    59 MGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNA--- 115
                    R Y   V       +D+ S  E  +++  E      +   E  N +   A   
Sbjct:   125 YVHNDMFR-YEDEVFGDSEPELDEES--EDEVEEEQEDRQPSPEPVQENANSAYYEAHPV 181

Query:   116 VNAAQDYLPASVEEPVGEPQKHTYASILR 144
              N  ++ L  S  EP  EP+  T    L+
Sbjct:   182 TNGIEEPLEESSHEPEPEPESETKTEELK 210

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006810 "transport" evidence=IEA

UNIPROTKB|Q2KJ17 G3BP2 "GTPase activating protein (SH3 domain) binding protein 2" [Bos taurus (taxid:9913)]

 Score = 111 (44.1 bits), Expect = 4.0e-06, Sum P(2) = 4.0e-06
 Identities = 42/149 (28%), Positives = 61/149 (40%)

Query:     1 MSLNYSGIEIKTAH--SLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHL 58
             +SLN+S    K  H  +  + + GV+V V G +        RKF+QTF LAP+  VPN  
Sbjct:    66 LSLNFSECHTKIRHVDAHATLSDGVVVQVMGLLS-NSGQPERKFMQTFVLAPEGSVPNKF 124

Query:    59 MGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNA--- 115
                    R Y   V       +D+ S  E  +++  E      +   E  N     A   
Sbjct:   125 YVHNDMFR-YEDEVFGDSEPELDEES--EDEVEEEQEERQPSPEPVQENANSGYYEAHPV 181

Query:   116 VNAAQDYLPASVEEPVGEPQKHTYASILR 144
              N  ++ L  S  EP  EP+  T    L+
Sbjct:   182 TNGIEEPLEESSHEPEPEPESETKTEELK 210

GO:0005737 "cytoplasm" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q9UN86 G3BP2 "Ras GTPase-activating protein-binding protein 2" [Homo sapiens (taxid:9606)]

 Score = 111 (44.1 bits), Expect = 4.9e-06, Sum P(2) = 4.9e-06
 Identities = 42/149 (28%), Positives = 61/149 (40%)

Query:     1 MSLNYSGIEIKTAH--SLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHL 58
             +SLN+S    K  H  +  + + GV+V V G +        RKF+QTF LAP+  VPN  
Sbjct:    66 LSLNFSECHTKIRHVDAHATLSDGVVVQVMGLLS-NSGQPERKFMQTFVLAPEGSVPNKF 124

Query:    59 MGGEIQAREYVSPVDVKQNGLIDDYSFPEQRLQQVPESENILEDSPAEELNGSLQNA--- 115
                    R Y   V       +D+ S  E  +++  E      +   E  N     A   
Sbjct:   125 YVHNDMFR-YEDEVFGDSEPELDEES--EDEVEEEQEERQPSPEPVQENANSGYYEAHPV 181

Query:   116 VNAAQDYLPASVEEPVGEPQKHTYASILR 144
              N  ++ L  S  EP  EP+  T    L+
Sbjct:   182 TNGIEEPLEESSHEPEPEPESETKTEELK 210

GO:0000166 "nucleotide binding" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA;NAS

GO:0003723 "RNA binding" evidence=NAS

GO:0007265 "Ras protein signal transduction" evidence=NAS

GO:0007253 "cytoplasmic sequestering of NF-kappaB" evidence=NAS

GO:0030159 "receptor signaling complex scaffold activity" evidence=NAS

GO:0005829 "cytosol" evidence=TAS

GO:0007264 "small GTPase mediated signal transduction" evidence=TAS

GO:0051056 "regulation of small GTPase mediated signal transduction" evidence=TAS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.X.4619.1 hypothetical protein (380 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	275
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-13
smart00360	73	smart00360, RRM, RNA recognition motif	2e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	6e-11
cd00780	119	cd00780, NTF2, Nuclear transport factor 2 (NTF2) d	1e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-09
pfam02136	116	pfam02136, NTF2, Nuclear transport factor 2 (NTF2)	4e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	8e-09
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-08
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-07
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	4e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	4e-07
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-07
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	9e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-06
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	5e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	6e-06
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	6e-06
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	8e-06
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	1e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	1e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	1e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	1e-05
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	3e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	4e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	4e-05
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	5e-05
cd12356	79	cd12356, RRM_PPARGC1B, RNA recognition motif in pe	5e-05
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	7e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	7e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	7e-05
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	8e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-04
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	2e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-04
cd12780	80	cd12780, RRM1_hnRNPL, RNA recognition motif 1 in v	2e-04
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	3e-04
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	4e-04
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	4e-04
cd12525	72	cd12525, RRM1_MEI2_fungi, RNA recognition motif 1	4e-04
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	5e-04
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	5e-04
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	6e-04
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	6e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	7e-04
cd12308	79	cd12308, RRM1_Spen, RNA recognition motif 1 in the	7e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	8e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	9e-04
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.001
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	0.001
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	0.001
cd12689	80	cd12689, RRM1_hnRNPL_like, RNA recognition motif 1	0.001
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	0.001
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	0.001
cd12724	92	cd12724, RRM1_CPEB2_like, RNA recognition motif 1	0.001
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	0.001
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	0.001
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.002
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.002
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	0.002
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	0.002
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	0.002
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.002
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.002
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.002
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.003
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	0.003
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.003
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	0.003
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	0.003
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	0.004
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	0.004

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

 Score = 63.0 bits (154), Expect = 3e-13
 Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 2/60 (3%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC 270
           +YVRNLPPSV+E ++ E F  +G++  EGV +   KD    +AFVEF        A++  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKV--EGVRLVRNKDRPRGFAFVEFASPEDAEAALKKL 58

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

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

 Score = 60.7 bits (148), Expect = 2e-12
 Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 4/61 (6%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMTGVRNAV 267
           +++V NLPP  +E E+ E F KFG++ S  V +   K+ G    +AFVEFE       A+
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVES--VRLVRDKETGKSKGFAFVEFESEEDAEKAL 58

Query: 268 E 268
           E
Sbjct: 59  E 59

Length = 73

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

 Score = 56.9 bits (138), Expect = 6e-11
 Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 3/59 (5%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGV-VIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++V NLPP  +E ++ E F KFGE+ S  V ++R +      +AFVEFE       A+E
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIES--VRIVRDKDGKSKGFAFVEFESPEDAEKALE 57

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|238403 cd00780, NTF2, Nuclear transport factor 2 (NTF2) domain plays an important role in the trafficking of macromolecules, ions and small molecules between the cytoplasm and nucleus

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 23/55 (41%), Positives = 33/55 (60%), Gaps = 3/55 (5%)

Query: 1   MSLNYSGI--EIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK 53
            SL +     +I T  S  + +GGV+VMV+GS+++ +    RKF QTF LAPQ  
Sbjct: 53  SSLPFQKTKHKITTVDSQPTPSGGVIVMVTGSLKLDE-QPPRKFSQTFVLAPQNG 106

This bi-directional transport of macromolecules across the nuclear envelope requires many soluble factors that includes GDP-binding protein Ran (RanGDP). RanGDP is required for both import and export of proteins and poly(A) RNA. RanGDP also has been implicated in cell cycle control, specifically in mitotic spindle assembly. In interphase cells, RanGDP is predominately nuclear and thought to be GTP bound, but it is also present in the cytoplasm, probably in the GDP-bound state. NTF2 mediates the nuclear import of RanGDP. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins. Length = 119

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

 Score = 53.0 bits (128), Expect = 1e-09
 Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 7/61 (11%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGI---CYAFVEFEDMTGVRNAV 267
           ++V NLPP  +E ++ + F KFG + S    IR  +D       +AFVEFED      A+
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIES----IRIVRDETGRSKGFAFVEFEDEEDAEKAL 56

Query: 268 E 268
           E
Sbjct: 57  E 57

(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|216894 pfam02136, NTF2, Nuclear transport factor 2 (NTF2) domain

 Score = 53.1 bits (128), Expect = 4e-09
 Identities = 23/57 (40%), Positives = 30/57 (52%), Gaps = 4/57 (7%)

Query: 1   MSLNYSGIEIKTAH---SLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKV 54
            SL ++ I+           S + GVLVMV+G + V DF  RR+F QTF L PQ   
Sbjct: 51  DSLPFTRIQHLITSVDAQPASHSDGVLVMVTGELTVDDFP-RRRFSQTFLLTPQRGG 106

This family includes the NTF2-like Delta-5-3-ketosteroid isomerase proteins. Length = 116

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

 Score = 55.6 bits (134), Expect = 8e-09
 Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 201 AVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDM 260
                ++  ++YV+NL PSV+E ++ E F KFGE++S   V++        +AFV FE  
Sbjct: 171 EAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITS-AAVMKDGSGRSRGFAFVNFEKH 229

Query: 261 TGVRNAVE 268
                AVE
Sbjct: 230 EDAAKAVE 237

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

 Score = 49.5 bits (119), Expect = 2e-08
 Identities = 25/57 (43%), Positives = 34/57 (59%), Gaps = 5/57 (8%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
           VYV NL P  ++ E+ +EF+K+G L S  V   +R   G  +AFVEFED     +AV
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWV---ARNPPG--FAFVEFEDPRDAEDAV 53

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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 8/61 (13%)

Query: 208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
           +K +YVRNLP S +E ++ E F ++GE+  E V     KD    YAFV FE+      A+
Sbjct: 1   VKVLYVRNLPLSTTEEQLRELFSEYGEV--ERVKK--IKD----YAFVHFEERDDAVKAM 52

Query: 268 E 268
           E
Sbjct: 53  E 53

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGI---CYAFVEFEDMTGVRNAV 267
           +YVRNL   + E ++   F KFGE+ S  +  +  +  G     +AFV F+D +   NA+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 268 EV 269
           ++
Sbjct: 63  QL 64

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

 Score = 46.4 bits (111), Expect = 4e-07
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 14/68 (20%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGV 263
           ++V++RNLP   +E E+ E F +FGE+    +V       S+   G   AFV+F+     
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSK---GT--AFVKFKT---- 51

Query: 264 RNAVEVCI 271
           + + + C+
Sbjct: 52  KESAQKCL 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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 46.4 bits (111), Expect = 4e-07
 Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 4/50 (8%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFE 258
           ++V  L PSV+ES++ E F +FG +S   V I  +KD G    +A+++  
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSD--VEIIKKKDAGPDRGFAYIDLR 49

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

 Score = 49.9 bits (118), Expect = 5e-07
 Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 4/82 (4%)

Query: 189 EKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV 248
           E+ +  +    S  + +EE  +++V NLP  V+E ++ E FKKFG +    V +   ++ 
Sbjct: 96  EELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKR--VRLVRDRET 153

Query: 249 GIC--YAFVEFEDMTGVRNAVE 268
           G    +AFVEFE       A+E
Sbjct: 154 GKSRGFAFVEFESEESAEKAIE 175

Length = 306

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

 Score = 45.1 bits (107), Expect = 9e-07
 Identities = 21/57 (36%), Positives = 35/57 (61%), Gaps = 3/57 (5%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
           +YV NLP  + E +I + F K+G + +  + +++R+  G  +AFVEFED     +AV
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPIKA--IDLKNRRR-GPPFAFVEFEDPRDAEDAV 55

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 10/62 (16%)

Query: 212 YVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGVRNA 266
           YV NLP +V+E ++ + F +FGE++S  V+      RSR      + FVE E       A
Sbjct: 3   YVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRG-----FGFVEMETAEEANAA 57

Query: 267 VE 268
           +E
Sbjct: 58  IE 59

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

 Score = 43.2 bits (102), Expect = 5e-06
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 4/57 (7%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
           +YV NLPP +   +I + F K+G +    + +++R+  G  +AFVEFED     +AV
Sbjct: 2   IYVGNLPPDIRTKDIEDLFYKYGAIRD--IDLKNRR--GPPFAFVEFEDPRDAEDAV 54

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

 Score = 43.0 bits (102), Expect = 6e-06
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 6/58 (10%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++V  L P  S +E+  EF +FG +      I         YA++E+E +   + A E
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRR----IDYDPGRN--YAYIEYESIEAAQAAKE 52

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|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 42.8 bits (101), Expect = 6e-06
 Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNA 266
            ++V NLP +V E  I+E FK++G + S  ++ +   D G+  AFV+F D+   + A
Sbjct: 1   HLWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVA-AFVDFVDIKSAQKA 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|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 42.7 bits (101), Expect = 8e-06
 Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 4/66 (6%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV 269
           +++V  L  +   +++ + F K+G++    +V  +R     C+ FV    +         
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVE----EAAK 56

Query: 270 CILMWH 275
           CI   H
Sbjct: 57  CIQHLH 62

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|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +SV+V       SE ++ + F  FG + +  V++   KD G+ YA VEF+   GV   + 
Sbjct: 3   RSVFVSGFKRGTSEEQLMDYFSAFGPVMN--VIM--DKDKGV-YAIVEFDSKEGVDKVLS 57

Query: 269 VC 270
             
Sbjct: 58  EP 59

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

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

 Score = 42.0 bits (99), Expect = 1e-05
 Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 4/59 (6%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +VY    P S   S++   F+  G +    ++ R+ +     +AF+ FE++   + A+E
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQ----PHAFITFENLEAAQLAIE 55

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

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 17/53 (32%), Positives = 33/53 (62%), Gaps = 3/53 (5%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-RSRKDVGICYAFVEFEDM 260
           ++++V NL  +++E E+   F+++G +  E V I R  +  G  YAFV+F ++
Sbjct: 3   RTLFVGNLEITITEEELRRAFERYGVV--EDVDIKRPPRGQGNAYAFVKFLNL 53

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|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 = 42.2 bits (100), Expect = 1e-05
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 4/59 (6%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMTGVRNAV 267
           V +R LP S +E +I + F     +  +G+ I    D G     A+VEF      R A+
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLD-IPPDGIHIV-YDDDGRPTGEAYVEFASPEDARRAL 58

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 = 42.0 bits (99), Expect = 2e-05
 Identities = 21/53 (39%), Positives = 29/53 (54%)

Query: 207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED 259
           E   ++VRNLP S  E ++ + F KFGELS   V I  +      +A+V F D
Sbjct: 1   ETGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLD 53

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 8/66 (12%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV----GICYAFVEFEDMTGVR 264
            +++V  L    +E  + E F ++G++      +R  +D+       YAFVE+E      
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDIRR----LRLVRDIVTGFSKGYAFVEYEHERDAL 59

Query: 265 NAVEVC 270
            A    
Sbjct: 60  RAYRDA 65

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 14/58 (24%), Positives = 28/58 (48%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNA 266
            S+YVRN+  +    ++   F K+G +    + +         +A+V+FED+    +A
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDA 58

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

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 4/60 (6%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAV 267
           S++V N+    +  E+ E FK  G ++   + I   K  G    +A++EF D + V NA+
Sbjct: 1   SIFVGNVDYGTTPEELQEHFKSCGTINR--ITILCDKFTGQPKGFAYIEFLDKSSVENAL 58

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|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 = 40.7 bits (96), Expect = 4e-05
 Identities = 16/58 (27%), Positives = 30/58 (51%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +++  LP  +SE ++ E  + FG+L +  +V  S   +   YAF E+ D +    A+ 
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

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

 Score = 40.6 bits (96), Expect = 4e-05
 Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           VYV+NL   + + ++ E F K+G+++S   V++  +     + FV FE+    + AVE
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITS-AKVMKDDEGKSKGFGFVNFENHEAAQKAVE 60

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

 Score = 40.6 bits (96), Expect = 4e-05
 Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 12/56 (21%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIR------SRKDVGICYAFVEFED 259
           S+YV +L P V+E+ + E F   G + S    IR      +R+ +G  YA+V F++
Sbjct: 1   SLYVGDLHPDVTEAMLYEIFSPAGPVLS----IRVCRDLITRRSLG--YAYVNFQN 50

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|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 = 40.4 bits (95), Expect = 5e-05
 Identities = 17/48 (35%), Positives = 26/48 (54%)

Query: 212 YVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED 259
           +VRNLP + +E E+ E F+ FGE+S   + +         +AFV F  
Sbjct: 3   FVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMF 50

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|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1-beta) and similar proteins

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 16/41 (39%), Positives = 28/41 (68%)

Query: 207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD 247
           E + +Y+RNL  S+S +E+ + F+ FGE+    V+I+SR +
Sbjct: 1   EGRVIYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRGE 41

This subfamily corresponds to the RRM of PGC-1beta, also termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or PGC-1-related estrogen receptor alpha coactivator, which is one of the members of PGC-1 transcriptional coactivators family, including PGC-1alpha and PGC-1-related coactivator (PRC). PGC-1beta plays a nonredundant role in controlling mitochondrial oxidative energy metabolism and affects both, insulin sensitivity and mitochondrial biogenesis, and functions in a number of oxidative tissues. It is involved in maintaining baseline mitochondrial function and cardiac contractile function following pressure overload hypertrophy by preserving glucose metabolism and preventing oxidative stress. PGC-1beta induces hypertriglyceridemia in response to dietary fats through activating hepatic lipogenesis and lipoprotein secretion. It can stimulate apolipoprotein C3 (APOC3) expression, further mediating hypolipidemic effect of nicotinic acid. PGC-1beta also drives nuclear respiratory factor 1 (NRF-1) target gene expression and NRF-1 and estrogen related receptor alpha (ERRalpha)-dependent mitochondrial biogenesis. The modulation of the expression of PGC-1beta can trigger ERRalpha-induced adipogenesis. PGC-1beta is also a potent regulator inducing angiogenesis in skeletal muscle. The transcriptional activity of PGC-1beta can be increased through binding to host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. PGC-1beta is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, two glutamic/aspartic acid-rich acidic domains, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha, PGC-1beta lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 79

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

 Score = 40.1 bits (94), Expect = 7e-05
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 3/58 (5%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           VYV NLP  + E E+ + F K+G +    + +  R      YAF+EFED     +A+ 
Sbjct: 2   VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPP---GYAFIEFEDARDAEDAIR 56

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

 Score = 40.3 bits (95), Expect = 7e-05
 Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 13/66 (19%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI--------RSRKDVGICYAFVEFEDMTG 262
           +YV NL P V+E  + +EF +FG L+S  V I        R R     C  FV F +   
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLAS--VKIMWPRTEEERRRN--RNC-GFVAFMNRAD 58

Query: 263 VRNAVE 268
              A++
Sbjct: 59  AERALD 64

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

 Score = 39.9 bits (94), Expect = 7e-05
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
           I ++YV  L   V+E ++ + F +FGE+ S  VV R +       AFV F        A 
Sbjct: 1   ITTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQ------CAFVTFTTREAAEKAA 54

Query: 268 E 268
           E
Sbjct: 55  E 55

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

 Score = 40.1 bits (94), Expect = 8e-05
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 9/61 (14%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++VY+ NLP S SE E+ E+ +KFG +  + + I   K++    AFV F     + NA++
Sbjct: 4   RNVYIGNLPESYSEEELREDLEKFGPI--DQIKIVKEKNI----AFVHF---LSIANAIK 54

Query: 269 V 269
           V
Sbjct: 55  V 55

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

 Score = 42.5 bits (100), Expect = 1e-04
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 9/62 (14%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----RSRKDVGICYAFVEFEDMTGVRNA 266
           ++V+NL  SV    + + F KFG + S  V      +SR      Y FV FE     + A
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRG-----YGFVHFEKEESAKAA 145

Query: 267 VE 268
           ++
Sbjct: 146 IQ 147

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

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

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           S++V  L P V++ E+ E F + G++    V +  R +    +AF++FE       AVE
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILE--VNLIKRANHTNAFAFIKFEREQAAARAVE 61

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 6/61 (9%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR---KDVGICYAFVEFEDMTGVRNAV 267
           ++V  LP   ++  + + F +FGE+  E VVI  R   K  G  Y FV F+D      A 
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEI-EEAVVITDRQTGKSRG--YGFVTFKDKESAERAC 59

Query: 268 E 268
           +
Sbjct: 60  K 60

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

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 1/65 (1%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC 270
           ++V  +PP  +E E+ + F +FG +  +  +I  R  V   Y FV FE        + + 
Sbjct: 5   IFVGGIPPDTTEEELRDFFSRFGSV-KDVKIITDRAGVSKGYGFVTFETQEDAEKILAMG 63

Query: 271 ILMWH 275
            L + 
Sbjct: 64  NLNFR 68

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

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 4/59 (6%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGV-VIRSRKD-VGICYAFVEFEDMTGVRNA 266
           SV+V NLP  + E E+ + F+  G++  E V ++R RK  +G  + +V F+    V  A
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDV--EAVRIVRDRKTGIGKGFGYVLFKTKDSVALA 57

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 4/58 (6%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMTGVRNA 266
           ++V NLP +V   E+ E F +FG++ S  V     K+ G+   Y FV F    G+ NA
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPF--DKETGLSKGYGFVSFSSRDGLENA 57

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGI-CYAFVEFEDMTGVRNAVE 268
           +++V NL  S  + ++ E FK+ GE+    V I    D     +  VEF    G + A+E
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVD--VRIAQDDDGRSKGFGHVEFATEEGAQKALE 58

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|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 6/63 (9%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV- 267
           +S++V N+P  V+ES +   F+ +G++     V   R   GI    V F D+   + AV 
Sbjct: 2   RSLFVINVPRDVTESTLRRLFEVYGDVRG---VQTERISEGIV--TVHFYDIRDAKRAVR 56

Query: 268 EVC 270
           E+C
Sbjct: 57  ELC 59

This subfamily corresponds to the RRM1 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 protein 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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 13/63 (20%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC-----YAFVEFEDMTGVRN 265
           +YVRNLP  +S  E+ + F K+G +      IR    +G        AFV +ED+   +N
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAI----RQIR----IGNTKETRGTAFVVYEDIYDAKN 56

Query: 266 AVE 268
           A +
Sbjct: 57  ACD 59

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|241224 cd12780, RRM1_hnRNPL, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein L (hnRNP-L)

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 23/57 (40%), Positives = 33/57 (57%), Gaps = 6/57 (10%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
           V+VR L   V E+++ E  ++FG +S   V+ + R+      A VEFEDM G  NAV
Sbjct: 5   VHVRGLIDGVVEADLVEALQEFGTISYVVVMPKKRQ------ALVEFEDMNGACNAV 55

This subgroup corresponds to the RRM1 of hnRNP-L, 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-L shows significant sequence homology to polypyrimidine tract-binding protein (PTB or hnRNP I). Both, hnRNP-L and PTB, are localized in the nucleus but excluded from the nucleolus. hnRNP-L is an RNA-binding protein with three RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 80

>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 = 38.5 bits (90), Expect = 2e-04
 Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 3/62 (4%)

Query: 207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSS-EGVVIRSRKDVGICYAFVEFEDMTGVRN 265
           E   ++V  LP SV++ E+ + FKK G + S   V  RS K  G   A+VE+E+ +    
Sbjct: 1   EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKG--LAYVEYENESSASQ 58

Query: 266 AV 267
           AV
Sbjct: 59  AV 60

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           + V+NLP  V+E  + E F+  GE+ ++  V+R+R      + FV F+     + AV+
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEV-TDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVK 59

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

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 3/57 (5%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
           +YV NLP  V E ++ + F K+G +    + +++R+ + + +AFV FED     +AV
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRIRD--IELKNRRGL-VPFAFVRFEDPRDAEDAV 55

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 14/49 (28%), Positives = 22/49 (44%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED 259
           +YV  L   V E  +   F  FG++    + +         +AFVEFE+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEE 49

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

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED 259
           +YV NL  +V+E  +AE F + G + S  ++     D    YAFVE+ D
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGND---PYAFVEYYD 46

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|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 41.3 bits (97), Expect = 4e-04
 Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 6/59 (10%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
             V+VRNLP  V E+++ E    FG +S   ++   R+      A VEFED    +  V
Sbjct: 3   PVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQ------ALVEFEDEESAKACV 55

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

>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal Mei2-like proteins

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 7/57 (12%)

Query: 213 VRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV 269
           V  +P  VS S + E F+K G++   G+ ++     GI    V F D   +R A++ 
Sbjct: 6   VTGVPKDVSTSNLKEIFEKMGDVK--GIFVKKLLSKGIVI--VSFHD---LRQAIKA 55

This subgroup corresponds to the RRM1 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif. . Length = 72

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

 Score = 38.0 bits (88), Expect = 5e-04
 Identities = 18/58 (31%), Positives = 36/58 (62%), Gaps = 1/58 (1%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDM 260
           +D+   +++++ NL  +VSE E+   F K+G +  E V+ R  +  G  YAF++F+++
Sbjct: 3   DDQRATRNLFIGNLDHNVSEVELRRAFDKYGII-EEVVIKRPARGQGGAYAFLKFQNL 59

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

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 23/62 (37%), Positives = 35/62 (56%), Gaps = 3/62 (4%)

Query: 206 EEIK-SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVR 264
           EEI+ ++YV NL P+ +  ++ E F + GE+    V +   +     YAFVEF + T V 
Sbjct: 1   EEIRRTIYVGNLDPTTTADQLLEFFSQAGEVKY--VRMAGDETQPTRYAFVEFAEQTSVI 58

Query: 265 NA 266
           NA
Sbjct: 59  NA 60

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|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGI--CYAFVEF 257
            ++ +R LP SV+E +I       G +  + V +  RK  G    +AFVEF
Sbjct: 3   NTIMLRGLPLSVTEEDIRNALVSHG-VEPKDVRLMRRKTTGASRGFAFVEF 52

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, 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. Both, RBM5 and RBM10, 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 = 81

>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 = 37.2 bits (87), Expect = 6e-04
 Identities = 15/59 (25%), Positives = 34/59 (57%), Gaps = 6/59 (10%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV 269
           +++RNLPP V+ES++      FG++++  +++R +       A VE + +   ++ V+ 
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNV-LLLRGKNQ-----ALVEMDSVESAKSMVDY 54

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

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 13/57 (22%), Positives = 25/57 (43%)

Query: 213 VRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV 269
           V  LP  +++ E+   F+  G + S  +V        + Y FV++ D    + A+  
Sbjct: 5   VNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

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|240754 cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split end) protein family

 Score = 37.2 bits (87), Expect = 7e-04
 Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 8/62 (12%)

Query: 209 KSVYVRNLPPSVSESEIAE----EFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVR 264
           K++ V NLP  +S+ +I +    EFKKFG++S    V           A+V F      R
Sbjct: 2   KTLCVSNLPSKLSDEDIEDVLYHEFKKFGDVS----VRVLHDGEDERVAYVNFRHPEDAR 57

Query: 265 NA 266
            A
Sbjct: 58  EA 59

This subfamily corresponds to the RRM1 domain in the Spen (split end) 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 possesses 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 known as 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 36.8 bits (86), Expect = 8e-04
 Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 8/58 (13%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++V NLP + +  E+   F+K+G ++   VV    K+    Y FV  E+     +A++
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVV----KN----YGFVHMEEEEDAEDAIK 51

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

 Score = 36.9 bits (85), Expect = 9e-04
 Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 8/61 (13%)

Query: 208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
           +K ++VRNL  +V+E  + + F +FG+L      ++  KD    YAF+ F++  G   A+
Sbjct: 1   VKVLFVRNLANTVTEEILEKAFGQFGKLER----VKKLKD----YAFIHFDERDGAVKAM 52

Query: 268 E 268
           E
Sbjct: 53  E 53

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|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 15/69 (21%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----------RSRKDVGICYAFVEFED 259
            VY+ NL  S SE ++ E  K F  +S   V+I          R  + +GI  A+ EF  
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDFEPVS---VLIPSQTVRGFRSRRVRPLGI--AYAEFSS 55

Query: 260 MTGVRNAVE 268
                  V+
Sbjct: 56  PEQAEKVVK 64

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR-KDVGICYAFVEFEDMTGVRNAVE 268
           ++ V+NL P VS   + + F +FGE+    V++  R +  G     VEF    G + A++
Sbjct: 1   ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTG--EGIVEFSRKPGAQAAIK 58

Query: 269 VC 270
            C
Sbjct: 59  RC 60

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|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 3/54 (5%)

Query: 213 VRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNA 266
           VR+LPP +SE +  +  K FG  +S   V+  R  +    AF  F++      A
Sbjct: 4   VRHLPPELSEDDKEDLLKHFG--ASSVRVMSRRGKLKNT-AFATFDNEQAASQA 54

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|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 6/60 (10%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC 270
           V+VR LP  V+E+++ E   +FG +S   ++ + R+      A VEFED++  +  V   
Sbjct: 5   VHVRGLPDGVTEADLVEALSEFGPISYVTMMPKKRQ------ALVEFEDISDAKACVNHA 58

This subfamily corresponds to the RRM1 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). . Length = 80

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

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 17/60 (28%), Positives = 32/60 (53%), Gaps = 4/60 (6%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMTGVRNAVE 268
           VY+R LPP+ ++ ++ +  + FG++ S   ++   K    C  Y FV+F+       A+E
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAIL--DKKTNKCKGYGFVDFDSPEAALKAIE 60

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

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 4/57 (7%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNA 266
           +V V+NLP   +E++I + FK  GE+    +V    +  G   A +EFE       A
Sbjct: 2   TVKVKNLPKDTTENKIRQFFKDCGEIREVKIV----ESEGGLVAVIEFETEDEALAA 54

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|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 10/70 (14%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGEL------SSEGVVIRSRKDVGICYAFVEFEDMTG 262
           + V+V  LPP + E EI   F++FG L       +E       K     YAF+ F++ + 
Sbjct: 1   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKG----YAFLLFQEESS 56

Query: 263 VRNAVEVCIL 272
           V+  ++ CI 
Sbjct: 57  VQALIDACIE 66

This subgroup corresponds to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and CPEB-4, all well-conserved in both, vertebrates and invertebrates. Due to the high sequence similarity, members in this family may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All family members contain an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. In addition, they do have conserved nuclear export signals that are not present in CPEB-1. . Length = 92

>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 = 36.4 bits (85), Expect = 0.001
 Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 4/60 (6%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI--RSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++V  L    +E E+   F KFG +    ++    + +  G  + FV FE +     A+ 
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRG--FGFVTFESVEDADAAIR 61

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

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 5/58 (8%)

Query: 213 VRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMTGVRNAVE 268
           VRNLP   +E+++ + F  FG +    V I  RK  G    +AFV+F        A++
Sbjct: 4   VRNLPFKCTEADLKKLFSPFGFVWE--VTI-PRKPDGKKKGFAFVQFTSKADAEKAIK 58

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFED 259
           VY+ +LP    E E+ + F +FG + +   + RS+K      YAFVEFE 
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTV-TRLRLSRSKKTGKSKGYAFVEFES 50

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 12/26 (46%), Positives = 18/26 (69%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELS 236
           ++V NLP  ++E E  E F K+GE+S
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVS 29

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 21/57 (36%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNA 266
           +V+V NL  SV E E+ + F K GE+ ++  ++++ K     YA+VEFE+   V+ A
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEI-TDVRLVKNYKGKSKGYAYVEFENEESVQEA 56

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|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 212 YVRNLPPSVSESEIAEEFKKFGELSSEGVVIRS--RKDVGICYAFVEFED 259
           +V  +P + ++ EI EEF K  E   + +V RS   K+    +AFVE+E 
Sbjct: 5   FVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYES 54

This subfamily corresponds to the RRM2 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 bind 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), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

>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 = 35.7 bits (83), Expect = 0.002
 Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 6/49 (12%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFE 258
           +VYV NLP  ++E E+   F  FG +      +R  KD G  YAFV F+
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEE----VRVFKDKG--YAFVRFD 44

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

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 12/52 (23%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDM 260
           +YVR  PP  SES I E F  +G +          K+V +   +AFVEFE +
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAV----------KEVKMISNFAFVEFESL 43

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

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 12/59 (20%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGI--CYAFVEFEDMTGVRNAV 267
           VY+  LP    E ++   FK +G +          +++ +   + FVEFED     +AV
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRI----------REINLKNGFGFVEFEDPRDADDAV 50

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

 Score = 38.8 bits (90), Expect = 0.002
 Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 13/71 (18%)

Query: 192 WADTGEEISAVEDEEEIKSV---YVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV 248
           WA+  EE+    DE+ +  V   YVRNL  + +E  I + F +F     E V  +  +D 
Sbjct: 218 WAEPEEEV----DEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERV--KKIRD- 270

Query: 249 GICYAFVEFED 259
              YAFV FED
Sbjct: 271 ---YAFVHFED 278

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 17/63 (26%)

Query: 211 VYVRNLPPS-VSESEIAEEFKKFGELSSEGVVIRSRKDVGIC----YAFVEFEDMTGVRN 265
           V+V NL    VS+ ++ E F K+G            K +GI     Y FV+F++    R 
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYG------------KILGISLHKGYGFVQFDNEEDARA 50

Query: 266 AVE 268
           AV 
Sbjct: 51  AVA 53

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|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 = 35.3 bits (82), Expect = 0.003
 Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 6/54 (11%)

Query: 213 VRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNA 266
           V+NLP   +E E+ E F+KFG L    +++   + + +    VEF + +  R A
Sbjct: 5   VKNLPFGTTEEELRELFEKFGSLGR--LLLPPSRTIAL----VEFLEPSDARKA 52

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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 2/34 (5%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRS 244
           V+V NLP +  + ++ + FK+FG + S  V  RS
Sbjct: 3   VFVGNLPLTTKKKDLKKLFKQFGPIES--VRFRS 34

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

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 4/60 (6%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG-IC-YAFVEFEDMTGVRNAVE 268
           VYV  LP + +   +   F K+G +    V +   K  G I  +AF+EFE     + A +
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTV--VYVSLPRYKHTGDIKGFAFIEFETPEEAQKACK 59

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|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 35.0 bits (81), Expect = 0.003
 Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 6/54 (11%)

Query: 213 VRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNA 266
           V+NLP     +E+ E F KFG L    V++      GI  A VEF + +  + A
Sbjct: 5   VKNLPAGTLTAELRELFSKFGSLGR--VLLPPA---GIT-AIVEFLEPSEAKLA 52

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

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 14/62 (22%), Positives = 36/62 (58%)

Query: 207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNA 266
           E  ++++ +LP   +++++A+ F  FG + S  V I  + ++  C+ FV +++    + A
Sbjct: 3   EGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAA 62

Query: 267 VE 268
           ++
Sbjct: 63  IQ 64

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

 Score = 35.2 bits (82), Expect = 0.004
 Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 12/56 (21%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGV-VIR------SRKDVGICYAFVEF 257
            ++ +R L    +E +I +       +  + V +IR      SR      +AFVEF
Sbjct: 3   NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSR-----GFAFVEF 53

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	275
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	100.0
KOG2104	126	consensus Nuclear transport factor 2 [Intracellula	99.77
cd00780	119	NTF2 Nuclear transport factor 2 (NTF2) domain play	99.43
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.43
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.34
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.31
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.26
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.22
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.19
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.18
PLN03120	260	nucleic acid binding protein; Provisional	99.18
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.16
PF02136	118	NTF2: Nuclear transport factor 2 (NTF2) domain; In	99.15
PLN03121	243	nucleic acid binding protein; Provisional	99.13
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.09
smart00362	72	RRM_2 RNA recognition motif.	99.07
KOG0122	270	consensus Translation initiation factor 3, subunit	99.07
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.06
PLN03213	759	repressor of silencing 3; Provisional	99.05
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.05
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.01
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.99
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.99
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	98.99
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	98.98
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.95
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	98.95
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.94
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	98.94
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.9
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.88
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	98.86
smart00360	71	RRM RNA recognition motif.	98.85
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	98.84
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.82
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.82
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.82
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.75
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	98.75
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.73
KOG4353	139	consensus RNA export factor NXT1 [RNA processing a	98.73
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.67
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.67
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.66
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.6
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.6
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.6
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	98.59
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.57
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.54
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	98.53
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.53
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.53
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.52
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.52
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.5
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.46
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.41
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.35
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.33
smart00361	70	RRM_1 RNA recognition motif.	98.29
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.29
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.27
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.24
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.23
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.23
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.22
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.18
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.16
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.12
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.11
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.05
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.04
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	97.99
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	97.95
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.87
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	97.82
KOG0226	290	consensus RNA-binding proteins [General function p	97.76
KOG0151	877	consensus Predicted splicing regulator, contains R	97.76
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	97.71
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.68
KOG4660	549	consensus Protein Mei2, essential for commitment t	97.63
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.59
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	97.48
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.47
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.4
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.36
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.3
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.26
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.2
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.13
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.08
KOG4210	285	consensus Nuclear localization sequence binding pr	96.72
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	96.59
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	96.57
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.47
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.33
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	95.97
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	95.8
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	95.74
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	95.72
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	95.66
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	95.29
KOG1995	351	consensus Conserved Zn-finger protein [General fun	95.08
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	94.76
KOG1855	484	consensus Predicted RNA-binding protein [General f	94.71
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	94.58
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	94.55
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	94.55
COG5175	480	MOT2 Transcriptional repressor [Transcription]	94.44
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.36
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	92.89
KOG2314	698	consensus Translation initiation factor 3, subunit	92.85
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	91.91
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	90.7
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	90.29
KOG3152	278	consensus TBP-binding protein, activator of basal	89.96
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	89.92
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	89.77
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	89.68
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	89.19
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	88.86
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	88.31
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	85.86
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	85.3
PF10429	166	Mtr2: Nuclear pore RNA shuttling protein Mtr2; Int	83.68
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	83.2
KOG2068	327	consensus MOT2 transcription factor [Transcription	83.06
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	83.05
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	82.92

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

Probab=100.00  E-value=5e-39  Score=303.24  Aligned_cols=264  Identities=28%  Similarity=0.463  Sum_probs=158.1

Q ss_pred             CCCCcc--ceEEeeeeecccCCCcEEEEEEeEEEecCccccccceeEEEeeecCCCCeEeecCccc-cccccCCCC----
Q 023954            1 MSLNYS--GIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQ-AREYVSPVD----   73 (275)
Q Consensus         1 ~sl~f~--~~~i~t~D~q~s~~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~~-~~~~~~~~~----   73 (275)
                      |+|+|+  +++|+|+|+|.||++||||||||.|+.+| ..+|+|+|||||+||++|| ||+||.|+ ..+.+.++.    
T Consensus        68 ~sld~~~~s~eI~tvdsQ~S~~~GvvI~VtG~lt~~~-~~rRkF~QtFfLapq~~~y-fVlNDiFRfvde~~~~e~~~~~  145 (419)
T KOG0116|consen   68 MSLDYEVCSVEISTVDSQASLEKGVVIMVTGYLTNKD-GPRRKFSQTFFLAPQEKGY-FVLNDIFRFVDEEFEPEANTDE  145 (419)
T ss_pred             eecCCCceeEEEEEEehhhhccCCeEEEEEEEEEeCC-CcceEEEEEEEEeecCCce-EEEechhhhccccccccccccc
Confidence            789999  89999999999999999999999999999 8899999999999999865 99999975 221111111    


Q ss_pred             CCCCC------------CCCCCCCCccccccCCCccc-cccC--CCccc-ccccCCCcCCCCCCCCCCCCCCCCCCCCCC
Q 023954           74 VKQNG------------LIDDYSFPEQRLQQVPESEN-ILED--SPAEE-LNGSLQNAVNAAQDYLPASVEEPVGEPQKH  137 (275)
Q Consensus        74 ~~~~~------------~~~~~~~~e~~~~~~~e~~~-v~e~--~~~ee-~~~~~~~~~~~~~~~~~~~~~~~~ee~pkk  137 (275)
                      +.+..            .+......+.+.......+. |.++  ..++. ...+.+.... ++......+..++.+++|+
T Consensus       146 vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~~~~~~~~~~~~~~~ee~v-~~~~~~~~p~~~~~~~~~~  224 (419)
T KOG0116|consen  146 VPEANPAVVVSVEKASQLVEAVVESEPEPEPEPKAEDEVEVPEEATVEDEAKEKTKEELV-IQQTVSEAPAAPQGDAPKK  224 (419)
T ss_pred             CCCCCcceeecccccccccccccccCCCCcccccccCceeccccccccccccccCchhhc-ccccccCCCccccccccch
Confidence            11000            00000000000000000000 1110  11110 1111111111 1111111222337899999


Q ss_pred             chHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCcccccCccccCCCCCCCCcCCccccccCCCcEEEEcCC
Q 023954          138 TYASILRVAKGQSTPSVTPQPSVSKNISPVSDWNH-VPQPTTQQETVSSYAYEKSWADTGEEISAVEDEEEIKSVYVRNL  216 (275)
Q Consensus       138 syAsiv~~~k~~~~~~~~~~~p~~~~~~p~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ifV~nL  216 (275)
                      +||||++.++....+......|...     .++++ ...+.+.....++........   .+.+..+.......|||+||
T Consensus       225 s~asv~~~~~~~~~~~~~~~~p~~~-----~~~~~p~~~~~~~~~s~~~~p~~~~~~---~n~~~~~~~~~~~~i~V~nl  296 (419)
T KOG0116|consen  225 SFASVVKVLKKSAAVQQSKGSPPQI-----QPQQQPSTKPQAERQSKPPSPVRESKS---GNSNNQEPRADGLGIFVKNL  296 (419)
T ss_pred             hhhhhhhhcccccccceeccCCCcc-----ccccCCccCcchhhccCCCCccccccc---cccCCcceeecccceEeecC
Confidence            9999999987766552222211111     11111 011110011111111111111   12233444556777999999


Q ss_pred             CCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccCC
Q 023954          217 PPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMWH  275 (275)
Q Consensus       217 p~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~ig  275 (275)
                      |++++.++|+++|++||.|+.++|.++...+.+.|||||+|++.+++++||+|++++||
T Consensus       297 P~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig  355 (419)
T KOG0116|consen  297 PPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIG  355 (419)
T ss_pred             CCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccC
Confidence            99999999999999999999888888875444469999999999999999999999997

>KOG2104 consensus Nuclear transport factor 2 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.77  E-value=4.5e-19  Score=137.85  Aligned_cols=63  Identities=27%  Similarity=0.440  Sum_probs=59.3

Q ss_pred             CCCCcc--ceEEeeeeecccCCCcEEEEEEeEEEecCccccccceeEEEeeecCCCCeEeecCccc
Q 023954            1 MSLNYS--GIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQ   64 (275)
Q Consensus         1 ~sl~f~--~~~i~t~D~q~s~~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~~   64 (275)
                      .||||+  +|.|+|+||||+..|||||||+|+|++++ ++.++|+|+|+|.|..+|.|||.||.|+
T Consensus        56 ~sLpFqkiqh~IttvD~QPt~~g~ilv~V~G~Lk~dE-d~~~~FsQvF~L~~n~~~~~~v~ndiFR  120 (126)
T KOG2104|consen   56 TSLPFQKIQHSITTVDSQPTPDGGILVMVVGQLKLDE-DPILRFSQVFLLKPNIQGSYYVFNDIFR  120 (126)
T ss_pred             hcCChhhhhceeeecccccCCCCcEEEEEeeeeeecc-CCccceeeEEEEeEcCCCCEEEEeeeEE
Confidence            489999  89999999999999999999999999996 9999999999999998888899999974

>cd00780 NTF2 Nuclear transport factor 2 (NTF2) domain plays an important role in the trafficking of macromolecules, ions and small molecules between the cytoplasm and nucleus

Probab=99.43  E-value=2.3e-13  Score=108.46  Aligned_cols=61  Identities=38%  Similarity=0.554  Sum_probs=55.2

Q ss_pred             CCCCcc--ceEEeeeeecccCCCcEEEEEEeEEEecCccccccceeEEEeeecCCCCeEeecCcc
Q 023954            1 MSLNYS--GIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEI   63 (275)
Q Consensus         1 ~sl~f~--~~~i~t~D~q~s~~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~   63 (275)
                      ++|+++  +|+|.++|||++.++||||+|+|.|+.++ +..|+|+|+|+|.+++ +.|||.||.+
T Consensus        53 ~~lp~~~~~~~i~~~d~q~~~~~~ili~V~G~~~~~~-~~~~~F~q~F~L~~~~-~~~~I~nD~f  115 (119)
T cd00780          53 SSLPFQKTKHKITTVDSQPTPSGGVIVMVTGSLKLDE-QPPRKFSQTFVLAPQN-GGYFVLNDIF  115 (119)
T ss_pred             HhCCCcceEEEEEEEeeeEcCCCCEEEEEEEEEEECC-CCceeEeEEEEEEecC-CeEEEEeeEE
Confidence            367853  99999999999999999999999999998 8899999999999999 4559999986

This bi-directional transport of macromolecules across the nuclear envelope requires many soluble factors that includes GDP-binding protein Ran (RanGDP). RanGDP is required for both import and export of proteins and poly(A) RNA. RanGDP also has been implicated in cell cycle control, specifically in mitotic spindle assembly. In interphase cells, RanGDP is predominately nuclear and thought to be GTP bound, but it is also present in the cytoplasm, probably in the GDP-bound state. NTF2 mediates the nuclear import of RanGDP. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins.

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

Probab=99.43  E-value=3.3e-13  Score=117.29  Aligned_cols=68  Identities=22%  Similarity=0.384  Sum_probs=60.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc-CccCC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC-ILMWH  275 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~-pi~ig  275 (275)
                      ...++||||||+|.++.+.|++.|++||+|.  ...|..|+.++  ||||||+|.|.++|.||++.. ||+.|
T Consensus        10 T~~TKifVggL~w~T~~~~l~~yFeqfGeI~--eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdG   80 (247)
T KOG0149|consen   10 TTFTKIFVGGLAWETHKETLRRYFEQFGEIV--EAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDG   80 (247)
T ss_pred             ceEEEEEEcCcccccchHHHHHHHHHhCceE--EEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccc
Confidence            4678999999999999999999999999999  78888888766  899999999999999999876 66544

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

Probab=99.34  E-value=4.7e-12  Score=104.60  Aligned_cols=62  Identities=16%  Similarity=0.400  Sum_probs=56.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+||++++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|++||+..
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~--~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~l   96 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVV--DAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM   96 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeE--EEEEEecCCCCCcceEEEEEECCHHHHHHHHHHc
Confidence            468999999999999999999999999999  88887776554  899999999999999999853

>PF00076 RRM_1: RNA recognition motif

Probab=99.31  E-value=7.5e-12  Score=88.92  Aligned_cols=58  Identities=36%  Similarity=0.646  Sum_probs=52.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCceeEceEEEecC-CCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR-KDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       211 ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~-~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      |||+|||.++++++|+++|++||.|.  .+.+..+ .+..+|||||+|.+.++|++||+..
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~--~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l   59 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIE--SIKVMRNSSGKSKGYAFVEFESEEDAEKALEEL   59 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEE--EEEEEEETTSSEEEEEEEEESSHHHHHHHHHHH
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcc--cccccccccccccceEEEEEcCHHHHHHHHHHc
Confidence            79999999999999999999999998  8888774 4444899999999999999999843

(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=99.26  E-value=3.4e-11  Score=112.10  Aligned_cols=63  Identities=22%  Similarity=0.308  Sum_probs=56.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..+++|||+|||+++++++|+++|++||.|.  .++|..++.++  ||||||.|.+.++|.+||++.
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~--~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~l  331 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQ--NVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL  331 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeE--EEEEeEcCCCCCccceEEEEECCHHHHHHHHHHh
Confidence            4567899999999999999999999999999  88887776444  999999999999999999864

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

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.22  E-value=4e-11  Score=85.97  Aligned_cols=62  Identities=34%  Similarity=0.563  Sum_probs=52.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhcC-ccC
Q 023954          211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVCI-LMW  274 (275)
Q Consensus       211 ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~p-i~i  274 (275)
                      |||+|||+++++++|+++|..||.|.  .+.+..++. ..+|+|||+|.+.++|.+||+... .+|
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~--~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~   64 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVE--KVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEI   64 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEE--EEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcc--eEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEE
Confidence            79999999999999999999999998  888877654 338999999999999999999886 554

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 ....

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

Probab=99.19  E-value=8.4e-11  Score=106.63  Aligned_cols=62  Identities=23%  Similarity=0.315  Sum_probs=56.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||.|||+...+.||+.+|.+||+|.  +|.|+.+..-+||||||+|++.++|+||-++.
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~Vl--dVEIIfNERGSKGFGFVTmen~~dadRARa~L  156 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVL--DVEIIFNERGSKGFGFVTMENPADADRARAEL  156 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCcee--eEEEEeccCCCCccceEEecChhhHHHHHHHh
Confidence            468999999999999999999999999999  89988876556999999999999999997765

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.18  E-value=7e-11  Score=109.99  Aligned_cols=60  Identities=25%  Similarity=0.444  Sum_probs=55.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..+|||+|||.++++++|+++|++||.|.  .|+|+.++.++  +|||||+|.+.++|.+||+.
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~--~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~   64 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIE--SCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS   64 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEE--EEEEEEcCCCCccceEEEEEECcHHHHHHHHhh
Confidence            57999999999999999999999999999  88888876554  89999999999999999975

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

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.18  E-value=8.6e-11  Score=104.94  Aligned_cols=64  Identities=25%  Similarity=0.344  Sum_probs=56.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      .++|||+||++.+++++|+++|+.||.|.  .|.|..++. .+|||||+|.+.+++..||.-+...|
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~--~V~I~~d~~-~~GfAFVtF~d~eaAe~AllLnG~~l   67 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIE--YVEMQSENE-RSQIAYVTFKDPQGAETALLLSGATI   67 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEeecCC-CCCEEEEEeCcHHHHHHHHHhcCCee
Confidence            58999999999999999999999999999  888877754 47999999999999999998665444

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.16  E-value=1.2e-10  Score=109.10  Aligned_cols=64  Identities=22%  Similarity=0.408  Sum_probs=57.4

Q ss_pred             ccCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          204 DEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       204 ~~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .....++|||+|||+++++++|+++|+.||.|.  .|+|+.++.++  ||||||+|.+.++|.+||+.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~--~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~  168 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPIN--TCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKN  168 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEecCCCCccCcEEEEEEccHHHHHHHHHH
Confidence            445689999999999999999999999999999  88887776554  89999999999999999975

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).

>PF02136 NTF2: Nuclear transport factor 2 (NTF2) domain; InterPro: IPR002075 Nuclear transport factor 2 (NTF2) is a homodimer which stimulates efficient nuclear import of a cargo protein

Probab=99.15  E-value=4.8e-11  Score=94.18  Aligned_cols=61  Identities=28%  Similarity=0.400  Sum_probs=52.7

Q ss_pred             CCCcc--ceEEeeeeec--ccCCCcEEEEEEeEEEecCccccccceeEEEeeecCCCCeEeecCcc
Q 023954            2 SLNYS--GIEIKTAHSL--ESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEI   63 (275)
Q Consensus         2 sl~f~--~~~i~t~D~q--~s~~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~   63 (275)
                      +|++.  ++.|+++|||  .+.+++|+|.|+|.++.++....|+|+|+|+|.+.+ +.|||.||.+
T Consensus        52 ~l~~~~~~~~i~~~d~qp~~~~~~~i~i~v~G~~~~~~~~~~~~F~q~FvL~~~~-~~~~I~nd~~  116 (118)
T PF02136_consen   52 SLPATGVQHRITSVDCQPSPSSDGSILITVTGQFKEDDNPNPRRFSQTFVLVPQN-NGYFIANDIF  116 (118)
T ss_dssp             HHTTSSEEEEEEEEEEEEEEECCSEEEEEEEEEEEETTSEEEEEEEEEEEEEEET-TEEEEEEEEE
T ss_pred             cCCCcccEEEecccccccccccCCcEEEEEEeEEEecCCCcccEEEEEEEEEEcC-CEEEEEeeEE
Confidence            35666  7999999999  578999999999999999944479999999999999 5569999975

NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins. NTF2 folds into a cone with a deep hydrophobic cavity, the opening of which is surrounded by several negatively charged residues. RanGDP binds to NTF2 by inserting a conserved phenylalanine residue into the hydrophobic pocket of NTF2 and making electrostatic interactions with the conserved negatively charged residues that surround the cavity []. This entry represent the main structural domain of NTF2 and related domains which are found in other nuclear import proteins.; GO: 0006810 transport, 0005622 intracellular; PDB: 3UJM_B 1JKG_B 1JN5_B 1M98_A 3MG1_A 3MG2_A 3MG3_B 2Z76_A 2Z7A_D 2Z77_A ....

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.13  E-value=2.2e-10  Score=101.03  Aligned_cols=65  Identities=25%  Similarity=0.342  Sum_probs=58.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      .+++|||+||++.+|+++|+++|+.||.|.  .|.|..++.+ +|||||+|.+.+++..||..+.-.|
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~--~V~I~~D~et-~gfAfVtF~d~~aaetAllLnGa~l   68 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIE--HVEIIRSGEY-ACTAYVTFKDAYALETAVLLSGATI   68 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeE--EEEEecCCCc-ceEEEEEECCHHHHHHHHhcCCCee
Confidence            579999999999999999999999999999  8998887543 5899999999999999998775544

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

Probab=99.09  E-value=3.1e-10  Score=101.83  Aligned_cols=67  Identities=27%  Similarity=0.453  Sum_probs=61.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc-CccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC-ILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~-pi~i  274 (275)
                      +..++|||+-|++++++..|+..|.+||.|+  .|.|+.++.+|  +|||||+|++.-++..|.+.. .++|
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~Ik--rirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~I  168 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIK--RIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKI  168 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcce--eEEEeeecccCCccceEEEEeccHHHHHHHHHhccCcee
Confidence            5789999999999999999999999999999  99999987776  899999999999999998876 6665

>smart00362 RRM_2 RNA recognition motif

Probab=99.07  E-value=7.9e-10  Score=77.38  Aligned_cols=60  Identities=37%  Similarity=0.622  Sum_probs=53.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcC
Q 023954          210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCI  271 (275)
Q Consensus       210 ~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~p  271 (275)
                      +|||+|||.+++.++|+++|.+||.+.  .+.+..+++..+|+|||+|.+.+.|++|++...
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~--~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~   60 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIE--SVKIPKDTGKSKGFAFVEFESEEDAEKAIEALN   60 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEE--EEEEecCCCCCCceEEEEeCCHHHHHHHHHHhC
Confidence            589999999999999999999999999  777776655558999999999999999998654

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

Probab=99.07  E-value=3.3e-10  Score=99.22  Aligned_cols=63  Identities=29%  Similarity=0.502  Sum_probs=58.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+..+|-|.||+.++++.+|+++|.+||.|.  .+.|..++.+|  ||||||.|.++++|.+||...
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~--rvylardK~TG~~kGFAFVtF~sRddA~rAI~~L  251 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPIT--RVYLARDKETGLSKGFAFVTFESRDDAARAIADL  251 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccc--eeEEEEccccCcccceEEEEEecHHHHHHHHHHc
Confidence            3678899999999999999999999999999  89999998888  999999999999999999764

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

Probab=99.06  E-value=4.1e-10  Score=111.87  Aligned_cols=62  Identities=26%  Similarity=0.399  Sum_probs=56.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+||++++++++|+++|.+||.|.  .|.+..++.++  ||||||+|.+.++|++||+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~--sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~l  169 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIK--SINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM  169 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEE--EEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhc
Confidence            568999999999999999999999999999  88887776554  899999999999999999753

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.

>PLN03213 repressor of silencing 3; Provisional

Probab=99.05  E-value=4.3e-10  Score=106.79  Aligned_cols=61  Identities=16%  Similarity=0.300  Sum_probs=53.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCH--HHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDM--TGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~--~~a~~Ai~a~  270 (275)
                      ..+.+||||||++.+++++|+.+|..||.|.  .+.|+  +.+|||||||+|...  .++.+||.+.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVk--dVEIp--RETGRGFAFVEMssdddaEeeKAISaL   70 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVD--AVEFV--RTKGRSFAYIDFSPSSTNSLTKLFSTY   70 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCee--EEEEe--cccCCceEEEEecCCcHHHHHHHHHHh
Confidence            4578999999999999999999999999999  88888  445699999999987  6789998754

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.05  E-value=5.1e-10  Score=104.95  Aligned_cols=61  Identities=26%  Similarity=0.449  Sum_probs=55.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++|||+|||.++++++|+++|++||.|.  .+.|..++.++  ||||||+|.+.++|++||++.
T Consensus       193 ~~~lfV~nLp~~vtee~L~~~F~~fG~V~--~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~l  255 (346)
T TIGR01659       193 DTNLYVTNLPRTITDDQLDTIFGKYGQIV--QKNILRDKLTGTPRGVAFVRFNKREEAQEAISAL  255 (346)
T ss_pred             cceeEEeCCCCcccHHHHHHHHHhcCCEE--EEEEeecCCCCccceEEEEEECCHHHHHHHHHHh
Confidence            46899999999999999999999999999  78887776554  899999999999999999864

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

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

Probab=99.01  E-value=8.3e-10  Score=109.69  Aligned_cols=62  Identities=23%  Similarity=0.497  Sum_probs=56.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC--CccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV--GICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~--grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+||++++++++|+++|++||.|.  .++|..++.+  .||||||+|++.++|.+||++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~--svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~am  266 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIV--KCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM  266 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCee--EEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHh
Confidence            468999999999999999999999999999  8888877554  4899999999999999999865

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.

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

Probab=98.99  E-value=1.2e-09  Score=102.17  Aligned_cols=67  Identities=19%  Similarity=0.370  Sum_probs=61.4

Q ss_pred             ccCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCc
Q 023954          204 DEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCIL  272 (275)
Q Consensus       204 ~~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi  272 (275)
                      .+.+.-++||+.+|+.++|.+|+.+|++||.+.  .|.|.+||.++  +|||||.|.+++++.+||.|++-
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~--einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn   98 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVY--EINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHN   98 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCcee--EEEeecccccCcccceEEEEeccHHHHHHHHHHhhc
Confidence            345678999999999999999999999999999  89999998877  99999999999999999998853

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

Probab=98.99  E-value=1.4e-09  Score=105.02  Aligned_cols=66  Identities=26%  Similarity=0.346  Sum_probs=58.5

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCc
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCIL  272 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi  272 (275)
                      ....++|||+|||.++++++|+++|++||.|.  .|.|+.++.++  +|||||+|.+.++|.+||.....
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~--~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~  153 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVR--DVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQ  153 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCee--EEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCC
Confidence            34578999999999999999999999999999  88888776555  89999999999999999986643

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.

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

Probab=98.99  E-value=7e-10  Score=88.53  Aligned_cols=62  Identities=24%  Similarity=0.374  Sum_probs=54.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+||++.+++++|.++|+++|.|+  .|.+-.++.+.  .|||||+|-+.++|..||+-
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~ir--riiMGLdr~kktpCGFCFVeyy~~~dA~~Alry   97 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIR--RIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRY   97 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchh--eeEeccccCCcCccceEEEEEecchhHHHHHHH
Confidence            4679999999999999999999999999999  66665555443  79999999999999999863

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

Probab=98.98  E-value=7.9e-10  Score=92.53  Aligned_cols=59  Identities=34%  Similarity=0.506  Sum_probs=52.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      -.++|||+||+..+++.+|+.+|.+||.|.  .|+|-.+   ..|||||+|++..+|..|+.+.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lr--svWvArn---PPGfAFVEFed~RDA~DAvr~L   67 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLR--SVWVARN---PPGFAFVEFEDPRDAEDAVRYL   67 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcce--eEEEeec---CCCceEEeccCcccHHHHHhhc
Confidence            468999999999999999999999999999  8888653   3689999999999999998765

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

Probab=98.95  E-value=2.5e-09  Score=102.67  Aligned_cols=66  Identities=41%  Similarity=0.627  Sum_probs=59.9

Q ss_pred             cccCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       203 ~~~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ++...+.+|||+|||+++|+++|..+|.+||.|.  .+.|..++.++  +|.|||.|.+...++.||++.
T Consensus       287 en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~--ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~A  354 (678)
T KOG0127|consen  287 ENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVK--YAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAA  354 (678)
T ss_pred             ccccccceEEEecCCccccHHHHHHHHHhhccce--eEEEEeccCCCCcccceEEEeccHHHHHHHHHhc
Confidence            3445789999999999999999999999999999  88888777766  899999999999999999876

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

Probab=98.95  E-value=2.1e-09  Score=82.87  Aligned_cols=60  Identities=28%  Similarity=0.513  Sum_probs=52.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..+-|||+|||+++|.+++.++|++||.|.  .|+|-..+++ +|-|||.|++..+|.+|++-
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~Ir--QIRiG~~k~T-rGTAFVVYedi~dAk~A~dh   76 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIR--QIRIGNTKET-RGTAFVVYEDIFDAKKACDH   76 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceE--EEEecCccCc-CceEEEEehHhhhHHHHHHH
Confidence            467899999999999999999999999999  6766554432 89999999999999999874

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

Probab=98.94  E-value=2.3e-09  Score=106.18  Aligned_cols=62  Identities=24%  Similarity=0.331  Sum_probs=55.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+++|||+|||+++++++|+++|++||.|.  .++|+++. +.+||||||+|.+.++|++||+..
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~--~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~l  119 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIY--ELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLL  119 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEE--EEEEEECCCCCccceEEEEeCCHHHHHHHHHHc
Confidence            469999999999999999999999999999  78887663 344999999999999999999874

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.

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

Probab=98.94  E-value=2.8e-09  Score=104.23  Aligned_cols=62  Identities=27%  Similarity=0.466  Sum_probs=55.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+.+++++|+++|+.||.|.  .+.+..+..+|  +|||||+|.+.+.|..||+..
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~--~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l  357 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLK--AFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL  357 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCee--EEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHc
Confidence            568999999999999999999999999999  78877665444  899999999999999999864

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

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

Probab=98.94  E-value=2.3e-09  Score=106.44  Aligned_cols=59  Identities=29%  Similarity=0.539  Sum_probs=54.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       210 ~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +|||+|||.++|+++|+++|++||.|.  .|+|..++.++  +|||||+|.+.++|++||+..
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~--~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~l   62 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVL--SVRVCRDSVTRRSLGYGYVNFQNPADAERALETM   62 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEecCCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            799999999999999999999999999  89988876544  899999999999999999765

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

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

Probab=98.90  E-value=4.8e-09  Score=91.26  Aligned_cols=62  Identities=34%  Similarity=0.547  Sum_probs=56.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC--CccEEEEEeCCHHHHHHHHHhcC
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV--GICYAFVEFEDMTGVRNAVEVCI  271 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~--grgfgFV~F~~~~~a~~Ai~a~p  271 (275)
                      .++|||+||++.+++++|+++|++||.+.  .+.+..++.+  .+|||||+|.+.+++..||+...
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~--~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~  178 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVK--RVRLVRDRETGKSRGFAFVEFESEESAEKAIEELN  178 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCcee--EEEeeeccccCccCceEEEEecCHHHHHHHHHHcC
Confidence            69999999999999999999999999998  8888877644  49999999999999999998763

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

Probab=98.88  E-value=2.3e-09  Score=90.60  Aligned_cols=61  Identities=33%  Similarity=0.569  Sum_probs=54.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||.++.+.+|+++|-+||.|.  .|.|....+ ..+||||+|++..+|+.||...
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~--~ieLK~r~g-~ppfafVeFEd~RDAeDAiygR   65 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIR--EIELKNRPG-PPPFAFVEFEDPRDAEDAIYGR   65 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceE--EEEeccCCC-CCCeeEEEecCccchhhhhhcc
Confidence            468999999999999999999999999999  888765432 3789999999999999999764

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

Probab=98.86  E-value=5.4e-09  Score=98.32  Aligned_cols=62  Identities=26%  Similarity=0.359  Sum_probs=58.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++.||||+||.++.+++|.-+|++.|+|-  .++|++++.+|  ||||||.|-+.+.|++||+.+
T Consensus        82 ~G~EVfvGkIPrD~~EdeLvplfEkiG~I~--elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~l  145 (506)
T KOG0117|consen   82 RGCEVFVGKIPRDVFEDELVPLFEKIGKIY--ELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKEL  145 (506)
T ss_pred             CCceEEecCCCccccchhhHHHHHhcccee--eEEEeecccCCCCcceEEEEeecHHHHHHHHHHh
Confidence            589999999999999999999999999999  99999986555  999999999999999999875

>smart00360 RRM RNA recognition motif

Probab=98.85  E-value=1.2e-08  Score=70.93  Aligned_cols=57  Identities=42%  Similarity=0.640  Sum_probs=49.7

Q ss_pred             EcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC--CCccEEEEEeCCHHHHHHHHHhcC
Q 023954          213 VRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD--VGICYAFVEFEDMTGVRNAVEVCI  271 (275)
Q Consensus       213 V~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~--~grgfgFV~F~~~~~a~~Ai~a~p  271 (275)
                      |+|||..+++++|+++|++||.|.  .+.+..++.  ..+|||||+|.+.+.|.+|++...
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~--~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~   59 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIE--SVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALN   59 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEe--EEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcC
Confidence            589999999999999999999999  777776643  348999999999999999998653

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

Probab=98.84  E-value=9.6e-09  Score=101.96  Aligned_cols=63  Identities=24%  Similarity=0.399  Sum_probs=55.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..+.+|||+||+.++++++|+++|++||.|.  .+.++.+. +.++|||||+|.+.++|.+||+..
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~--~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~  346 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEIT--SAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEM  346 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeE--EEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHh
Confidence            4578899999999999999999999999999  78776653 445999999999999999999764

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

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

Probab=98.82  E-value=1.1e-08  Score=98.67  Aligned_cols=61  Identities=28%  Similarity=0.581  Sum_probs=55.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++|||+|||..+++++|+++|++||.|.  .|.+..+..++  +|||||+|.+.++|.+||+..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~--~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l  248 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIE--DVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM  248 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeE--EEEEEEcCCCCccceEEEEEECCHHHHHHHHHhc
Confidence            68999999999999999999999999999  88887766543  899999999999999999754

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=98.82  E-value=2.3e-08  Score=70.20  Aligned_cols=59  Identities=42%  Similarity=0.701  Sum_probs=52.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhc
Q 023954          210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       210 ~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +|||+|||..+++++|+++|+.||.|.  .+.+..++. .++|+|||+|.+.++|..|++..
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~--~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~   60 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVE--SVRIVRDKDTKSKGFAFVEFEDEEDAEKALEAL   60 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEE--EEEEeeCCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            489999999999999999999999998  777766543 34899999999999999999865

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).

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

Probab=98.82  E-value=1.1e-08  Score=100.06  Aligned_cols=56  Identities=38%  Similarity=0.530  Sum_probs=51.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .+.|||+|||+++++++|+++|++||.|.  .+.++.    +||||||+|++.++|++||+.
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~--~v~i~~----~k~~afVef~~~e~A~~Ai~~   57 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVS--YVMMLP----GKRQALVEFEDEESAKACVNF   57 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCee--EEEEEC----CCCEEEEEeCchHHHHHHHHH
Confidence            47899999999999999999999999999  777764    357999999999999999985

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).

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.75  E-value=1.4e-08  Score=90.30  Aligned_cols=67  Identities=21%  Similarity=0.503  Sum_probs=56.6

Q ss_pred             ccCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          204 DEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       204 ~~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +..++|+|||-+||.+..+.+|-.+|-.||.|.+..|.+.+-.+.+||||||.|++..+++.||.+-
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAM  347 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM  347 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHh
Confidence            4457999999999999999999999999999995444443333445999999999999999999874

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

Probab=98.75  E-value=2.1e-08  Score=89.16  Aligned_cols=59  Identities=29%  Similarity=0.474  Sum_probs=53.5

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..+.++||+||++.-+++++|++.|..||.|.  .|++-.+    +||+||.|++.|+|..||..
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~--EVRvFk~----qGYaFVrF~tkEaAahAIv~  219 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQ--EVRVFKD----QGYAFVRFETKEAAAHAIVQ  219 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcce--EEEEecc----cceEEEEecchhhHHHHHHH
Confidence            34679999999999999999999999999999  8888765    57999999999999999965

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

Probab=98.73  E-value=1.6e-08  Score=86.82  Aligned_cols=67  Identities=25%  Similarity=0.393  Sum_probs=60.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc-CccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC-ILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~-pi~i  274 (275)
                      ....+|-|-||.+.++.++|+.+|++||.|-  +|.|..++.+.  +|||||.|.+..+|+.|+++. .+||
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vg--DVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~l   80 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVG--DVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVL   80 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCccc--ceecccccccccccceeEEEeeecchHHHHHHhhcceee
Confidence            4578999999999999999999999999999  99999988776  999999999999999999886 4443

>KOG4353 consensus RNA export factor NXT1 [RNA processing and modification]

Probab=98.73  E-value=1.3e-08  Score=80.88  Aligned_cols=52  Identities=31%  Similarity=0.414  Sum_probs=46.5

Q ss_pred             CCccceEEeeeeecccCCC------cEEEEEEeEEEecCccccccceeEEEeeecCCCC
Q 023954            3 LNYSGIEIKTAHSLESWNG------GVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVP   55 (275)
Q Consensus         3 l~f~~~~i~t~D~q~s~~~------gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~   55 (275)
                      ||..+|.|.++||||-+++      +|||+|.|.++.+| +..|.|.|+|.|.++..-|
T Consensus        64 LPsS~~qi~~lD~Qpv~dqat~~q~~vLvvvsGtVkFdG-~k~r~F~qt~ll~~e~~~~  121 (139)
T KOG4353|consen   64 LPSSEFQINDLDCQPVHDQATGSQTTVLVVVSGTVKFDG-NKQRVFNQTFLLTAEDPPF  121 (139)
T ss_pred             CCCccccccccccccchhhcccccceEEEEEeeeEEEcC-CccccccceeEEeecCCcc
Confidence            7888999999999987644      69999999999999 8899999999999987555

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

Probab=98.67  E-value=1.9e-08  Score=89.05  Aligned_cols=63  Identities=21%  Similarity=0.373  Sum_probs=56.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      -++.+|||.+||..+|..+|+.+|++||.|.  .-+|..+..+|  ||.|||.|+.+.+|+.||+..
T Consensus       125 Ik~aNLYvSGlPktMtqkelE~iFs~fGrII--tSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~l  189 (360)
T KOG0145|consen  125 IKDANLYVSGLPKTMTQKELEQIFSPFGRII--TSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGL  189 (360)
T ss_pred             hcccceEEecCCccchHHHHHHHHHHhhhhh--hhhhhhhcccceecceeEEEecchhHHHHHHHhc
Confidence            3678999999999999999999999999998  56666666666  999999999999999999864

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

Probab=98.67  E-value=3.6e-08  Score=79.48  Aligned_cols=63  Identities=22%  Similarity=0.476  Sum_probs=59.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++--|||.++...++++++.+.|..||.|+  .|.+..++.+|  +||++|+|++...|++||.+.
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiK--NihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~  134 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIK--NIHLNLDRRTGYVKGYALVEYETLKEAQAAIDAL  134 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhccccc--ceeeccccccccccceeeeehHhHHHHHHHHHhc
Confidence            4678899999999999999999999999999  99999998888  999999999999999999876

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

Probab=98.66  E-value=1.6e-08  Score=94.90  Aligned_cols=62  Identities=24%  Similarity=0.386  Sum_probs=55.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEec-CCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRS-RKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~-~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +.++||||-|+..+||.+++++|.+||.|+  ++.|.+ ..+.+||||||.|.+.+.|..||++-
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ie--d~~ilrd~~~~sRGcaFV~fstke~A~~Aika~  185 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIE--DCYILRDPDGLSRGCAFVKFSTKEMAVAAIKAL  185 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccc--hhhheecccccccceeEEEEehHHHHHHHHHhh
Confidence            468999999999999999999999999999  777655 44566999999999999999999875

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

Probab=98.60  E-value=6.3e-08  Score=81.71  Aligned_cols=63  Identities=25%  Similarity=0.364  Sum_probs=57.1

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .....+|||+||+..++++.|.++|-+.|.+.  .+.+..++-+.  +||||++|.++++|+-||+-
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv--~i~iPkDrv~~~~qGygF~Ef~~eedadYAiki   70 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVV--NLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKI   70 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCcee--eeecchhhhcccccceeEEEEechhhhHHHHHH
Confidence            34679999999999999999999999999999  88888887655  89999999999999999874

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

Probab=98.60  E-value=1.4e-07  Score=92.29  Aligned_cols=62  Identities=19%  Similarity=0.272  Sum_probs=53.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCc--eeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGE--LSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~--I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...+|||+|||.++++++|+++|+.||.  +.  .+++...+...+|||||+|++.++|.+||...
T Consensus       393 ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~--~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~l  456 (481)
T TIGR01649       393 PSATLHLSNIPLSVSEEDLKELFAENGVHKVK--KFKFFPKDNERSKMGLLEWESVEDAVEALIAL  456 (481)
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHHhcCCccce--EEEEecCCCCcceeEEEEcCCHHHHHHHHHHh
Confidence            4678999999999999999999999998  66  67775544444799999999999999999875

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=98.60  E-value=7e-08  Score=92.89  Aligned_cols=62  Identities=23%  Similarity=0.343  Sum_probs=57.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+.+|||++||+.++.++|.++|+.+|.|+  .+.+..+++++  ||||||.|.-.+++++||+..
T Consensus         4 ~g~TlfV~~lp~~~~~~qL~e~FS~vGPik--~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~   67 (678)
T KOG0127|consen    4 SGATLFVSRLPFSSTGEQLEEFFSYVGPIK--HAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAET   67 (678)
T ss_pred             CCceEEEecCCCccchhHHHHhhhcccCcc--eeEEecCCCcccccCccceeeehHhHHHHHHHHh
Confidence            458999999999999999999999999999  88888888876  999999999999999999753

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

Probab=98.59  E-value=1.1e-07  Score=84.75  Aligned_cols=61  Identities=28%  Similarity=0.538  Sum_probs=55.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .-..+||+.|...++-++|++.|.+||+|.  ..+|.+|..++  ||||||.|-+.++|++||..
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS--~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~  123 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVS--DAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQ  123 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccc--cceEeecccCCcccceeEEeccchHHHHHHHHH
Confidence            357899999999999999999999999999  78887776554  89999999999999999975

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

Probab=98.57  E-value=2.3e-08  Score=84.35  Aligned_cols=56  Identities=25%  Similarity=0.527  Sum_probs=50.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHH
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGV  263 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a  263 (275)
                      .+..-|||||||+..|+.+|--.|++||.|.  .|.+++++.+|  +||||+.|++..+-
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~v--dinLiRDk~TGKSKGFaFLcYEDQRST   90 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIV--DINLIRDKKTGKSKGFAFLCYEDQRST   90 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceE--EEEEEecCCCCcccceEEEEecCccce
Confidence            3567899999999999999999999999999  99999998887  89999999986543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.54  E-value=6.7e-08  Score=89.04  Aligned_cols=66  Identities=23%  Similarity=0.405  Sum_probs=60.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      +.++|||++|++.++++.|++.|.+||++.  .+.++.++.++  |||+||+|++.+...++|.+.++.|
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~--d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~   72 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVT--DCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKL   72 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCcee--eEEEeccCCCCCcccccceecCCCcchheeeccccccc
Confidence            679999999999999999999999999999  88888877666  8999999999999999999887755

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

Probab=98.53  E-value=1.2e-07  Score=89.32  Aligned_cols=57  Identities=32%  Similarity=0.534  Sum_probs=50.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..-+-||||||+.++|++.|+++|++||.|.  .|+..+|      ||||.|.++++|.+||+..
T Consensus       257 s~VKvLYVRNL~~~tTeE~lk~~F~~~G~ve--RVkk~rD------YaFVHf~eR~davkAm~~~  313 (506)
T KOG0117|consen  257 SKVKVLYVRNLMESTTEETLKKLFNEFGKVE--RVKKPRD------YAFVHFAEREDAVKAMKET  313 (506)
T ss_pred             hheeeeeeeccchhhhHHHHHHHHHhccceE--Eeecccc------eeEEeecchHHHHHHHHHh
Confidence            3568899999999999999999999999999  5555433      9999999999999999753

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

Probab=98.53  E-value=3.9e-07  Score=88.22  Aligned_cols=64  Identities=19%  Similarity=0.448  Sum_probs=56.4

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC-C-ccEEEEEeCCHHHHHHHHHhc
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV-G-ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~-g-rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..-+++|||.+|...+...+|+.+|++||+|.  +..|..+..+ | ||||||++.+.+.|-+||.-.
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVv--GAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hL  467 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVV--GAKVVTNARSPGARCYGFVTMSTSAEATKCIEHL  467 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhccee--ceeeeecCCCCCcceeEEEEecchHHHHHHHHHh
Confidence            34578999999999999999999999999999  8888877554 3 999999999999999999754

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

Probab=98.53  E-value=7.1e-08  Score=88.95  Aligned_cols=67  Identities=25%  Similarity=0.351  Sum_probs=59.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc-CccCC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC-ILMWH  275 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~-pi~ig  275 (275)
                      -.++||||.+.+...++.|+..|..||.|+  .|.+.++..++  +||+||+|+-.+.|+-|++.- ..|+|
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIK--SInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlG  181 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIK--SINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLG  181 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcc--eeecccccccccccceEEEEEeCcHHHHHHHHHhcccccc
Confidence            368999999999999999999999999999  88888887766  899999999999999999864 55554

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

Probab=98.52  E-value=2.2e-07  Score=90.84  Aligned_cols=63  Identities=22%  Similarity=0.429  Sum_probs=49.0

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccC------------ceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCc
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFG------------ELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCIL  272 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG------------~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi  272 (275)
                      ....++|||||||+.+|+++|+++|.+|+            .|.  .+.+.    ..+|||||+|.+.++|..||....+
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~--~~~~~----~~kg~afVeF~~~e~A~~Al~l~g~  245 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVS--SVNIN----KEKNFAFLEFRTVEEATFAMALDSI  245 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceE--EEEEC----CCCCEEEEEeCCHHHHhhhhcCCCe
Confidence            34679999999999999999999999762            222  23332    2478999999999999999965444


Q ss_pred             c
Q 023954          273 M  273 (275)
Q Consensus       273 ~  273 (275)
                      +
T Consensus       246 ~  246 (509)
T TIGR01642       246 I  246 (509)
T ss_pred             E
Confidence            3

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

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

Probab=98.52  E-value=1.6e-07  Score=90.23  Aligned_cols=60  Identities=25%  Similarity=0.404  Sum_probs=56.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +.+||||+|+++++++|..+|+..|.|.  .+++..|+.+|  |||||++|.+.+.+.+|++..
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~--s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~l   80 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVL--SFRLVYDRETGKPKGFGFCEFTDEETAERAIRNL   80 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccc--eeeecccccCCCcCceeeEecCchhhHHHHHHhc
Confidence            8999999999999999999999999999  89999988877  899999999999999999865

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

Probab=98.50  E-value=3.7e-07  Score=90.66  Aligned_cols=56  Identities=36%  Similarity=0.542  Sum_probs=49.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcc--CceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKF--GELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~f--G~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+||+.++++++|+++|++|  |.|.  .|.+.      ++||||+|.+.++|.+||++.
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~--rV~~~------rgfAFVeF~s~e~A~kAi~~l  289 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVE--RVKKI------RDYAFVHFEDREDAVKAMDEL  289 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceE--EEEee------cCeEEEEeCCHHHHHHHHHHh
Confidence            45789999999999999999999999  9999  66553      469999999999999999853

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.

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

Probab=98.46  E-value=8.4e-08  Score=83.19  Aligned_cols=61  Identities=25%  Similarity=0.472  Sum_probs=55.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++||||+|-..+++.-|...|-.||.|.  .|++..+-.+.  ||||||+|+..++|..||..
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~--dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDN   71 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIK--DIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDN   71 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchh--hcccccchhcccccceeEEEeeccchhHHHhhc
Confidence            568999999999999999999999999999  99998875544  99999999999999999863

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

Probab=98.41  E-value=2e-07  Score=89.80  Aligned_cols=62  Identities=24%  Similarity=0.501  Sum_probs=55.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||||.+++++++|+.+|+.||.|.  .|++..+..+|  +|||||+|.+.+.|.+|++..
T Consensus       277 p~~rl~vgnLHfNite~~lr~ifepfg~Ie--~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~l  340 (549)
T KOG0147|consen  277 PMRRLYVGNLHFNITEDMLRGIFEPFGKIE--NVQLTKDSETGRSKGFGFITFVNKEDARKALEQL  340 (549)
T ss_pred             chhhhhhcccccCchHHHHhhhccCcccce--eeeeccccccccccCcceEEEecHHHHHHHHHHh
Confidence            345599999999999999999999999999  89998885445  999999999999999997653

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

Probab=98.35  E-value=8.7e-07  Score=83.87  Aligned_cols=58  Identities=24%  Similarity=0.519  Sum_probs=52.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       210 ~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .|||+||+..++...|.++|+.||.|.  .+++..+..-.+|| ||.|++.++|++||+..
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~il--S~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~  135 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNIL--SCKVATDENGSKGY-FVQFESEESAKKAIEKL  135 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCee--EEEEEEcCCCceee-EEEeCCHHHHHHHHHHh
Confidence            399999999999999999999999999  88888776556999 99999999999999854

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.33  E-value=6.7e-07  Score=79.66  Aligned_cols=63  Identities=22%  Similarity=0.392  Sum_probs=55.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +.++||||-|.+.-.|++++++|..||.|.. ...++...+.+|||+||.|.+..+++.||.+.
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e-~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aL   80 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEE-CTVLRGPDGNSKGCAFVKFSSHAEAQAAINAL   80 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcce-eEEecCCCCCCCCceEEEeccchHHHHHHHHh
Confidence            5689999999999999999999999999993 44556666777999999999999999999875

>smart00361 RRM_1 RNA recognition motif

Probab=98.29  E-value=2.2e-06  Score=61.74  Aligned_cols=47  Identities=19%  Similarity=0.321  Sum_probs=38.0

Q ss_pred             HHHHHHHHh----ccCceeEceEE-EecCC----CCCccEEEEEeCCHHHHHHHHHhc
Q 023954          222 ESEIAEEFK----KFGELSSEGVV-IRSRK----DVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       222 e~~L~~~F~----~fG~I~~~~v~-v~~~~----~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +++|+++|+    +||.|.  .+. +..++    +..+|||||.|.+.++|.+||+..
T Consensus         2 ~~~l~~~~~~~~~~fG~v~--~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l   57 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVG--KINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDL   57 (70)
T ss_pred             chhHHHHHHHHHHhcCCee--EEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHh
Confidence            467888888    999999  664 44444    345999999999999999999863

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

Probab=98.29  E-value=6.4e-07  Score=80.57  Aligned_cols=54  Identities=28%  Similarity=0.535  Sum_probs=49.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+|||||||..+++.+|+.+|++||++.  .+.|.++      ||||..++...+..||+..
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVl--ECDIvKN------YgFVHiEdktaaedairNL   56 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVL--ECDIVKN------YGFVHIEDKTAAEDAIRNL   56 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceE--eeeeecc------cceEEeecccccHHHHhhc
Confidence            4799999999999999999999999999  7777754      9999999999999999854

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

Probab=98.27  E-value=3.5e-06  Score=74.89  Aligned_cols=61  Identities=21%  Similarity=0.424  Sum_probs=55.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|.|.-||.++|.++|+.+|...|+|.  .+++.+||.+|  -|||||.|-+..+|++||..
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiE--ScKLvRDKitGqSLGYGFVNYv~p~DAe~Aint  102 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIE--SCKLVRDKITGQSLGYGFVNYVRPKDAEKAINT  102 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhccccee--eeeeeeccccccccccceeeecChHHHHHHHhh
Confidence            457788989999999999999999999999  89999998777  79999999999999999864

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

Probab=98.24  E-value=1.4e-06  Score=73.71  Aligned_cols=63  Identities=24%  Similarity=0.358  Sum_probs=53.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC--CCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD--VGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~--~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      -+.++||+||.+.+++..|.+.|+.||.|.. .-.++.+..  .++|||||.|.+.+.+.+||++.
T Consensus        95 vganlfvgNLd~~vDe~~L~dtFsafG~l~~-~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~  159 (203)
T KOG0131|consen   95 VGANLFVGNLDPEVDEKLLYDTFSAFGVLIS-PPKIMRDPDTGNPKGFGFINYASFEASDAAIGSM  159 (203)
T ss_pred             ccccccccccCcchhHHHHHHHHHhcccccc-CCcccccccCCCCCCCeEEechhHHHHHHHHHHh
Confidence            4689999999999999999999999999973 234555444  44899999999999999999864

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

Probab=98.23  E-value=1.3e-06  Score=80.80  Aligned_cols=64  Identities=23%  Similarity=0.555  Sum_probs=55.1

Q ss_pred             ccCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CC-ccEEEEEeCCHHHHHHHHHh
Q 023954          204 DEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VG-ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       204 ~~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~g-rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      +.....+|||..+..+.++++|+..|+.||+|.  .|.+.+... .+ |||||++|.+..+...||..
T Consensus       206 eAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~--~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAias  271 (544)
T KOG0124|consen  206 EAKKFNRIYVASVHPDLSETDIKSVFEAFGEIV--KCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  271 (544)
T ss_pred             HHHhhheEEeeecCCCccHHHHHHHHHhhccee--eEEeeccCCCCCccceeeEEeccccchHHHhhh
Confidence            345689999999999999999999999999999  888866543 23 99999999999999988854

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

Probab=98.23  E-value=9.6e-07  Score=87.40  Aligned_cols=62  Identities=24%  Similarity=0.434  Sum_probs=54.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC--CCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD--VGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~--~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+++|+|+|||+.++..+++.+|..||.++  .|+|....+  .+||||||+|-+...+.+|+++.
T Consensus       612 ~~tKIlVRNipFeAt~rEVr~LF~aFGqlk--svRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al  675 (725)
T KOG0110|consen  612 KGTKILVRNIPFEATKREVRKLFTAFGQLK--SVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDAL  675 (725)
T ss_pred             ccceeeeeccchHHHHHHHHHHHhccccee--eeccchhhcchhhccceeeeccCcHHHHHHHHhh
Confidence            378999999999999999999999999999  888866533  34999999999999999998764

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

Probab=98.22  E-value=1.5e-06  Score=80.00  Aligned_cols=62  Identities=23%  Similarity=0.489  Sum_probs=55.6

Q ss_pred             ccCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHH
Q 023954          204 DEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAV  267 (275)
Q Consensus       204 ~~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai  267 (275)
                      ......-|||..|.+-+++++|+-+|+.||.|.  .+.|..++.+|  -+||||+|++.+++++|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~--sceVIRD~ktgdsLqyaFiEFen~escE~Ay  298 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIV--SCEVIRDRKTGDSLQYAFIEFENKESCEQAY  298 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccce--eeeEEecccccchhheeeeeecchhhHHHHH
Confidence            334568899999999999999999999999999  88888888777  799999999999999985

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

Probab=98.18  E-value=3.9e-06  Score=72.24  Aligned_cols=60  Identities=35%  Similarity=0.522  Sum_probs=50.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcc-CceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHH
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKF-GELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~f-G~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~  268 (275)
                      ...-+||+.+|+...+.++..+|.+| |.+.  .+++.+++.+|  +|||||+|++.+-|.-|-+
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~--r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAE  110 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVT--RFRLSRNKRTGNSKGYAFVEFESEEVAKIAAE  110 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeE--EEEeecccccCCcCceEEEEeccHHHHHHHHH
Confidence            45678999999999999999999998 6666  67775666666  9999999999998887754

>PF13893 RRM_5: RNA recognition motif

Probab=98.16  E-value=6.2e-06  Score=56.50  Aligned_cols=41  Identities=34%  Similarity=0.571  Sum_probs=34.5

Q ss_pred             HHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          225 IAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       225 L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      |.++|++||.|.  .+.+..++   +|+|||+|.+.++|.+|++..
T Consensus         1 L~~~f~~fG~V~--~i~~~~~~---~~~a~V~f~~~~~A~~a~~~l   41 (56)
T PF13893_consen    1 LYKLFSKFGEVK--KIKIFKKK---RGFAFVEFASVEDAQKAIEQL   41 (56)
T ss_dssp             HHHHHTTTS-EE--EEEEETTS---TTEEEEEESSHHHHHHHHHHH
T ss_pred             ChHHhCCcccEE--EEEEEeCC---CCEEEEEECCHHHHHHHHHHh
Confidence            678999999999  77776654   589999999999999999854

(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 ....

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

Probab=98.12  E-value=4.6e-06  Score=76.66  Aligned_cols=59  Identities=31%  Similarity=0.509  Sum_probs=53.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ....+||||+|-..+++.+|+++|-+||.|+  .+.+...    +|+|||+|.+.++|+.|.+.+
T Consensus       226 ~~I~tLyIg~l~d~v~e~dIrdhFyqyGeir--si~~~~~----~~CAFv~ftTR~aAE~Aae~~  284 (377)
T KOG0153|consen  226 TSIKTLYIGGLNDEVLEQDIRDHFYQYGEIR--SIRILPR----KGCAFVTFTTREAAEKAAEKS  284 (377)
T ss_pred             cceeEEEecccccchhHHHHHHHHhhcCCee--eEEeecc----cccceeeehhhHHHHHHHHhh
Confidence            4578999999999999999999999999999  7777653    569999999999999998876

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.11  E-value=2.3e-06  Score=78.99  Aligned_cols=62  Identities=27%  Similarity=0.524  Sum_probs=55.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||++|+.++++.+|++.|.+||.|.  .+.++.++.+.  ||||||.|++.+++.+++...
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~--~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~  159 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVA--DVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQK  159 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeE--eeEEeecccccccccceeeEeccccccceecccc
Confidence            468999999999999999999999999998  88888877665  899999999999999887654

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

Probab=98.05  E-value=1.2e-05  Score=70.09  Aligned_cols=60  Identities=20%  Similarity=0.337  Sum_probs=50.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHH----HHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIAE----EFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~----~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..+|||+||+..+..++|++    +|++||.|.  +|.... ....||-|||.|.+.+.|-.|+++.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~il--dI~a~k-t~KmRGQA~VvFk~~~~As~A~r~l   72 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKIL--DISAFK-TPKMRGQAFVVFKETEAASAALRAL   72 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeE--EEEecC-CCCccCceEEEecChhHHHHHHHHh
Confidence            34999999999999999888    999999999  665543 2234899999999999999888764

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

Probab=98.04  E-value=7.2e-06  Score=82.02  Aligned_cols=57  Identities=21%  Similarity=0.483  Sum_probs=50.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++||||+|+.++++.+|..+|+.||.|.  .|.+..    .||||||.+..+.+|.+||.+.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiq--Si~li~----~R~cAfI~M~~RqdA~kalqkl  477 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQ--SIILIP----PRGCAFIKMVRRQDAEKALQKL  477 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccce--eEeecc----CCceeEEEEeehhHHHHHHHHH
Confidence            46899999999999999999999999999  666654    3789999999999999998764

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

Probab=97.99  E-value=1.8e-05  Score=74.87  Aligned_cols=62  Identities=26%  Similarity=0.341  Sum_probs=54.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHH-hccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEF-KKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F-~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...+++||.|||+++...+|+++| .+.|+|.  .|.+..|. ++.||||.|+|++.+.+++|++.
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~--yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~  105 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVE--YVELLFDESGKARGCAVVEFKDPENVQKALEK  105 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceE--eeeeecccCCCcCCceEEEeeCHHHHHHHHHH
Confidence            346779999999999999999999 5789999  88887764 44599999999999999999875

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

Probab=97.95  E-value=1.5e-05  Score=79.03  Aligned_cols=60  Identities=23%  Similarity=0.448  Sum_probs=51.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC-----CccEEEEEeCCHHHHHHHHHhc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV-----GICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~-----grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ++|||+||++++|.+.|+.+|.+.|.|.  .+.|...+..     +.|||||+|.+.++|++|+++.
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~Vl--S~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~l  580 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVL--SIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKAL  580 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEE--EEEEeccccccccccccceeEEEecCHHHHHHHHHHh
Confidence            4499999999999999999999999999  7766554321     2599999999999999999985

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

Probab=97.87  E-value=9.5e-05  Score=64.61  Aligned_cols=63  Identities=21%  Similarity=0.346  Sum_probs=52.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC---ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG---ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g---rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..-++|||.+||.++...+|..+|..|-.-.  +..++...+.+   +-+||+.|.+...|..|+.+.
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYE--gslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaL   97 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYE--GSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNAL   97 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCcc--ceeeeeccCCCccccceEEEEecchHHHHHHHHHh
Confidence            4579999999999999999999999997777  66665532222   579999999999999999876

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

Probab=97.82  E-value=3.6e-05  Score=72.98  Aligned_cols=57  Identities=23%  Similarity=0.458  Sum_probs=52.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcC
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCI  271 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~p  271 (275)
                      .+||||   +++|+.+|.++|+.+|.+.  .++|..+. ++-|||||.|.+..+|.+||++..
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~--s~rvc~d~-tslgy~yvnf~~~~da~~A~~~~n   58 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVL--SIRVCRDA-TSLGYAYVNFQQPADAERALDTMN   58 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCce--eEEEeecC-CccceEEEecCCHHHHHHHHHHcC
Confidence            468999   9999999999999999999  89998888 689999999999999999998763

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

Probab=97.76  E-value=5.8e-05  Score=66.99  Aligned_cols=76  Identities=25%  Similarity=0.341  Sum_probs=62.6

Q ss_pred             CCCCcCCccccccCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          193 ADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +.+.++-+-.+......+||.|.|.-+++++.|.+.|++|-...  ...+.+++.++  +|||||.|.+..++.+|++..
T Consensus       175 gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~--~akviRdkRTgKSkgygfVSf~~pad~~rAmrem  252 (290)
T KOG0226|consen  175 GTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQ--KAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREM  252 (290)
T ss_pred             ccccCCcccccCccccceeecccccccccHHHHHHHHHhccchh--hccccccccccccccceeeeecCHHHHHHHHHhh
Confidence            33344444455667789999999999999999999999998887  66777777666  899999999999999999864

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.76  E-value=8e-05  Score=74.13  Aligned_cols=64  Identities=28%  Similarity=0.424  Sum_probs=56.2

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-----CCCccEEEEEeCCHHHHHHHHHhc
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-----DVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-----~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +...+++||+||++.+++..|-..|+.||.|-  .++|+..+     ...+-||||-|.+..++++|++..
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPla--svKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~l  239 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLA--SVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKEL  239 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCccc--ceeeecccchhhhccccccceeeehhhhhHHHHHHHh
Confidence            45678999999999999999999999999999  88887653     234789999999999999999875

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

Probab=97.71  E-value=7.1e-05  Score=70.92  Aligned_cols=60  Identities=17%  Similarity=0.238  Sum_probs=51.1

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..+.++|||+|||+++|...|++-|..||.++  ...| +.++..+|  .|.|.+.+.|++||..
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~--yadi-me~GkskG--VVrF~s~edAEra~a~  592 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVL--YADI-MENGKSKG--VVRFFSPEDAERACAL  592 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhcccee--hhhh-hccCCccc--eEEecCHHHHHHHHHH
Confidence            45678999999999999999999999999999  7777 34444444  8999999999999864

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

Probab=97.68  E-value=2.9e-05  Score=68.00  Aligned_cols=54  Identities=30%  Similarity=0.530  Sum_probs=47.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++|||+|++.+.+.+|+.+|..||.+.  .+.+.      .|||||+|++.-+|..||-..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~--d~~mk------~gf~fv~fed~rda~Dav~~l   55 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIP--DADMK------NGFGFVEFEDPRDADDAVHDL   55 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccc--cceee------cccceeccCchhhhhcccchh
Confidence            5799999999999999999999999999  65553      369999999999999887654

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

Probab=97.63  E-value=7.9e-05  Score=72.35  Aligned_cols=60  Identities=27%  Similarity=0.367  Sum_probs=51.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|+|-|||..++.++|+++|+.||+|+  +|+.-..   .+|..||+|-|..+|++|+++.
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir--~ir~t~~---~~~~~~v~FyDvR~A~~Alk~l  132 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGEIR--EIRETPN---KRGIVFVEFYDVRDAERALKAL  132 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHhhcchh--hhhcccc---cCceEEEEEeehHhHHHHHHHH
Confidence            3568999999999999999999999999999  6544322   3789999999999999999874

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

Probab=97.59  E-value=8.5e-05  Score=66.05  Aligned_cols=63  Identities=27%  Similarity=0.350  Sum_probs=56.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+...+||+|+.+.+|.++++..|+.||.|.  .+.+..++..+  +||+||+|.+.+.+..||+..
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~--~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~  163 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGIN--RVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLD  163 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCcc--ceeeeccccCCCcceeEEEecccHhhhHHHhhcC
Confidence            4679999999999999999999999999998  78887776654  999999999999999999844

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

Probab=97.48  E-value=0.00012  Score=66.10  Aligned_cols=54  Identities=26%  Similarity=0.485  Sum_probs=49.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHH
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~  268 (275)
                      ...+|+|+||.+.++..+|+..|.+||.+.  .+.|.+      +|+||.|+-.+++..||+
T Consensus        77 ~stkl~vgNis~tctn~ElRa~fe~ygpvi--ecdivk------dy~fvh~d~~eda~~air  130 (346)
T KOG0109|consen   77 ASTKLHVGNISPTCTNQELRAKFEKYGPVI--ECDIVK------DYAFVHFDRAEDAVEAIR  130 (346)
T ss_pred             CccccccCCCCccccCHHHhhhhcccCCce--eeeeec------ceeEEEEeeccchHHHHh
Confidence            568999999999999999999999999999  666654      599999999999999994

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

Probab=97.47  E-value=0.00011  Score=64.23  Aligned_cols=59  Identities=24%  Similarity=0.498  Sum_probs=49.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...+|||.||..++++++|+.+|+.|-...  .++|+..  .|.|.+|++|++.+.|..||..
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~--~l~~~~~--~g~~vaf~~~~~~~~at~am~~  267 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFH--ILKIRAR--GGMPVAFADFEEIEQATDAMNH  267 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCce--EEEEecC--CCcceEeecHHHHHHHHHHHHH
Confidence            456899999999999999999999998877  5566543  2578999999999988888753

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

Probab=97.40  E-value=0.00042  Score=61.91  Aligned_cols=62  Identities=29%  Similarity=0.399  Sum_probs=53.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...+|+|.||++.++.++|+++|..||.++  .+.|..++. ...|.|-|.|...++|.+|++..
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~--r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~  144 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELK--RVAVHYDRAGRSLGTADVSFNRRDDAERAVKKY  144 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccce--EEeeccCCCCCCCccceeeecchHhHHHHHHHh
Confidence            458899999999999999999999999888  666655543 33799999999999999999865

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

Probab=97.36  E-value=0.00088  Score=51.65  Aligned_cols=58  Identities=17%  Similarity=0.299  Sum_probs=45.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcc--CceeEceEEEecCCCC--CccEEEEEeCCHHHHHHHHH
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKF--GELSSEGVVIRSRKDV--GICYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~f--G~I~~~~v~v~~~~~~--grgfgFV~F~~~~~a~~Ai~  268 (275)
                      ++|.|+|||...|.++|.+++...  |...  .+-++.|-.+  ..|||||.|.+.+.+.+-.+
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yD--F~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~   63 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYD--FFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYK   63 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcce--EEEeeeeccCCCceEEEEEEcCCHHHHHHHHH
Confidence            579999999999999998888543  4444  7777776444  48999999999998876544

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

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

Probab=97.30  E-value=0.00066  Score=62.73  Aligned_cols=63  Identities=25%  Similarity=0.303  Sum_probs=52.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEc------eEEE-ecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSE------GVVI-RSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~------~v~v-~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...+|||.|||.++|.+++.++|++||-|.++      .|.| +.+.|.-+|=|.+.|...+++.-||+-
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~i  202 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKI  202 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHH
Confidence            56789999999999999999999999999864      3454 334444599999999999999999874

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.26  E-value=0.00078  Score=64.76  Aligned_cols=65  Identities=28%  Similarity=0.292  Sum_probs=52.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...-|-+++|||++|+++|.++|+.++ |.  .+.+.+..++..|=|||+|.+.+++++||+..-.++
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~--~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~m   73 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IE--NLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESM   73 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-ee--EEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHh
Confidence            456777899999999999999999996 55  455555555567999999999999999999764443

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.20  E-value=0.00094  Score=52.22  Aligned_cols=57  Identities=25%  Similarity=0.317  Sum_probs=36.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      |+-|+|.++...++.++|+.+|++||.|.  .|.+..    |-.-|||.|.+.++|++|+++.
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~--yVD~~~----G~~~g~VRf~~~~~A~~a~~~~   57 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVA--YVDFSR----GDTEGYVRFKTPEAAQKALEKL   57 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EE--EEE--T----T-SEEEEEESS---HHHHHHHH
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcc--eEEecC----CCCEEEEEECCcchHHHHHHHH
Confidence            35688999999999999999999999999  776654    3347999999999999998753

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.13  E-value=0.00071  Score=65.41  Aligned_cols=63  Identities=27%  Similarity=0.514  Sum_probs=50.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCC----cc---EEEEEeCCHHHHHHHHHhcC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVG----IC---YAFVEFEDMTGVRNAVEVCI  271 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~g----rg---fgFV~F~~~~~a~~Ai~a~p  271 (275)
                      .-.++||||+||++++++.|...|..||.+..   .+..+. ..+    +|   |.|+.|+++.+++.-|.+|.
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~V---dWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVKV---DWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceEe---ecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            34678999999999999999999999999973   333211 111    56   99999999999999888873

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

Probab=97.08  E-value=0.00026  Score=61.71  Aligned_cols=61  Identities=28%  Similarity=0.316  Sum_probs=53.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|+...++++.|.++|-+-|.+.  .|.|+..+...--||||.|.++-++.-|++-
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~--kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L   68 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVY--KVGIPSGQDQEQKFAYVFFPNENSVQLAGQL   68 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceE--EEeCCCCccCCCceeeeecccccchhhhhhh
Confidence            358999999999999999999999999999  8888877665534999999999999988763

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=96.72  E-value=0.00093  Score=61.27  Aligned_cols=61  Identities=21%  Similarity=0.421  Sum_probs=54.4

Q ss_pred             CCcEEE-EcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVY-VRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~if-V~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++| +++|++.+++++|+.+|..+|.|.  .++++.+..++  +|||||.|.+......++..
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~--~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~  246 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEIT--SVRLPTDEESGDSKGFAYVDFSAGNSKKLALND  246 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcce--eeccCCCCCccchhhhhhhhhhhchhHHHHhhc
Confidence            345666 999999999999999999999999  88888887776  89999999999999999884

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=96.59  E-value=0.0044  Score=59.71  Aligned_cols=67  Identities=24%  Similarity=0.267  Sum_probs=51.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecC-CCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR-KDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~-~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ....|-+++||+.||+++|.++|.-.--+. ++|.+..+ ++...|=|||.|++.+.+++||...--.|
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~-~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rhre~i  169 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVP-DGILLPMDQRGRPTGEAFVQFESQESAEIALGRHRENI  169 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccc-cceeeeccCCCCcccceEEEecCHHHHHHHHHHHHHhh
Confidence            346788899999999999999998764433 35655444 44447899999999999999998764333

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

Probab=96.57  E-value=0.00067  Score=65.93  Aligned_cols=66  Identities=23%  Similarity=0.349  Sum_probs=58.4

Q ss_pred             cccCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       203 ~~~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++.+.+++|+--|...++..+|.++|+.+|.|.  .|+++.++.++  +|.|||+|.|.+++..||.-+
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVr--dVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLs  241 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVR--DVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALS  241 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcc--eeEeeccccchhhcceeEEEEecccchhhHhhhc
Confidence            3456789999999999999999999999999999  99998887765  899999999999999888544

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.47  E-value=0.0066  Score=58.88  Aligned_cols=67  Identities=19%  Similarity=0.270  Sum_probs=58.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHh-ccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFK-KFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~-~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      +..++||||+||.-++..+|-.+|. -||.|.  .+-|-.|..-+  +|-|-|+|.+..+..+||.+.=|.|
T Consensus       368 DprrTVFVGgvprpl~A~eLA~imd~lyGgV~--yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql  437 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTAEELAMIMEDLFGGVL--YVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQL  437 (520)
T ss_pred             CccceEEecCCCCcchHHHHHHHHHHhcCceE--EEEeccCcccCCCCCcceeeecccHHHHHHHhhheEEE
Confidence            4568999999999999999999997 799999  88887774433  8999999999999999999875543

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.33  E-value=0.011  Score=40.30  Aligned_cols=52  Identities=19%  Similarity=0.529  Sum_probs=38.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHH
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV  267 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai  267 (275)
                      +.|-|.+.+.+..+. +...|..||+|.  .+.+..    ..-+.||.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~--~~~~~~----~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIV--DIYVPE----STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEE--EEEcCC----CCcEEEEEECCHHHHHhhC
Confidence            345677777666554 555899999999  666652    2448999999999999986

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=95.97  E-value=0.0087  Score=56.63  Aligned_cols=53  Identities=30%  Similarity=0.401  Sum_probs=44.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHH
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRN  265 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~  265 (275)
                      ..+-|.+||||++++|++|-.++..||.|.  .+.+..    |+.-+|++|.+.++|..
T Consensus        27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vt--n~~~lk----GknQAflem~d~~sAvt   79 (492)
T KOG1190|consen   27 PSKVVHLRNLPWEVTEEELISLGLPFGKVT--NLLMLK----GKNQAFLEMADEESAVT   79 (492)
T ss_pred             CcceeEeccCCccccHHHHHHhccccccee--eeeeec----cchhhhhhhcchhhhhh
Confidence            568899999999999999999999999998  444432    44589999999988765

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=95.80  E-value=0.0095  Score=53.19  Aligned_cols=61  Identities=25%  Similarity=0.423  Sum_probs=53.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..|||.||...++-+.|...|..||.|.. .|.+..+++...+=++|.|...-.+.+|++.|
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~-av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~   92 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIER-AVAKVDDRGKPTREGIVEFAKKPNARKAARRC   92 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccch-heeeecccccccccchhhhhcchhHHHHHHHh
Confidence            78999999999999999999999999985 55556666666788999999999999998887

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

Probab=95.74  E-value=0.028  Score=49.33  Aligned_cols=59  Identities=17%  Similarity=0.300  Sum_probs=49.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ....+|+.|||..++.+.|..+|.+|...+  .|++...+   ++.+||+|.+...+..|..+.
T Consensus       145 pn~ilf~~niP~es~~e~l~~lf~qf~g~k--eir~i~~~---~~iAfve~~~d~~a~~a~~~l  203 (221)
T KOG4206|consen  145 PNNILFLTNIPSESESEMLSDLFEQFPGFK--EIRLIPPR---SGIAFVEFLSDRQASAAQQAL  203 (221)
T ss_pred             CceEEEEecCCcchhHHHHHHHHhhCcccc--eeEeccCC---CceeEEecchhhhhHHHhhhh
Confidence            468899999999999999999999999998  77776532   579999999987766666554

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=95.72  E-value=0.022  Score=53.68  Aligned_cols=67  Identities=16%  Similarity=0.045  Sum_probs=49.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhcc---C-ceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccCC
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKF---G-ELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMWH  275 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~f---G-~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~ig  275 (275)
                      .--|-.|+||+++++.++.++|..-   + ... +.+.|.+..++--|=|||.|...+.|+.||..+--+||
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~e-gvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~iG  231 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTE-GVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQNIG  231 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCcc-ceEEEECCCCCcccceEEEecCHHHHHHHHHHHHHHHh
Confidence            4567779999999999999999732   2 222 13344443444578999999999999999988755554

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

Probab=95.66  E-value=0.009  Score=58.45  Aligned_cols=63  Identities=21%  Similarity=0.367  Sum_probs=54.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC--CccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV--GICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~--grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ....+|||++||...++.+++++...||.++  ...+..+..+  ++||+|.+|-+..-...||...
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk--~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agL  351 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLK--AFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGL  351 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccch--hheeecccccccccceeeeeeeCCcchhhhhccc
Confidence            3568999999999999999999999999999  7777777664  4999999999988887777654

>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=95.29  E-value=0.065  Score=41.53  Aligned_cols=64  Identities=16%  Similarity=0.285  Sum_probs=42.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEE-EecC--------CCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVV-IRSR--------KDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~-v~~~--------~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      .+.|-|-+.|... ...+-+.|++||.|.  ... +..+        ...+..+-.|.|++..+|.+||+.+..+|
T Consensus         6 ~~wVtVFGfp~~~-~~~Vl~~F~~~G~Il--e~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~   78 (100)
T PF05172_consen    6 ETWVTVFGFPPSA-SNQVLRHFSSFGTIL--EHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIF   78 (100)
T ss_dssp             CCEEEEE---GGG-HHHHHHHHHCCS-EE--CEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEE
T ss_pred             CeEEEEEccCHHH-HHHHHHHHHhcceEE--EeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEE
Confidence            4557777888774 456777899999998  332 1110        11246789999999999999999986655

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.

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

Probab=95.08  E-value=0.033  Score=51.87  Aligned_cols=64  Identities=27%  Similarity=0.425  Sum_probs=53.1

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEc------eEEEecCCCCC--ccEEEEEeCCHHHHHHHHH
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSE------GVVIRSRKDVG--ICYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~------~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~  268 (275)
                      .....+|||.+|+..+++.+|.++|.++|.|+.+      .|.|-.++.++  ||=|.|.|++...|+.||.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~  134 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIE  134 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhh
Confidence            3456899999999999999999999999999743      24444455555  8999999999999999985

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=94.76  E-value=0.0033  Score=64.04  Aligned_cols=63  Identities=27%  Similarity=0.358  Sum_probs=53.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEec--CCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRS--RKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~--~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ....++||+||+..+.+.+|...|..+|.+.  .+++..  +++.-||+||++|.+.+.+.+||...
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e--~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~  729 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIE--VVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFR  729 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhh--hHHHHHHhhccccccceeeEeecCCchhhhhhhh
Confidence            4567899999999999999999999999998  666653  33334899999999999999998754

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=94.71  E-value=0.042  Score=52.40  Aligned_cols=65  Identities=25%  Similarity=0.365  Sum_probs=52.6

Q ss_pred             ccCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecC---C--CCC----------ccEEEEEeCCHHHHHHHHH
Q 023954          204 DEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR---K--DVG----------ICYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       204 ~~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~---~--~~g----------rgfgFV~F~~~~~a~~Ai~  268 (275)
                      ++...++|.+-|||.+-.-+-|.++|+.+|.|+  .|+|...   .  .++          +-+|||+|+..+.|.+|-+
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~Ik--sIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e  304 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIK--SIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARE  304 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhccccee--eeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHH
Confidence            345789999999999988899999999999999  8888765   1  111          4569999999999888865


Q ss_pred             hc
Q 023954          269 VC  270 (275)
Q Consensus       269 a~  270 (275)
                      ..
T Consensus       305 ~~  306 (484)
T KOG1855|consen  305 LL  306 (484)
T ss_pred             hh
Confidence            43

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

Probab=94.58  E-value=0.021  Score=50.22  Aligned_cols=56  Identities=30%  Similarity=0.404  Sum_probs=48.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..+++.+.||..++...+|.+.|.++|.+.  ...+      .++++||.|...+++.+||...
T Consensus        98 s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~--~~~~------~~~~~~v~Fs~~~da~ra~~~l  153 (216)
T KOG0106|consen   98 THFRLIVRNLSLRVSWQDLKDHFRPAGEVT--YVDA------RRNFAFVEFSEQEDAKRALEKL  153 (216)
T ss_pred             ccceeeeccchhhhhHHHHhhhhcccCCCc--hhhh------hccccceeehhhhhhhhcchhc
Confidence            468999999999999999999999999995  3333      2569999999999999999876

>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=94.55  E-value=0.12  Score=38.73  Aligned_cols=52  Identities=19%  Similarity=0.217  Sum_probs=34.7

Q ss_pred             cEEEEcCCCCCCCHHH----HHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          209 KSVYVRNLPPSVSESE----IAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~----L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .-|||.|||.+.+...    |+.++..+|.-.   +.|.      .|-|+|.|.+.+.|.+|.+.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkV---l~v~------~~tAilrF~~~~~A~RA~KR   58 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKV---LSVS------GGTAILRFPNQEFAERAQKR   58 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--E---EE--------TT-EEEEESSHHHHHHHHHH
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEE---EEEe------CCEEEEEeCCHHHHHHHHHh
Confidence            4689999999988754    667777886522   2332      36899999999999999874

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

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=94.55  E-value=0.031  Score=52.06  Aligned_cols=62  Identities=15%  Similarity=0.211  Sum_probs=45.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcc-----CceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKF-----GELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCI  271 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~f-----G~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~p  271 (275)
                      ....+|||||-|++|+++|-+.....     -.|+  ...-| .++.+||||+|...+..+.++-++-.|
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmK--FFENR-~NGQSKG~AL~~~~SdAa~Kq~MeiLP  145 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMK--FFENR-TNGQSKGYALLVLNSDAAVKQTMEILP  145 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhh--hhhcc-cCCcccceEEEEecchHHHHHHHHhcc
Confidence            45789999999999999997776544     3444  22222 234459999999999888888877554

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=94.44  E-value=0.08  Score=49.20  Aligned_cols=61  Identities=18%  Similarity=0.467  Sum_probs=44.9

Q ss_pred             CcEEEEcCCCCCCCHHH----H--HHHHhccCceeEceEEEecCCCC---Ccc-E-EEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESE----I--AEEFKKFGELSSEGVVIRSRKDV---GIC-Y-AFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~----L--~~~F~~fG~I~~~~v~v~~~~~~---grg-f-gFV~F~~~~~a~~Ai~a~  270 (275)
                      ..-+||-+|++.+-.++    |  .++|++||.|.  .|.|......   -.+ + -||+|...++|.+||.+-
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~--KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~v  185 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIK--KIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEV  185 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhcccee--EEEecccccccccccccceEEEEecchHHHHHHHHHh
Confidence            35689999988876655    3  57899999999  7766543311   123 2 389999999999999864

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.36  E-value=0.31  Score=34.45  Aligned_cols=54  Identities=19%  Similarity=0.282  Sum_probs=43.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcc----CceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKF----GELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~f----G~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...+|+|+|+ -+++.++++.+|..|    +..   .|.+..+.     -|-|.|.+.+.|.+||.+
T Consensus         4 rpeavhirGv-d~lsT~dI~~y~~~y~~~~~~~---~IEWIdDt-----ScNvvf~d~~~A~~AL~~   61 (62)
T PF10309_consen    4 RPEAVHIRGV-DELSTDDIKAYFSEYFDEEGPF---RIEWIDDT-----SCNVVFKDEETAARALVA   61 (62)
T ss_pred             eeceEEEEcC-CCCCHHHHHHHHHHhcccCCCc---eEEEecCC-----cEEEEECCHHHHHHHHHc
Confidence            3568999999 568888999999988    433   67777765     367999999999999976

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=92.89  E-value=0.12  Score=49.45  Aligned_cols=56  Identities=27%  Similarity=0.431  Sum_probs=42.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++||+||...++..+|+.+|+..-.-..+.+.+.      .||+||++.+...+.+||+..
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~   57 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETL   57 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhh
Confidence            46899999999999999999975422111122221      479999999999999999875

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

Probab=92.85  E-value=0.16  Score=50.19  Aligned_cols=62  Identities=23%  Similarity=0.298  Sum_probs=47.3

Q ss_pred             CCcEEEEcCCCCCCCH------HHHHHHHhccCceeEceEEEecCCCCC-ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSE------SEIAEEFKKFGELSSEGVVIRSRKDVG-ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te------~~L~~~F~~fG~I~~~~v~v~~~~~~g-rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ....|+|-|+|---..      .-|..+|+++|+|.  .+.+..+...| +||.|++|.+..+|+.|++..
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~v--n~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l  125 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIV--NMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSL  125 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhcccc--ceeeccCccCCeeeEEEEEecChhhHHHHHHhc
Confidence            3467888888764322      23567899999999  77776554444 999999999999999999865

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

Probab=91.91  E-value=0.52  Score=40.54  Aligned_cols=57  Identities=21%  Similarity=0.276  Sum_probs=49.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++.|.+||...+..+|+++..+-|.+.  ...+-.+     |+|.|+|-..++++-||+..
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvC--fadv~rD-----g~GvV~~~r~eDMkYAvr~l  170 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVC--FADVQRD-----GVGVVEYLRKEDMKYAVRKL  170 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCee--eeeeecc-----cceeeeeeehhhHHHHHHhh
Confidence            457899999999999999999999999987  6666544     58999999999999998754

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=90.70  E-value=0.25  Score=51.20  Aligned_cols=58  Identities=22%  Similarity=0.382  Sum_probs=48.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...+++|+++|..|+....|..+|..||.|.  .|.++.    |--|+||.|++...++.|++.
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir--~Idy~h----gq~yayi~yes~~~aq~a~~~  510 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIR--IIDYRH----GQPYAYIQYESPPAAQAATHD  510 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcce--eeeccc----CCcceeeecccCccchhhHHH
Confidence            3568999999999999999999999999999  655543    345999999999988888753

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=90.29  E-value=0.99  Score=33.85  Aligned_cols=54  Identities=19%  Similarity=0.271  Sum_probs=40.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+-.||. .|......+|.++|+.||.|.   |.+..+.     -|||...+.+.+..++...
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~---VsWi~dT-----SAfV~l~~r~~~~~v~~~~   62 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY---VSWINDT-----SAFVALHNRDQAKVVMNTL   62 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE---EEEECTT-----EEEEEECCCHHHHHHHHHH
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE---EEEEcCC-----cEEEEeecHHHHHHHHHHh
Confidence            4556665 999999999999999999996   5555553     5999999999998887654

; 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.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=89.96  E-value=0.22  Score=44.69  Aligned_cols=60  Identities=25%  Similarity=0.486  Sum_probs=45.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC--------C--c----cEEEEEeCCHHHHHHHHH
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV--------G--I----CYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~--------g--r----gfgFV~F~~~~~a~~Ai~  268 (275)
                      ...-||+++||+.+...-|+++|..||.|-  .|.+-....+        |  +    -=|.|+|.+...|.++-.
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVG--RvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe  146 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVG--RVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAE  146 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccc--eEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHH
Confidence            567899999999999999999999999998  7777544322        1  1    125688888877776543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=89.92  E-value=1  Score=43.07  Aligned_cols=58  Identities=22%  Similarity=0.240  Sum_probs=49.9

Q ss_pred             CcEEEEcCCCCC-CCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPS-VSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~-~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...|.|.||... +|.+-|..+|+-||.|.  .|.|..++..   -|.|.|.|...|+-|+...
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVq--RVkil~nkkd---~ALIQmsd~~qAqLA~~hL  355 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQ--RVKILYNKKD---NALIQMSDGQQAQLAMEHL  355 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceE--EEEeeecCCc---ceeeeecchhHHHHHHHHh
Confidence            577888898665 89999999999999999  8998887654   5999999999999998764

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=89.77  E-value=0.16  Score=52.17  Aligned_cols=60  Identities=15%  Similarity=0.129  Sum_probs=49.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHh
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...+||+|+|+..|.+.|+.++.++|.++  .+.+...+ +..+|.+||.|.+...+.++...
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~--~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s  796 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVT--SLRLVTVRAGKPKGKARVDYNTEADASRKVAS  796 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCcc--ccchhhhhccccccceeccCCCcchhhhhccc
Confidence            45799999999999999999999999999  55555444 34489999999999988887543

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=89.68  E-value=0.27  Score=46.54  Aligned_cols=64  Identities=20%  Similarity=0.291  Sum_probs=49.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeE-ceEEEecC-CCCCccEEEEEeCCHHHHHHHHHhcC
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSS-EGVVIRSR-KDVGICYAFVEFEDMTGVRNAVEVCI  271 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~-~~v~v~~~-~~~grgfgFV~F~~~~~a~~Ai~a~p  271 (275)
                      ...|-+|+||+.++.++|-.+|+.|..-.+ -+|.+..+ .+...|=|||.|.+.+.+..|...+.
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~h  345 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCH  345 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHH
Confidence            456788999999999999999998865431 13555443 33347999999999999999887663

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=89.19  E-value=0.32  Score=46.09  Aligned_cols=57  Identities=21%  Similarity=0.367  Sum_probs=46.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC-----ccEEEEEeCCHHHHHHH
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG-----ICYAFVEFEDMTGVRNA  266 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g-----rgfgFV~F~~~~~a~~A  266 (275)
                      ..-|-|.||.+.++.++++.||+..|+|.  .+.|..+-+..     ...|||.|.|...+..|
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~--elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~va   68 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIP--ELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVA   68 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccc--cccccCCCCCccCcceeeeEEEeccCCcceeHH
Confidence            34889999999999999999999999999  77665432211     56899999998877665

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

Probab=88.86  E-value=0.89  Score=43.02  Aligned_cols=56  Identities=34%  Similarity=0.500  Sum_probs=46.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHH
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~  268 (275)
                      ..--+.||+|-..+++.+|-+..+.||.|.  .+..+..    +.-+.|+|++.+.+..++.
T Consensus        30 ~spvvhvr~l~~~v~eadl~eal~~fG~i~--yvt~~P~----~r~alvefedi~~akn~Vn   85 (494)
T KOG1456|consen   30 PSPVVHVRGLHQGVVEADLVEALSNFGPIA--YVTCMPH----KRQALVEFEDIEGAKNCVN   85 (494)
T ss_pred             CCceEEEeccccccchhHHHHHHhcCCceE--EEEeccc----cceeeeeeccccchhhhee
Confidence            456799999999999999999999999998  6655543    2369999999999888864

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=88.31  E-value=0.12  Score=53.52  Aligned_cols=65  Identities=25%  Similarity=0.381  Sum_probs=53.0

Q ss_pred             ccccCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecC-CCCCccEEEEEeCCHHHHHHHHH
Q 023954          202 VEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR-KDVGICYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       202 ~~~~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~-~~~grgfgFV~F~~~~~a~~Ai~  268 (275)
                      .++.....+||+|||+..+++.+|+..|..+|.+.  .|.|... .+++--||||.|.+...+.+|+.
T Consensus       366 ~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve--~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~  431 (975)
T KOG0112|consen  366 LDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVE--EVDIKTPHIKTESAYAFVSLLNTDMTPSAKF  431 (975)
T ss_pred             ccchhhhhhhhhcCcccchhhhhhhhhhhhhcccc--ccccccCCCCcccchhhhhhhccccCcccch
Confidence            44555678999999999999999999999999999  7777654 34457899999998887766643

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=85.86  E-value=1  Score=45.80  Aligned_cols=61  Identities=26%  Similarity=0.306  Sum_probs=48.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       210 ~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      -|-+.|||+.+...||+.+|+-. +|-.++|+|...   --|=+||.|.+-++|.-|+-..-.||
T Consensus         4 IIRLqnLP~tAga~DIR~FFSGL-~IPdGgVHIIGG---e~GeaFI~FsTDeDARlaM~kdr~~i   64 (944)
T KOG4307|consen    4 IIRLQNLPMTAGASDIRTFFSGL-KIPDGGVHIIGG---EEGEAFIGFSTDEDARLAMTKDRLMI   64 (944)
T ss_pred             EEEecCCcccccchHHHHhhccc-ccCCCceEEecc---cccceEEEecccchhhhhhhhcccce
Confidence            35678999999999999999865 455467777642   16889999999999999988776666

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=85.30  E-value=2.2  Score=43.48  Aligned_cols=61  Identities=23%  Similarity=0.254  Sum_probs=49.8

Q ss_pred             Cc-EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecC-CCCCccEEEEEeCCHHHHHHHHHh
Q 023954          208 IK-SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR-KDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       208 ~~-~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~-~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ++ -|-+.|+|++++-++|-++|..|-.+. +.|.++.+ ++..-|=|.|-|++.+.|.+|...
T Consensus       866 Gp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p-~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~d  928 (944)
T KOG4307|consen  866 GPRVLSCNNFPFDVTLEDIVEFFNDYEPDP-NSIRIRRNDDGVPTGECMVAFESQEEARRASMD  928 (944)
T ss_pred             CCeEEEecCCCccccHHHHHHHhcccccCC-CceeEeecCCCCcccceeEeecCHHHHHhhhhc
Confidence            44 678899999999999999999997665 57777654 444478999999999999999754

>PF10429 Mtr2: Nuclear pore RNA shuttling protein Mtr2; InterPro: IPR019488 Mtr2 is a monomeric, dual-action, RNA-shuttle protein found in yeasts

Probab=83.68  E-value=1.8  Score=36.43  Aligned_cols=44  Identities=16%  Similarity=0.143  Sum_probs=34.2

Q ss_pred             ceEEeeeeecccCC-CcEEEEEEeEEEecCccccccceeEEEeeec
Q 023954            7 GIEIKTAHSLESWN-GGVLVMVSGSVQVKDFSARRKFVQTFFLAPQ   51 (275)
Q Consensus         7 ~~~i~t~D~q~s~~-~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~   51 (275)
                      +|+++++||+...+ |++||-|+|.|..|+ ..+-|--|+.-|.+.
T Consensus        65 qH~L~s~D~H~IPGsgt~i~N~n~KVRFDE-sGrdk~G~~a~l~~~  109 (166)
T PF10429_consen   65 QHQLTSFDCHVIPGSGTFIINVNCKVRFDE-SGRDKLGEDADLPQP  109 (166)
T ss_dssp             EEEEEEEEEEEETTTTEEEEEEEEEEEEB--SSB-TTS-B--TTS-
T ss_pred             eeeeeeeeeeEeCCCCeEEEeeeEEEEecC-CCCCCCCCceeeccc
Confidence            89999999999864 569999999999987 888899999998775

Transport across the nuclear-cytoplasmic membrane is via the macro-molecular membrane-spanning nuclear pore complex, NPC. The pore is lined by a subset of NPC members called nucleoporins that present FG (Phe-Gly) receptors, characteristically GLFG and FXFG motifs, for shuttling RNAs and proteins. RNA cargo is bound to soluble transport proteins (nuclear export factors) such as Mex67 in yeasts, and TAP in metazoa, which pass along the pore by binding to successive FG receptors. Mtr2 when bound to Mex67 maximises this FG-binding. Mtr2 also acts independently of Mex67 in transporting the large ribosomal RNA subunit through the pore []. ; PDB: 1Q40_A 1Q42_A 1OF5_B.

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=83.20  E-value=4.3  Score=37.24  Aligned_cols=49  Identities=16%  Similarity=0.242  Sum_probs=36.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHH
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMT  261 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~  261 (275)
                      ..-||++||++++...+|+..+.+.|-.-   ..|.. ++ .+|-||+.|.+..
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~p---m~isw-kg-~~~k~flh~~~~~  378 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTP---MSISW-KG-HFGKCFLHFGNRK  378 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCc---eeEee-ec-CCcceeEecCCcc
Confidence            45699999999999999999998887664   22222 21 2678999998854

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=83.06  E-value=0.76  Score=42.72  Aligned_cols=61  Identities=21%  Similarity=0.498  Sum_probs=44.5

Q ss_pred             cEEEEcCCCCCCCH-HHH--HHHHhccCceeEceEEEecCC----CCC-ccEEEEEeCCHHHHHHHHHhcC
Q 023954          209 KSVYVRNLPPSVSE-SEI--AEEFKKFGELSSEGVVIRSRK----DVG-ICYAFVEFEDMTGVRNAVEVCI  271 (275)
Q Consensus       209 ~~ifV~nLp~~~te-~~L--~~~F~~fG~I~~~~v~v~~~~----~~g-rgfgFV~F~~~~~a~~Ai~a~p  271 (275)
                      .-+||-+|+..... ..|  ...|++||.|.  .|.+..+.    +.+ .+-++|+|+..+++.+||....
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~--ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~  146 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKIN--KIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVD  146 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccce--EEeecCCcccccCCCCCCcccccccchHhhhhHHHHhh
Confidence            45788888877544 444  36789999999  66665544    112 5669999999999999998764

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=83.05  E-value=2.1  Score=43.18  Aligned_cols=55  Identities=24%  Similarity=0.271  Sum_probs=45.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++||+|+...+..+-++.+...+|.|.  .  +...+     |||++|.......+|+..+
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~--s--~kr~~-----fgf~~f~~~~~~~ra~r~~   93 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVP--S--WKRDK-----FGFCEFLKHIGDLRASRLL   93 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcch--h--hhhhh-----hcccchhhHHHHHHHHHHh
Confidence            458899999999999999999999999987  2  22222     9999999999999988765

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

Probab=82.92  E-value=2.4  Score=41.89  Aligned_cols=46  Identities=30%  Similarity=0.402  Sum_probs=36.6

Q ss_pred             HHHHHHHhccCceeEceEEEecCC-----CCCccEEEEEeCCHHHHHHHHHhc
Q 023954          223 SEIAEEFKKFGELSSEGVVIRSRK-----DVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       223 ~~L~~~F~~fG~I~~~~v~v~~~~-----~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ++++..+.+||.|.  .|.+...-     ..|-|--||+|.+.+++++|+++.
T Consensus       424 Edvr~ec~k~g~v~--~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L  474 (500)
T KOG0120|consen  424 EDVRTECAKFGAVR--SVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEEL  474 (500)
T ss_pred             HHHHHHhcccCcee--EEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHc
Confidence            45666788999999  88886651     234688899999999999999875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	275
3q90_A	140	RAS GTPase-activating protein-binding protein 1; s	6e-13
3ujm_A	120	Rasputin; NTF2-like fold, RAS signaling, signaling	7e-12
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	9e-12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-11
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-11
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-11
1gy6_A	127	Nuclear transport factor 2; 1.6A {Rattus norvegicu	8e-11
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-10
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-10
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-10
1zo2_A	129	NTF2, nuclear transport factor 2; structural genom	2e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-10
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-06
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-10
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	7e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-09
1gy7_A	125	Nuclear transport factor 2; protein transport; 1.6	1e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-09
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-09
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-09
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-09
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-09
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-09
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-09
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-08
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-08
1jkg_A	140	P15; NTF2-like domain, transport protein; 1.90A {H	2e-09
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-09
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-07
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-09
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	4e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-09
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	5e-09
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-09
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	7e-09
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-09
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	8e-09
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-06
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	8e-09
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	9e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	9e-09
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-08
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-08
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-08
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-08
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-08
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-06
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-08
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-08
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-08
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-08
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-08
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-08
2div_A	99	TRNA selenocysteine associated protein; structural	4e-08
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-08
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-08
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-08
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-06
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-08
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-08
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	6e-08
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	6e-08
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-08
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	7e-08
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	8e-08
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	8e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-06
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-08
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	9e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-08
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-07
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-07
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-07
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-07
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-07
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-07
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-07
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-06
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-06
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-07
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-07
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-07
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-07
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-07
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-07
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-07
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-07
3nv0_B	154	NTF2-related export protein; NTF2-like domain, bet	4e-07
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	5e-07
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-07
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	6e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	6e-07
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	7e-07
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	8e-07
1x5o_A	114	RNA binding motif, single-stranded interacting pro	8e-07
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	9e-07
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	9e-07
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-06
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-06
2qiy_A	154	UBP3-associated protein BRE5; deubiquitylation, ub	1e-06
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-06
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-06
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-06
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-06
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	5e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-04
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	6e-06
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	6e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	7e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-05
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-05
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-05
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-05
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-05
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	7e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	8e-05
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-04
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-04
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-04
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	3e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	4e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	5e-04

>3q90_A RAS GTPase-activating protein-binding protein 1; structural genomics, structural genomics consortium, SGC, NT (A+B proteins); 1.70A {Homo sapiens} Length = 140

 Score = 63.7 bits (155), Expect = 6e-13
 Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 3/58 (5%)

Query: 1   MSLNYSGI--EIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPN 56
           MS N++    +I+   +  + N GV+V V G +   +  A R+F+QTF LAP+  V N
Sbjct: 67  MSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNN-QALRRFMQTFVLAPEGSVAN 123

>3ujm_A Rasputin; NTF2-like fold, RAS signaling, signaling protein; HET: EPE; 2.74A {Drosophila melanogaster} Length = 120

 Score = 60.3 bits (146), Expect = 7e-12
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 3/54 (5%)

Query: 1   MSLNYSGI--EIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQE 52
             LN++    +I    +  +   GV+V V+G +        R+F QTF LA Q 
Sbjct: 54  QQLNFNDCHAKISQVDAQATLGNGVVVQVTGELSNDG-QPMRRFTQTFVLAAQS 106

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 59.3 bits (144), Expect = 9e-12
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRN 265
             ++SV+V   P  V  ++++E F  FG ++S    +   KD G  +A VE  D+     
Sbjct: 6   SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVAS----VVMDKDKG-VFAIVEMGDVGAREA 60

Query: 266 AVE 268
            + 
Sbjct: 61  VLS 63

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

 Score = 58.5 bits (142), Expect = 2e-11
 Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 5/59 (8%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
            VYV NL     + E+   F  +G L +  +           +AFVEFED     +AV 
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVR 55

>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 = 59.0 bits (143), Expect = 2e-11
 Identities = 24/98 (24%), Positives = 40/98 (40%), Gaps = 8/98 (8%)

Query: 173 VPQPTTQQETVSSYAYEKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKF 232
             Q T  + T  +Y        + EE    + E + +SVYV N+    +  ++   F   
Sbjct: 5   CMQTTHSKMTAGAYTEGPPQPLSAEE----KKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60

Query: 233 GELSSEGVVIRSRKDVGIC--YAFVEFEDMTGVRNAVE 268
           G ++   + I   K  G    YA++EF +   V  AV 
Sbjct: 61  GSINR--ITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96

>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 = 58.5 bits (142), Expect = 2e-11
 Identities = 21/58 (36%), Positives = 34/58 (58%), Gaps = 3/58 (5%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +YV NLPP +   +I + F K+G +    + +++R+  G  +AFVEFED     +AV 
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRD--IDLKNRRG-GPPFAFVEFEDPRDAEDAVY 79

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

 Score = 59.1 bits (143), Expect = 3e-11
 Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 5/59 (8%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
            VYV NL  + +++E+   F  +G L S  V           +AFVEFED     +AV 
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVR 128

>1gy6_A Nuclear transport factor 2; 1.6A {Rattus norvegicus} SCOP: d.17.4.2 PDB: 1a2k_A 1oun_A 1ar0_A 1u5o_A 1ask_A 1gy5_A 1jb5_A 1jb4_A 1jb2_A 1qma_A Length = 127

 Score = 57.6 bits (139), Expect = 8e-11
 Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 3/55 (5%)

Query: 1   MSLNYSGI--EIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK 53
            SL +  I   I       + +  ++ MV G ++  +      F Q F L     
Sbjct: 57  SSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADE-DPIMGFHQMFLLKNIND 110

>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 = 56.0 bits (136), Expect = 1e-10
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 4/66 (6%)

Query: 205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMTG 262
           E + +S+YV N+    +  E+   F   G ++   V I   K  G    +A++EF D   
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNR--VTILCDKFSGHPKGFAYIEFSDKES 60

Query: 263 VRNAVE 268
           VR ++ 
Sbjct: 61  VRTSLA 66

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 56.0 bits (135), Expect = 1e-10
 Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 6/62 (9%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
             V+VR L  SV E+++ E  +KFG +    V++   K      A VEFE++   +  V 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICY--VMMMPFK----RQALVEFENIDSAKECVT 69

Query: 269 VC 270
             
Sbjct: 70  FA 71

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 55.9 bits (135), Expect = 2e-10
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 6/60 (10%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
             V++R L   V E+++ E  ++FG + S  VV+  ++      A VEFED+ G  NAV 
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPI-SYVVVMPKKR-----QALVEFEDVLGACNAVN 75

>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 = 55.3 bits (134), Expect = 2e-10
 Identities = 12/60 (20%), Positives = 28/60 (46%), Gaps = 6/60 (10%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
             ++V  L P+ S + +A EF +FG + +  +           +A++++E +   + A  
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRT--IDHVKGDS----FAYIQYESLDAAQAACA 71

>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 = 55.4 bits (134), Expect = 2e-10
 Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 6/66 (9%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
           +    +K +YVRNL  S SE  I +EF      + E V     +D    YAFV F +   
Sbjct: 10  DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK--IRD----YAFVHFSNRED 63

Query: 263 VRNAVE 268
              A++
Sbjct: 64  AVEAMK 69

>1zo2_A NTF2, nuclear transport factor 2; structural genomics, structural genomics consortium, SGC, transport protein; 1.60A {Cryptosporidium parvum} SCOP: d.17.4.2 Length = 129

 Score = 56.1 bits (135), Expect = 2e-10
 Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 3/54 (5%)

Query: 1   MSLNYSGI--EIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQE 52
            SLN+  +  EI       S N G +V V+G V++ D     KF Q F L P  
Sbjct: 61  NSLNFQRVQFEITRVDCQPSPNNGSIVFVTGDVRIDD-GQPLKFSQVFNLMPSG 113

>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 = 56.8 bits (138), Expect = 3e-10
 Identities = 13/73 (17%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 196 GEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFV 255
           G  +    +     ++++ NL P+ S +E+     +    +    V+  R      + +V
Sbjct: 1   GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYV 59

Query: 256 EFEDMTGVRNAVE 268
           +FE    +  A+E
Sbjct: 60  DFESAEDLEKALE 72

>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 = 51.1 bits (123), Expect = 3e-08
 Identities = 14/68 (20%), Positives = 28/68 (41%), Gaps = 9/68 (13%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDM 260
           +     +++  +NL  +++E E+ E F+   E       IR     G     A++EF+  
Sbjct: 94  KKVRAARTLLAKNLSFNITEDELKEVFEDALE-------IRLVSQDGKSKGIAYIEFKSE 146

Query: 261 TGVRNAVE 268
                 +E
Sbjct: 147 ADAEKNLE 154

>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 = 55.4 bits (134), Expect = 3e-10
 Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 8/69 (11%)

Query: 200 SAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED 259
           S      ++K ++VRNL  +V+E  + + F +FG+L      ++  KD    YAF+ F++
Sbjct: 3   SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLER----VKKLKD----YAFIHFDE 54

Query: 260 MTGVRNAVE 268
             G   A+E
Sbjct: 55  RDGAVKAME 63

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 55.1 bits (133), Expect = 4e-10
 Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 200 SAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC-YAFVEFE 258
             ++++ + +SVY++  P   +  +I E  +  G++ +  + +R           FV F+
Sbjct: 3   WILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLN--IQMRRTLHKAFKGSIFVVFD 60

Query: 259 DMTGVRNAVE 268
            +   +  VE
Sbjct: 61  SIESAKKFVE 70

>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 = 55.2 bits (133), Expect = 4e-10
 Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVE 268
           +++  +P      EI EE  K  E   + +V  S  D      +AFVE+E       A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

>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 = 56.4 bits (137), Expect = 4e-10
 Identities = 13/61 (21%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           + +YV NL  +++E  + + F+  G +++   ++  + +  + YAFVE+        A++
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANI-KIMIDKNNKNVNYAFVEYHQSHDANIALQ 59

Query: 269 V 269
            
Sbjct: 60  T 60

>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 = 44.8 bits (107), Expect = 4e-06
 Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 10/64 (15%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGVR 264
           +++V +L  +V +  +   FK F    S  V+       SR      Y FV F      +
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSR-----GYGFVSFTSQDDAQ 143

Query: 265 NAVE 268
           NA++
Sbjct: 144 NAMD 147

>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 = 54.7 bits (132), Expect = 5e-10
 Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 10/71 (14%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEF 257
            D  E K+V++RNL     E  + E  ++FG+L    VV+      S+   G   AF +F
Sbjct: 10  SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSK---G--CAFAQF 64

Query: 258 EDMTGVRNAVE 268
                 +  + 
Sbjct: 65  MTQEAAQKCLA 75

>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 = 54.2 bits (131), Expect = 7e-10
 Identities = 12/78 (15%), Positives = 31/78 (39%), Gaps = 13/78 (16%)

Query: 197 EEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGI 250
           E+     +     ++++ NL P+ S +E+     +    +   + +       +R     
Sbjct: 6   EDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKND--LAVVDVRTGTNR----- 58

Query: 251 CYAFVEFEDMTGVRNAVE 268
            + +V+FE    +  A+E
Sbjct: 59  KFGYVDFESAEDLEKALE 76

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 8/66 (12%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
           E E     ++VR  P  V ESE+ E F  FG +      ++        +AFVEFE+   
Sbjct: 26  EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE----VKILNG----FAFVEFEEAES 77

Query: 263 VRNAVE 268
              A+E
Sbjct: 78  AAKAIE 83

>1gy7_A Nuclear transport factor 2; protein transport; 1.6A {Saccharomyces cerevisiae} SCOP: d.17.4.2 PDB: 1gyb_A Length = 125

 Score = 54.5 bits (131), Expect = 1e-09
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 3/56 (5%)

Query: 1   MSLNYSGI--EIKTAHSLES-WNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK 53
           +SL +  +   I T  +  +   G VLVM++G + + +    ++F Q F L P   
Sbjct: 55  VSLPFQKVQHRITTLDAQPASPYGDVLVMITGDLLIDEEQNPQRFSQVFHLIPDGN 110

>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 = 53.7 bits (129), Expect = 1e-09
 Identities = 13/65 (20%), Positives = 29/65 (44%), Gaps = 6/65 (9%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           + +++R LP  V+E+E+      FG++++  +++   K      AF+E          V 
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPFGKVTN--ILMLKGK----NQAFLELATEEAAITMVN 69

Query: 269 VCILM 273
               +
Sbjct: 70  YYSAV 74

>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 = 53.4 bits (129), Expect = 1e-09
 Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 6/58 (10%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++V NLPP ++E E+ + F+K+G+       +   KD G  + F+  E  T    A  
Sbjct: 18  LFVGNLPPDITEEEMRKLFEKYGKAGE----VFIHKDKG--FGFIRLETRTLAEIAKV 69

>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 = 52.9 bits (128), Expect = 1e-09
 Identities = 12/63 (19%), Positives = 31/63 (49%), Gaps = 10/63 (15%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGVRN 265
           +Y+R L P  ++ ++ +  + +G++ S   ++     + +      Y FV+F+  +  + 
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCK-----GYGFVDFDSPSAAQK 62

Query: 266 AVE 268
           AV 
Sbjct: 63  AVT 65

>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 = 54.0 bits (130), Expect = 1e-09
 Identities = 9/66 (13%), Positives = 27/66 (40%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
           +        ++ N+P S+++ ++ +  +      +   V+      G+  A V+F++   
Sbjct: 10  DVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDD 69

Query: 263 VRNAVE 268
            R +  
Sbjct: 70  ARKSER 75

>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 = 53.4 bits (129), Expect = 1e-09
 Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 193 ADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICY 252
           +   E+    +     +++  +NL  +++E E+ E F+   E+       +S+   G   
Sbjct: 1   SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSK---G--I 55

Query: 253 AFVEFEDMTGVRNAVE 268
           A++EF+        +E
Sbjct: 56  AYIEFKSEADAEKNLE 71

>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 = 53.9 bits (130), Expect = 1e-09
 Identities = 14/68 (20%), Positives = 31/68 (45%), Gaps = 4/68 (5%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDM 260
            +E + ++V+   L   +   ++ + F   G++    V I S ++       A+VEF ++
Sbjct: 20  PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRD--VRIISDRNSRRSKGIAYVEFCEI 77

Query: 261 TGVRNAVE 268
             V  A+ 
Sbjct: 78  QSVPLAIG 85

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 53.3 bits (128), Expect = 2e-09
 Identities = 13/65 (20%), Positives = 28/65 (43%), Gaps = 6/65 (9%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           + +++R LP  V+E E+      FG++++  +++   K      AF+E          V 
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPFGKVTN--LLMLKGK----NQAFIEMNTEEAANTMVN 70

Query: 269 VCILM 273
               +
Sbjct: 71  YYTSV 75

>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 = 53.0 bits (128), Expect = 2e-09
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 10/70 (14%)

Query: 204 DEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFE 258
           D + + ++ V NL    S   +   F+K+G +    +         R   G  +AFV F 
Sbjct: 9   DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPR---G--FAFVRFH 63

Query: 259 DMTGVRNAVE 268
           D    ++A  
Sbjct: 64  DRRDAQDAEA 73

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 9/66 (13%), Positives = 22/66 (33%), Gaps = 2/66 (3%)

Query: 205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGI--CYAFVEFEDMTG 262
              + ++ +RN+ P      I      +  L+   + +   K       +AFV+      
Sbjct: 6   HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMD 65

Query: 263 VRNAVE 268
               ++
Sbjct: 66  ASQLLQ 71

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

 Score = 52.6 bits (127), Expect = 2e-09
 Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 8/60 (13%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
             +++ NLP   +E EI   F+++G++      I         Y FV  ED T   +A+ 
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLE--CDIIKN------YGFVHIEDKTAAEDAIR 60

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

 Score = 52.6 bits (127), Expect = 2e-09
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 8/60 (13%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
             ++V N+ P+ +  E+  +F+++G +    +V    KD    YAFV  E       A+ 
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDIV----KD----YAFVHMERAEDAVEAIR 62

>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 = 56.1 bits (136), Expect = 2e-09
 Identities = 10/58 (17%), Positives = 25/58 (43%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +++ N PPS ++  I +  +    ++    +   R +    +A+++       R  VE
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177

>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 = 53.8 bits (130), Expect = 1e-08
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 2/62 (3%)

Query: 207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNA 266
           E+ +V V+NLP S +++++ + FK  G +    V    +K+    +A +EF    G   A
Sbjct: 40  ELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR--FARIEFARYDGALAA 97

Query: 267 VE 268
           + 
Sbjct: 98  IT 99

>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 = 51.1 bits (123), Expect = 8e-08
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 5/81 (6%)

Query: 192 WADTGEEISAVE-DEEEIKSVYVRNLPPSVS-ESEIAEEFKKFGELSSEGVVIRSRKDVG 249
            ++  E+    +    E + + +RNL   +  E+ + E F+ FG +     +   +K+  
Sbjct: 193 VSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEK-INIPAGQKEHS 251

Query: 250 IC--YAFVEFEDMTGVRNAVE 268
                AF+ FE+      A++
Sbjct: 252 FNNCCAFMVFENKDSAERALQ 272

>1jkg_A P15; NTF2-like domain, transport protein; 1.90A {Homo sapiens} SCOP: d.17.4.2 PDB: 1jn5_A Length = 140

 Score = 53.8 bits (129), Expect = 2e-09
 Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 7/62 (11%)

Query: 1   MSLNYSGIEIKTAHS------LESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKV 54
             L  S  +I                  VLV++ GSV+ +  + +R F Q F L  Q   
Sbjct: 63  EMLPSSEFQISVVDCQPVHDEATPSQTTVLVVICGSVKFEG-NKQRDFNQNFILTAQASP 121

Query: 55  PN 56
            N
Sbjct: 122 SN 123

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 53.6 bits (129), Expect = 2e-09
 Identities = 19/99 (19%), Positives = 36/99 (36%), Gaps = 10/99 (10%)

Query: 175 QPTTQQETVSSYAYEKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGE 234
            P +   T  +         +G    +       + +YV  L   V +  +   F  FG+
Sbjct: 30  LPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGD 89

Query: 235 LSSEGVVI-----RSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++   + +     + R   G  +AFVEFE       A++
Sbjct: 90  ITDIQIPLDYETEKHR---G--FAFVEFELAEDAAAAID 123

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 52.3 bits (126), Expect = 3e-09
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 6/60 (10%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
             +Y+ NL P+V+  ++ + F         G V+         YAFV++ D      A+E
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLP-LAGQVLLKSG-----YAFVDYPDQNWAIRAIE 62

>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 = 51.9 bits (125), Expect = 3e-09
 Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 10/73 (13%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
            +++ I ++YV  L  +++E+++   F +FGE+ +  + +  R+      AF++F     
Sbjct: 7   GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRT--ITVVQRQQ----CAFIQFAT--- 57

Query: 263 VRNAVEVCILMWH 275
            R A EV      
Sbjct: 58  -RQAAEVAAEKSF 69

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 52.6 bits (126), Expect = 4e-09
 Identities = 12/64 (18%), Positives = 28/64 (43%), Gaps = 6/64 (9%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           + +++R LP  V+E E+      FG++++  ++++ +       AF+E          V 
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTN-LLMLKGK-----NQAFIEMNTEEAANTMVN 85

Query: 269 VCIL 272
               
Sbjct: 86  YYTS 89

>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 = 55.1 bits (133), Expect = 4e-09
 Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 10/73 (13%)

Query: 200 SAVEDEEEIKS----VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFV 255
           S ++  E+  +    ++V NLP  ++E +    F+++GE S    + R R      + F+
Sbjct: 10  SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSE-VFINRDR-----GFGFI 63

Query: 256 EFEDMTGVRNAVE 268
             E  T    A  
Sbjct: 64  RLESRTLAEIAKA 76

>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 = 48.9 bits (117), Expect = 4e-07
 Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 9/64 (14%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----RSRKDVGICYAFVEFEDMTGVRNA 266
           + V+NL P VS   + + F +FG +    VV+    R+         FVEF      R A
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRAT-----GKGFVEFAAKPPARKA 153

Query: 267 VEVC 270
           +E C
Sbjct: 154 LERC 157

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 9/66 (13%)

Query: 207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----RSRKDVGICYAFVEFEDMTG 262
           E   +++  LP S ++ E+ E  K  G +    +V     + +   G   A+VE+E+ + 
Sbjct: 16  EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPK---G--LAYVEYENESQ 70

Query: 263 VRNAVE 268
              AV 
Sbjct: 71  ASQAVM 76

>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 = 51.9 bits (125), Expect = 4e-09
 Identities = 13/74 (17%), Positives = 32/74 (43%), Gaps = 8/74 (10%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR------KDVGIC--YAF 254
               +  +++V+ L  +V+   +A+ FK+ G + +     +        ++ G     A 
Sbjct: 8   HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 67

Query: 255 VEFEDMTGVRNAVE 268
           V F+D    + A++
Sbjct: 68  VSFDDPPSAKAAID 81

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 52.4 bits (126), Expect = 4e-09
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 7/62 (11%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI--RSRKDVGICYAFVEFEDMTGVRNA 266
           + +Y+RNLP  ++  E+ + F K+G +    V     +R       A+V +ED+   +NA
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR-----GTAYVVYEDIFDAKNA 63

Query: 267 VE 268
           V+
Sbjct: 64  VD 65

>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 = 52.1 bits (125), Expect = 4e-09
 Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 2/67 (2%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGI-CYAFVEFEDMT 261
            D      V +R LP   S+ EI + F     +   G+ +           AFV+F    
Sbjct: 10  PDTANDGFVRLRGLPFGCSKEEIVQFFSGLE-IVPNGMTLPVDFQGRSTGEAFVQFASQE 68

Query: 262 GVRNAVE 268
               A++
Sbjct: 69  IAEKALK 75

>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 = 55.0 bits (133), Expect = 5e-09
 Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 10/63 (15%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGVRN 265
           + V NLPPS+++ +  E  + FG L    +V      +S+      Y F E+        
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSK-----GYGFAEYMKKDSAAR 152

Query: 266 AVE 268
           A  
Sbjct: 153 AKS 155

>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 = 52.3 bits (126), Expect = 4e-08
 Identities = 10/66 (15%), Positives = 21/66 (31%), Gaps = 7/66 (10%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
                 + + +R LP  V+  E+ +    +        V + +       AFV   +   
Sbjct: 17  RQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCF--VDKYK-----GTAFVTLLNGEQ 69

Query: 263 VRNAVE 268
              A+ 
Sbjct: 70  AEAAIN 75

>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 = 49.2 bits (118), Expect = 4e-07
 Identities = 11/79 (13%), Positives = 25/79 (31%), Gaps = 5/79 (6%)

Query: 191 SWADTGEEISAVEDEEEIKSVYVRNLPPSVSESE-IAEEFKKFGELSSEGVVIRSRKDVG 249
            W D G+           + + V  LPP  ++ + +          +    +   +    
Sbjct: 170 HWTDAGQLT---PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTF-CQLACGQDGQL 225

Query: 250 ICYAFVEFEDMTGVRNAVE 268
             +A +E+E       A +
Sbjct: 226 KGFAVLEYETAEMAEEAQQ 244

>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 = 51.9 bits (125), Expect = 5e-09
 Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 8/69 (11%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI---RSRKDVGICYAFVEFED 259
           E +   K ++V N+P    + ++ + F +FG++    ++     S+      + FV FE+
Sbjct: 10  ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK-----GFGFVTFEN 64

Query: 260 MTGVRNAVE 268
                 A E
Sbjct: 65  SADADRARE 73

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 52.0 bits (125), Expect = 5e-09
 Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 4/62 (6%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI--RSRKDVGICYAFVEFEDMTGVRNA 266
           K V    L  +V E+ + +  +K+GE+    +++  R+RK +G   A V F    G +  
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLG--LARVLFTSTRGAKET 64

Query: 267 VE 268
           V+
Sbjct: 65  VK 66

>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 = 51.5 bits (124), Expect = 6e-09
 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 200 SAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED 259
             +ED+ + +++YV NL   V+E  I + F + G   S    + +       Y FVEF +
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKS--CKMITEHTSNDPYCFVEFYE 64

Query: 260 MTGVRNAVEV 269
                 A+  
Sbjct: 65  HRDAAAALAA 74

>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 = 51.9 bits (125), Expect = 7e-09
 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 9/69 (13%)

Query: 204 DEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----RSRKDVGICYAFVEFED 259
           + +    +++  L    +E  +   F K G +S   ++     +SR      +AF+ FE+
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSR-----GFAFITFEN 57

Query: 260 MTGVRNAVE 268
               +NA +
Sbjct: 58  PADAKNAAK 66

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 51.4 bits (123), Expect = 7e-09
 Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 5/66 (7%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
           E       VYV NLP     S++    ++ G +         R       AF+ + D   
Sbjct: 14  EGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPR-----RRAFLHYPDSAA 68

Query: 263 VRNAVE 268
            + AV 
Sbjct: 69  AQQAVS 74

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 51.5 bits (124), Expect = 8e-09
 Identities = 15/69 (21%), Positives = 33/69 (47%), Gaps = 8/69 (11%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI---RSRKDVGICYAFVEFED 259
           E++ + K ++V N+P    + ++ + F +FG++    ++     S+      + FV FE+
Sbjct: 24  ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK-----GFGFVTFEN 78

Query: 260 MTGVRNAVE 268
                 A E
Sbjct: 79  SADADRARE 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 = 52.6 bits (127), Expect = 8e-09
 Identities = 14/60 (23%), Positives = 30/60 (50%), Gaps = 2/60 (3%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVE 268
           ++ V  LP  +++ E+   F+  G +++   ++R  K      YAFV+F      + A++
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTC-RIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 46.8 bits (112), Expect = 1e-06
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 16/83 (19%)

Query: 191 SWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSR 245
           S+A  G E        +  ++YV NLP ++++ ++   F K+G +  + ++      R R
Sbjct: 78  SYARPGGE------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPR 131

Query: 246 KDVGICYAFVEFEDMTGVRNAVE 268
                  AFV +      + A+ 
Sbjct: 132 -----GVAFVRYNKREEAQEAIS 149

>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 = 50.7 bits (122), Expect = 8e-09
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 8/58 (13%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++V N+  + +  E+   F++ G +    VV    KD    YAFV  E     + A+ 
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVV----KD----YAFVHMEKEADAKAAIA 61

>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 = 51.6 bits (124), Expect = 9e-09
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 10/83 (12%)

Query: 196 GEEISAVEDEEEIK--SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR------KD 247
           G   S+ + +E+    ++YV+ L  SV+  ++A+ FK+ G +       +        K+
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 248 VGIC--YAFVEFEDMTGVRNAVE 268
            G     A V +ED    + AVE
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVE 83

>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 = 50.8 bits (122), Expect = 9e-09
 Identities = 15/69 (21%), Positives = 27/69 (39%)

Query: 200 SAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED 259
            +   +     + V+N+P +VS  EI + F  +  +     +  + K +    A V FE 
Sbjct: 7   GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66

Query: 260 MTGVRNAVE 268
                 AV 
Sbjct: 67  RDEATAAVI 75

>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 = 50.7 bits (122), Expect = 1e-08
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 10/71 (14%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEF 257
            + +    + V  L    +E ++ E F K+G ++   +V      RSR      +AFV F
Sbjct: 10  ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR-----GFAFVYF 64

Query: 258 EDMTGVRNAVE 268
           E++   + A E
Sbjct: 65  ENVDDAKEAKE 75

>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 = 51.2 bits (123), Expect = 1e-08
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 202 VEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGV-VIRSRKDVGIC--YAFVEFE 258
           V  ++    + VRN+P   ++ EI E F  FGEL +  V + +     G    + FV+F 
Sbjct: 9   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKT--VRLPKKMTGTGAHRGFGFVDFI 66

Query: 259 DMTGVRNAVE 268
                + A  
Sbjct: 67  TKQDAKKAFN 76

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 10/74 (13%)

Query: 200 SAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAF 254
           S+    E  K +Y++NL P V+E ++   F +F E     +       R R       AF
Sbjct: 17  SSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMR-----GQAF 71

Query: 255 VEFEDMTGVRNAVE 268
           + F +      A+ 
Sbjct: 72  ITFPNKEIAWQALH 85

>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 = 50.4 bits (121), Expect = 1e-08
 Identities = 16/69 (23%), Positives = 27/69 (39%)

Query: 200 SAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED 259
            A   +     + V+N+P +VS  EI + F  +  +     +  + K +    A V FE 
Sbjct: 7   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66

Query: 260 MTGVRNAVE 268
                 AV 
Sbjct: 67  RDEATAAVI 75

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 10/90 (11%)

Query: 184 SSYAYEKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI- 242
           S    ++    +        D E + S+ V NL    S   +   F+K+G +    +   
Sbjct: 23  SMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD 82

Query: 243 ----RSRKDVGICYAFVEFEDMTGVRNAVE 268
                SR   G  +AFV F D     +A++
Sbjct: 83  RYTKESR---G--FAFVRFHDKRDAEDAMD 107

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 49.5 bits (119), Expect = 2e-08
 Identities = 12/63 (19%), Positives = 25/63 (39%), Gaps = 8/63 (12%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI---RSRKDVGICYAFVEFEDMTGVRN 265
             ++VRNLP   +   + ++F + G +    + +   +S+         V+FE       
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSK-----GCGVVKFESPEVAER 63

Query: 266 AVE 268
           A  
Sbjct: 64  ACR 66

>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 = 51.4 bits (124), Expect = 3e-08
 Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVE 268
           ++ V  LP ++++ E    F   GE+ S   ++R +     + Y FV + D      A+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESC-KLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

>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 = 44.9 bits (107), Expect = 4e-06
 Identities = 12/63 (19%), Positives = 30/63 (47%), Gaps = 10/63 (15%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGVRN 265
           +YV  LP ++++ E+ + F ++G + +  +++      SR        F+ F+       
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSR-----GVGFIRFDKRIEAEE 145

Query: 266 AVE 268
           A++
Sbjct: 146 AIK 148

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 50.1 bits (120), Expect = 3e-08
 Identities = 14/74 (18%), Positives = 34/74 (45%), Gaps = 8/74 (10%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR------KDVGIC--YAF 254
           +D  +  +++V+ L  +V+   +A+ FK+ G + +     +        ++ G     A 
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 255 VEFEDMTGVRNAVE 268
           V F+D    + A++
Sbjct: 62  VSFDDPPSAKAAID 75

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

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 14/59 (23%), Positives = 33/59 (55%), Gaps = 9/59 (15%)

Query: 211 VYVRNLPP-SVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +++ NLP  +VS+ ++   F  +G +    + I++       + F++F++   VR+A+E
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQ--INIKNA------FGFIQFDNPQSVRDAIE 63

>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 = 49.6 bits (119), Expect = 3e-08
 Identities = 18/80 (22%), Positives = 31/80 (38%), Gaps = 9/80 (11%)

Query: 193 ADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----RSRKDV 248
             +G        EE  ++V+V NL   V E  + E F + G L+   +      + +   
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPK--- 57

Query: 249 GICYAFVEFEDMTGVRNAVE 268
              + FV F+    V  A+ 
Sbjct: 58  --SFGFVCFKHPESVSYAIA 75

>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 = 49.8 bits (119), Expect = 3e-08
 Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 6/60 (10%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
             +  +NLP     +EI E F +FG L    V++          A VEF +    R A  
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGR--VLLPEGG----ITAIVEFLEPLEARKAFR 64

>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 = 51.6 bits (124), Expect = 3e-08
 Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 10/63 (15%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGVRN 265
           +++  LP  +++ ++ E    FG L +  +V       S+      YAF E+ D+     
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK-----GYAFCEYVDINVTDQ 171

Query: 266 AVE 268
           A+ 
Sbjct: 172 AIA 174

>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 = 50.8 bits (122), Expect = 6e-08
 Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 5/65 (7%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSS-EGVVIRSRKDVGI----CYAFVEFEDMTGV 263
           + +YV N+P  ++E  + + F     L             V I     +AF+EF  +   
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 264 RNAVE 268
             A+ 
Sbjct: 65  TQAMA 69

>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 = 49.9 bits (120), Expect = 3e-08
 Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 8/61 (13%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI---RSRKDVGICYAFVEFEDMTGVRNAV 267
           ++++NL  S+    + + F  FG + S  VV     S+      Y FV FE       A+
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK-----GYGFVHFETQEAAERAI 62

Query: 268 E 268
           E
Sbjct: 63  E 63

>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 = 50.6 bits (121), Expect = 4e-08
 Identities = 19/84 (22%), Positives = 32/84 (38%), Gaps = 10/84 (11%)

Query: 190 KSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RS 244
            +  +         D E + S+ V NL    S   +   F+K+G +    +        S
Sbjct: 52  FTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKES 111

Query: 245 RKDVGICYAFVEFEDMTGVRNAVE 268
           R   G  +AFV F D     +A++
Sbjct: 112 R---G--FAFVRFHDKRDAEDAMD 130

>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 = 49.2 bits (118), Expect = 4e-08
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 5/68 (7%)

Query: 204 DEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIR---SRKDVGICYAFVEFEDM 260
                 S+++ +L P + E+ I+  F   GE      +IR   +    G  Y FVEF D+
Sbjct: 5   SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAG--YCFVEFADL 62

Query: 261 TGVRNAVE 268
                 + 
Sbjct: 63  ATAEKCLH 70

>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 = 50.1 bits (120), Expect = 4e-08
 Identities = 15/71 (21%), Positives = 37/71 (52%), Gaps = 10/71 (14%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEF 257
            + + ++++ V  +P +V E ++ + F+++G + S  +V      +SR      Y FV+F
Sbjct: 37  PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSR-----GYGFVKF 91

Query: 258 EDMTGVRNAVE 268
           +  +  + A+ 
Sbjct: 92  QSGSSAQQAIA 102

>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 = 49.7 bits (119), Expect = 4e-08
 Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 10/71 (14%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEF 257
           +D      V+V +L P ++  +I   F  FG +S   VV      +S+      Y FV F
Sbjct: 10  KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSK-----GYGFVSF 64

Query: 258 EDMTGVRNAVE 268
            +     NA++
Sbjct: 65  FNKWDAENAIQ 75

>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 = 48.7 bits (117), Expect = 4e-08
 Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMTGVRNAVE 268
           V++  L  +V++  I E F  +G++     +   R    +   YA+VEFE+      A++
Sbjct: 7   VHIGRLTRNVTKDHIMEIFSTYGKIKM-IDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

>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 = 48.9 bits (117), Expect = 4e-08
 Identities = 14/59 (23%), Positives = 33/59 (55%), Gaps = 9/59 (15%)

Query: 211 VYVRNLP-PSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +++ NLP  +VS+ ++   F  +G +    + I++       + F++F++   VR+A+E
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQ--INIKNA------FGFIQFDNPQSVRDAIE 75

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 48.8 bits (117), Expect = 5e-08
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 16/69 (23%)

Query: 206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGICYAFVEFED 259
            E K++ + NL  S +E  + E F+K        + +      +S+   G  YAF+EF  
Sbjct: 13  GESKTLVLSNLSYSATEETLQEVFEKATF-----IKVPQNQNGKSK---G--YAFIEFAS 62

Query: 260 MTGVRNAVE 268
               + A+ 
Sbjct: 63  FEDAKEALN 71

>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 = 50.3 bits (121), Expect = 5e-08
 Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 10/71 (14%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEF 257
           +       +++  LP  +++ ++ E    FG L +  +V       S+      YAF E+
Sbjct: 89  QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK-----GYAFCEY 143

Query: 258 EDMTGVRNAVE 268
            D+     A+ 
Sbjct: 144 VDINVTDQAIA 154

>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 = 49.9 bits (120), Expect = 9e-08
 Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 9/67 (13%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSS-----EGVVIR--SRKDVGICYAFVEFEDMT 261
           + +YV N+P  ++E  + + F     L          V+     +D    +AF+EF  + 
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN--FAFLEFRSVD 62

Query: 262 GVRNAVE 268
               A+ 
Sbjct: 63  ETTQAMA 69

>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 = 51.1 bits (123), Expect = 6e-08
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 8/70 (11%)

Query: 204 DEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGV-VIR---SRKDVGICYAFVEFED 259
               + S+YV +L P V+E+ + E+F   G + S  + V R   +R+ +G  YA+V F+ 
Sbjct: 11  PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILS--IRVCRDMITRRSLG--YAYVNFQQ 66

Query: 260 MTGVRNAVEV 269
                 A++ 
Sbjct: 67  PADAERALDT 76

>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 = 46.1 bits (110), Expect = 3e-06
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 8/62 (12%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI---RSRKDVGICYAFVEFEDMTGVRNA 266
           +++++NL  S+    + + F  FG + S  VV     S+      Y FV FE       A
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK-----GYGFVHFETQEAAERA 159

Query: 267 VE 268
           +E
Sbjct: 160 IE 161

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 51.2 bits (123), Expect = 6e-08
 Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 10/71 (14%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEF 257
                +  VYV ++   + E  I + F  FG + S  +       + +      +AFVE+
Sbjct: 23  GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK-----GFAFVEY 77

Query: 258 EDMTGVRNAVE 268
           E     + A+E
Sbjct: 78  EVPEAAQLALE 88

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 51.2 bits (123), Expect = 6e-08
 Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 10/71 (14%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEF 257
           E+      +YV ++   +S+ +I   F+ FG++ S  +       + +      Y F+E+
Sbjct: 120 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHK-----GYGFIEY 174

Query: 258 EDMTGVRNAVE 268
           E     ++AV 
Sbjct: 175 EKAQSSQDAVS 185

>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 = 48.8 bits (117), Expect = 6e-08
 Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 13/66 (19%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGICYAFVEFEDMTG 262
            +V+V  +   + E+EI   F ++G +    V I       S+      Y FV F +   
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKE--VKIITDRTGVSK-----GYGFVSFYNDVD 62

Query: 263 VRNAVE 268
           V+  VE
Sbjct: 63  VQKIVE 68

>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 = 48.8 bits (117), Expect = 6e-08
 Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 10/71 (14%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEF 257
              ++  ++ V NL     E+++ E F+ FG +S   +       +S+      +AF+ F
Sbjct: 10  RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSK-----GFAFISF 64

Query: 258 EDMTGVRNAVE 268
                   A+ 
Sbjct: 65  HRREDAARAIA 75

>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 = 48.3 bits (116), Expect = 6e-08
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 10/64 (15%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGVR 264
            V+V +L P ++ + IA  F  FG +S   VV      +S+      Y FV F +     
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSK-----GYGFVSFFNKWDAE 62

Query: 265 NAVE 268
           NA++
Sbjct: 63  NAIQ 66

>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 = 48.4 bits (116), Expect = 7e-08
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 10/65 (15%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGV 263
            +VYV NLP S++ +++   F K+G++    ++      +S+   G   AF+ F D    
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSK---G--VAFILFLDKDSA 71

Query: 264 RNAVE 268
           +N   
Sbjct: 72  QNCTR 76

>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 = 47.9 bits (115), Expect = 7e-08
 Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 10/64 (15%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGVR 264
           +++V +L  +V +  +   FK F    S  V+       SR      Y FV F      +
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSR-----GYGFVSFTSQDDAQ 57

Query: 265 NAVE 268
           NA++
Sbjct: 58  NAMD 61

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 48.8 bits (116), Expect = 8e-08
 Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGI--CYAFVEFEDMTGVRNA 266
           + V+V  LPP + E EI   F++FG L  +       K       YAF+ F++ + V+  
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

Query: 267 VEVCI 271
           ++ C+
Sbjct: 69  IDACL 73

>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 = 48.5 bits (116), Expect = 8e-08
 Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 6/59 (10%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +VY   +   +++  + + F  FG++      IR   + G  Y+FV F       +A+ 
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIME----IRVFPEKG--YSFVRFSTHESAAHAIV 79

>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 = 50.4 bits (121), Expect = 8e-08
 Identities = 14/73 (19%), Positives = 35/73 (47%), Gaps = 12/73 (16%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGICYAFVE 256
           ++ E+++ +++  L    ++  +   F+++G L ++ VV+      RSR      + FV 
Sbjct: 8   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL-TDCVVMRDPNTKRSR-----GFGFVT 61

Query: 257 FEDMTGVRNAVEV 269
           +  +  V  A+  
Sbjct: 62  YATVEEVDAAMNA 74

>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 = 44.6 bits (106), Expect = 8e-06
 Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 14/83 (16%)

Query: 193 ADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-------RSR 245
           A + E+         +K ++V  +     E  + + F+++G++  E + I       + R
Sbjct: 89  AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI--EVIEIMTDRGSGKKR 146

Query: 246 KDVGICYAFVEFEDMTGVRNAVE 268
                 +AFV F+D   V   V 
Sbjct: 147 -----GFAFVTFDDHDSVDKIVI 164

>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 = 48.0 bits (115), Expect = 8e-08
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 10/65 (15%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGV 263
           + VY+ ++P   +E +I +     G + +  ++      RS+   G  YAF+EF D+   
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSK---G--YAFIEFRDLESS 57

Query: 264 RNAVE 268
            +AV 
Sbjct: 58  ASAVR 62

>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 = 47.9 bits (115), Expect = 9e-08
 Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 10/65 (15%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGV 263
           + +YV  L   V +  +   F  FG+++   + +     + R   G  +AFVEFE     
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR---G--FAFVEFELAEDA 62

Query: 264 RNAVE 268
             A++
Sbjct: 63  AAAID 67

>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 = 48.0 bits (115), Expect = 9e-08
 Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 10/71 (14%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEF 257
                   ++VRNL  + SE ++ + F  +G LS     I     + +      +AFV F
Sbjct: 3   SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPK-----GFAFVTF 57

Query: 258 EDMTGVRNAVE 268
                   A  
Sbjct: 58  MFPEHAVKAYA 68

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 9/59 (15%), Positives = 25/59 (42%), Gaps = 6/59 (10%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           + Y+ N+P   +E+++   F+ FG +       +   + G    F++++        + 
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILD----FKHYPEKG--CCFIKYDTHEQAAVCIV 81

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 48.3 bits (115), Expect = 1e-07
 Identities = 16/79 (20%), Positives = 28/79 (35%), Gaps = 3/79 (3%)

Query: 193 ADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--- 249
             T  E++    +E    V +R LP + +  E+   F +   ++     I          
Sbjct: 8   GGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRP 67

Query: 250 ICYAFVEFEDMTGVRNAVE 268
              AFV F      +NA+ 
Sbjct: 68  TGDAFVLFACEEYAQNALR 86

>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 = 48.0 bits (115), Expect = 1e-07
 Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 9/62 (14%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----RSRKDVGICYAFVEFEDMTGVRNA 266
           + V NL   VS+++I E F +FG L    V      RS        A V FE       A
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSL-----GTADVHFERKADALKA 86

Query: 267 VE 268
           ++
Sbjct: 87  MK 88

>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 = 48.3 bits (115), Expect = 1e-07
 Identities = 12/58 (20%), Positives = 21/58 (36%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           VY++ LP       + + FKK   +     +            FVEF +    + A+ 
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC 85

>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 = 48.1 bits (115), Expect = 1e-07
 Identities = 13/63 (20%), Positives = 30/63 (47%), Gaps = 10/63 (15%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGVRN 265
           +++ +LP    + ++ + F  FG + S  V I      S+     C+ FV +++    + 
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK-----CFGFVSYDNPVSAQA 82

Query: 266 AVE 268
           A++
Sbjct: 83  AIQ 85

>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 = 47.6 bits (114), Expect = 1e-07
 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 10/71 (14%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEF 257
             +  ++SV+V N+P   +E ++ + F + G + S  +V      + +   G  Y F E+
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPK---G--YGFCEY 57

Query: 258 EDMTGVRNAVE 268
           +D     +A+ 
Sbjct: 58  QDQETALSAMR 68

>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 = 48.1 bits (115), Expect = 1e-07
 Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 9/73 (12%)

Query: 200 SAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----RSRKDVGICYAFV 255
            A++      +V+V NL   V   ++ E F   G +    ++     +SR         V
Sbjct: 7   GALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSR-----GIGTV 61

Query: 256 EFEDMTGVRNAVE 268
            FE       A+ 
Sbjct: 62  TFEQSIEAVQAIS 74

>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 = 51.0 bits (121), Expect = 2e-07
 Identities = 15/60 (25%), Positives = 31/60 (51%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           K+++V  +    +ES++  EF+ +G +    +V   R      YAF+E+E    + +A +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 49.1 bits (117), Expect = 2e-07
 Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 9/62 (14%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----RSRKDVGICYAFVEFEDMTGVRNA 266
           + V NL   VS+++I E F +FG L    V      RS    G   A V FE       A
Sbjct: 91  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL---G--TADVHFERRADALKA 145

Query: 267 VE 268
           ++
Sbjct: 146 MK 147

>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 = 49.1 bits (118), Expect = 2e-07
 Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 12/69 (17%)

Query: 206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGICYAFVEFED 259
           +E   +++  L    +E  + E F K+G + ++  ++      RSR      + F+ FE 
Sbjct: 1   KESCKMFIGGLNWDTTEDNLREYFGKYGTV-TDLKIMKDPATGRSR-----GFGFLSFEK 54

Query: 260 MTGVRNAVE 268
            + V   V+
Sbjct: 55  PSSVDEVVK 63

>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 = 45.6 bits (109), Expect = 2e-06
 Identities = 12/73 (16%), Positives = 29/73 (39%), Gaps = 14/73 (19%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-------RSRKDVGICYAFV 255
           +++++   ++V  + P V   E  E F ++G +      +       +SR      + FV
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTI--IDAQLMLDKDTGQSR-----GFGFV 134

Query: 256 EFEDMTGVRNAVE 268
            ++    V    +
Sbjct: 135 TYDSADAVDRVCQ 147

>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 = 47.6 bits (114), Expect = 2e-07
 Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 10/73 (13%)

Query: 202 VEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVE 256
           + +  +  +VYV  L   VSE  + E F + G + +  +       + +   G  Y FVE
Sbjct: 9   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQ---G--YGFVE 63

Query: 257 FEDMTGVRNAVEV 269
           F        A+++
Sbjct: 64  FLSEEDADYAIKI 76

>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 = 47.2 bits (113), Expect = 2e-07
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 10/65 (15%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGV 263
             +YV +L  +++E  +   F+ FG++ +  ++      RS+   G  Y F+ F D    
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSK---G--YGFITFSDSECA 60

Query: 264 RNAVE 268
           R A+E
Sbjct: 61  RRALE 65

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 10/63 (15%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGVRN 265
           +++ +LP   +++++A  F  FG + S  V I      S+     C+ FV F++    + 
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSK-----CFGFVSFDNPDSAQV 97

Query: 266 AVE 268
           A++
Sbjct: 98  AIK 100

>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 = 48.2 bits (115), Expect = 2e-07
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 10/71 (14%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEF 257
            + +    + V  L    +E ++ E F K+G ++   +V      RSR      +AFV F
Sbjct: 41  ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR-----GFAFVYF 95

Query: 258 EDMTGVRNAVE 268
           E++   + A E
Sbjct: 96  ENVDDAKEAKE 106

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 48.0 bits (114), Expect = 2e-07
 Identities = 16/86 (18%), Positives = 25/86 (29%), Gaps = 4/86 (4%)

Query: 185 SYAYEKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRS 244
           S+    +        S   D      V +R LP   ++ EI + F           +   
Sbjct: 19  SHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEI--VPNGITLP 76

Query: 245 RKDVGIC--YAFVEFEDMTGVRNAVE 268
               G     AFV+F        A+ 
Sbjct: 77  VDPEGKITGEAFVQFASQELAEKALG 102

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 201 AVEDEEEIKSVYVRNLPPSVSESEIAEE----FKKFGELSSEGVVIRSRKDVGICYAFVE 256
           AV +     ++Y+ NL   + + E+ +     F +FG++    +V RS K  G   AFV 
Sbjct: 1   AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI-LVSRSLKMRG--QAFVI 57

Query: 257 FEDMTGVRNAVE 268
           F++++   NA+ 
Sbjct: 58  FKEVSSATNALR 69

>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 = 48.8 bits (117), Expect = 2e-07
 Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 4/61 (6%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIR---SRKDVGICYAFVEFEDMTGVRNAV 267
           ++V  +P + SE ++ E F+++G +     V+R             FV F        A 
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYE-INVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 268 E 268
            
Sbjct: 65  N 65

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 46.8 bits (112), Expect = 1e-06
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 9/70 (12%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----RSRKDVGICYAFVEFE 258
            +  E + +++  +    +E++I   F  FG++    ++      SR       AFV F 
Sbjct: 90  NNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSR-----GCAFVTFT 144

Query: 259 DMTGVRNAVE 268
                + A++
Sbjct: 145 TRAMAQTAIK 154

>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 = 47.4 bits (113), Expect = 2e-07
 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 9/59 (15%)

Query: 211 VYVRNLPPS-VSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           V++ NL  + V +S++   F K+G ++     +         YAFV++ +    R AV 
Sbjct: 30  VFIGNLNTALVKKSDVETIFSKYGRVAG--CSVHKG------YAFVQYSNERHARAAVL 80

>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 = 46.8 bits (112), Expect = 3e-07
 Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 10/65 (15%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGV 263
           + +YV  L   V +  +   F  FG+++   + +     + R   G  +AFVEFE     
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR---G--FAFVEFELAEDA 67

Query: 264 RNAVE 268
             A++
Sbjct: 68  AAAID 72

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 47.6 bits (113), Expect = 3e-07
 Identities = 14/86 (16%), Positives = 31/86 (36%), Gaps = 7/86 (8%)

Query: 187 AYEKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEE----FKKFGELSSEGVVI 242
            +E+   D+ +  S     E  + V + N+ P V + ++           G++     ++
Sbjct: 8   KFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD---IV 64

Query: 243 RSRKDVGICYAFVEFEDMTGVRNAVE 268
               D     A++ F      +  VE
Sbjct: 65  VDLSDDNSGKAYIVFATQESAQAFVE 90

>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 = 47.4 bits (113), Expect = 3e-07
 Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 9/62 (14%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----RSRKDVGICYAFVEFEDMTGVRNA 266
           + V NL   VS+++I E F +FG L    V      RS    G   A V FE       A
Sbjct: 38  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL---G--TADVHFERRADALKA 92

Query: 267 VE 268
           ++
Sbjct: 93  MK 94

>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 = 47.3 bits (113), Expect = 3e-07
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 12/76 (15%)

Query: 199 ISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGICY 252
           +   + +     ++V  LP   +++ + + F+ FG++  E VVI      +SR      Y
Sbjct: 8   MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDI-EEAVVITDRQTGKSR-----GY 61

Query: 253 AFVEFEDMTGVRNAVE 268
            FV   D      A +
Sbjct: 62  GFVTMADRAAAERACK 77

>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 = 46.8 bits (112), Expect = 3e-07
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 8/61 (13%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI---RSRKDVGICYAFVEFEDMTGVRNAV 267
           +YV+NL   + +  + + F  FG ++S  V++   RS+      + FV F        AV
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSK-----GFGFVCFSSPEEATKAV 72

Query: 268 E 268
            
Sbjct: 73  T 73

>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 = 46.9 bits (112), Expect = 3e-07
 Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 200 SAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED 259
           S      + K ++V  L    SE ++   F+ FG +     V+R         AFV+F  
Sbjct: 8   SESRGGRDRK-LFVGMLNKQQSEEDVLRLFQPFGVIDEC-TVLRGPDGSSKGCAFVKFSS 65

Query: 260 MTGVRNAVE 268
            T  + A+ 
Sbjct: 66  HTEAQAAIH 74

>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 = 47.9 bits (114), Expect = 3e-07
 Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 10/81 (12%)

Query: 193 ADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKD 247
            D  E     +   E   ++V ++     E EI E+F  +GE+ +  + +      S+  
Sbjct: 57  EDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK-- 114

Query: 248 VGICYAFVEFEDMTGVRNAVE 268
               YA VE+E       A E
Sbjct: 115 ---GYALVEYETHKQALAAKE 132

>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 = 47.9 bits (114), Expect = 4e-07
 Identities = 16/60 (26%), Positives = 27/60 (45%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
            ++YV NL    +E +I E F K G++    + +   K     + FVE+       NA+ 
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 4/62 (6%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMTGVRNA 266
            + ++ NLP  V+E  I E F+     +    + R   +      + + EFED+  + +A
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGLNISAV--RLPREPSNPERLKGFGYAEFEDLDSLLSA 77

Query: 267 VE 268
           + 
Sbjct: 78  LS 79

>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 = 46.5 bits (111), Expect = 4e-07
 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 11/78 (14%)

Query: 196 GEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGI 250
           G   S+    +E K ++V  L    +E  + + F K+G++S   VV      RSR   G 
Sbjct: 1   GSSGSSGMASDEGK-LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSR---G- 55

Query: 251 CYAFVEFEDMTGVRNAVE 268
            + FV FE++   ++A+ 
Sbjct: 56  -FGFVTFENIDDAKDAMM 72

>3nv0_B NTF2-related export protein; NTF2-like domain, beta sheet heterodimer interface, nucleopo binding pocket, water mediated interface; 1.84A {Caenorhabditis elegans} Length = 154

 Score = 47.7 bits (113), Expect = 4e-07
 Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 18  SWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK 53
             +GG+L+ V+G+V V    ++R F QT  L  ++ 
Sbjct: 107 DMSGGMLLNVAGAVTVDG-DSKRAFTQTLLLGVEDG 141

>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 = 46.0 bits (110), Expect = 5e-07
 Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 11/65 (16%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGICYAFVEFEDMTGV 263
            +++ NL P + E  + + F  FG +     ++       S+   G  YAF+ F      
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSK---G--YAFINFASFDAS 61

Query: 264 RNAVE 268
             A+E
Sbjct: 62  DAAIE 66

>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 = 45.9 bits (109), Expect = 5e-07
 Identities = 13/58 (22%), Positives = 26/58 (44%), Gaps = 7/58 (12%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           + V+NLP   +  E+ +  K +        V R+++      AFV   +    +NA++
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDLKYCY--VDRNKR-----TAFVTLLNGEQAQNAIQ 58

>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 = 46.1 bits (110), Expect = 6e-07
 Identities = 17/64 (26%), Positives = 32/64 (50%), Gaps = 10/64 (15%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGVR 264
            +YV +L  +++E  +   F+ FG + S  +++     RS+   G  Y F+ F D    +
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK---G--YGFITFSDSECAK 82

Query: 265 NAVE 268
            A+E
Sbjct: 83  KALE 86

>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 = 47.8 bits (113), Expect = 6e-07
 Identities = 12/63 (19%), Positives = 23/63 (36%), Gaps = 3/63 (4%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC 270
           ++  N P  V+E    E   + G      V + S K        +E++      +A+E  
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDS---KSDALETL 182

Query: 271 ILM 273
             +
Sbjct: 183 GFL 185

>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 = 45.5 bits (108), Expect = 7e-07
 Identities = 12/65 (18%), Positives = 27/65 (41%), Gaps = 5/65 (7%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGE-----LSSEGVVIRSRKDVGICYAFVEFEDMTGV 263
           + +YV N+P  ++E  + + F           +    V+  + +    +AF+EF  +   
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66

Query: 264 RNAVE 268
             A+ 
Sbjct: 67  TQAMA 71

>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 = 45.7 bits (109), Expect = 8e-07
 Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 10/67 (14%)

Query: 207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMT 261
           E   ++V ++     E EI E+F  +GE+ +  + +      S+      YA VE+E   
Sbjct: 25  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK-----GYALVEYETHK 79

Query: 262 GVRNAVE 268
               A E
Sbjct: 80  QALAAKE 86

>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 = 45.7 bits (109), Expect = 8e-07
 Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 9/62 (14%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----RSRKDVGICYAFVEFEDMTGVRNA 266
           +Y+ NLP S+ E E+    K FG++ S  ++      SR        F   E        
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSR-----GVGFARMESTEKCEAV 82

Query: 267 VE 268
           + 
Sbjct: 83  IG 84

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 45.3 bits (108), Expect = 9e-07
 Identities = 14/72 (19%), Positives = 29/72 (40%), Gaps = 13/72 (18%)

Query: 205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSS--------EGVVIRSRKDVGICYAFVE 256
                 ++++NL  S +E  +   F K G + S        +  V+ S       + FVE
Sbjct: 2   SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSM-----GFGFVE 56

Query: 257 FEDMTGVRNAVE 268
           ++     + A++
Sbjct: 57  YKKPEQAQKALK 68

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 45.1 bits (107), Expect = 9e-07
 Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 3/67 (4%)

Query: 202 VEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMT 261
           V   + I+ + +RN+PP +    +     ++G + S     +   D       V +    
Sbjct: 9   VPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVES---CEQVNTDSETAVVNVTYSSKD 65

Query: 262 GVRNAVE 268
             R A++
Sbjct: 66  QARQALD 72

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 14/88 (15%), Positives = 27/88 (30%), Gaps = 2/88 (2%)

Query: 181 ETVSSYAYEKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGV 240
             ++S    +       +            V++R LP   +E++I   F     +     
Sbjct: 19  SHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIE 78

Query: 241 VIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +    +  G   A VEF        A+ 
Sbjct: 79  IGPDGRVTG--EADVEFATHEEAVAAMS 104

>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 = 44.9 bits (107), Expect = 1e-06
 Identities = 12/57 (21%), Positives = 30/57 (52%), Gaps = 10/57 (17%)

Query: 208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFED 259
           ++++YV NL  S +  ++ E F +FG++ +  ++      + +      + FVE ++
Sbjct: 1   MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPK-----GFGFVEMQE 52

>2qiy_A UBP3-associated protein BRE5; deubiquitylation, ubiquitin-specific processing proteases(UB NTF2, protein-protein recognition; 1.69A {Saccharomyces cerevisiae} SCOP: d.17.4.2 PDB: 1zx2_A Length = 154

 Score = 46.3 bits (109), Expect = 1e-06
 Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 3/48 (6%)

Query: 8   IEIKTAHSLES--WNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK 53
           +++ T     +   +  +L+M +G +     +   KF QTF L P   
Sbjct: 87  LKLDTIDFQYTGHLHKSILIMATGEMFWTG-TPVYKFCQTFILLPSSN 133

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 13/64 (20%), Positives = 30/64 (46%), Gaps = 10/64 (15%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDMTGVR 264
            ++V  +    +E +I ++F ++GE+ +  + +       +   G  Y  VE+E     +
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK---G--YTLVEYETYKEAQ 79

Query: 265 NAVE 268
            A+E
Sbjct: 80  AAME 83

>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 = 44.9 bits (107), Expect = 2e-06
 Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 4/62 (6%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMTGVRNA 266
            + ++ NLP  V+E  I E F+     +    + R   +      + + EFED+  + +A
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAV--RLPREPSNPERLKGFGYAEFEDLDSLLSA 73

Query: 267 VE 268
           + 
Sbjct: 74  LS 75

>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 = 47.2 bits (111), Expect = 2e-06
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 201 AVEDEEEIKSVYVRNLPPSVSESEIAEE----FKKFGELSSEGVVIRSRKDVGICYAFVE 256
           AV +     ++Y+ NL   + + E+ +     F +FG++    +V RS K  G   AFV 
Sbjct: 2   AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDI-LVSRSLKMRG--QAFVI 58

Query: 257 FEDMTGVRNAVE 268
           F++++   NA+ 
Sbjct: 59  FKEVSSATNALR 70

>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 = 39.5 bits (91), Expect = 6e-04
 Identities = 22/184 (11%), Positives = 50/184 (27%), Gaps = 10/184 (5%)

Query: 85  FPEQRLQQVPESENILEDSPAEELNGSLQNAVNAAQDYLPASVEEPVGEPQKHTYASILR 144
                + ++  +    +    +    S +                 VG  Q         
Sbjct: 89  TDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQ-GGGATPVVGAVQGPVPGMPPM 147

Query: 145 VAKGQSTPSVTPQPSVSKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADTGEEISAVED 204
               +    +  QP        +      P     Q    +   ++           + +
Sbjct: 148 TQAPRIMHHMPGQPPYMPPPGMI----PPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSE 203

Query: 205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVR 264
                 +++ NLP   +E  ++  F +F        ++  R D+    AFVEF++     
Sbjct: 204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEV-RLVPGRHDI----AFVEFDNEVQAG 258

Query: 265 NAVE 268
            A +
Sbjct: 259 AARD 262

>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 = 44.1 bits (104), Expect = 3e-06
 Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 2/68 (2%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDM 260
           E+ +++  +  + LP S +  ++   F      + E  +       G     A +E E  
Sbjct: 6   EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65

Query: 261 TGVRNAVE 268
             V+ A+E
Sbjct: 66  QDVQKALE 73

>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 = 44.7 bits (106), Expect = 3e-06
 Identities = 14/68 (20%), Positives = 31/68 (45%), Gaps = 10/68 (14%)

Query: 206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEFEDM 260
            E   ++V  +    +E +I ++F ++GE+ +  + +       +   G  Y  VE+E  
Sbjct: 20  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK---G--YTLVEYETY 74

Query: 261 TGVRNAVE 268
              + A+E
Sbjct: 75  KEAQAAME 82

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 44.0 bits (104), Expect = 3e-06
 Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 7/58 (12%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           V V  LPPS S  ++ +  ++ G++    V    R   G     VEF     +  AV 
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVY---RDGTG----VVEFVRKEDMTYAVR 68

>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 = 44.8 bits (106), Expect = 4e-06
 Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 15/68 (22%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI----------RSRKDVGICYAFVEFEDM 260
           +YV+NL   V E ++   F ++ + SSE   I          R +       AF+   + 
Sbjct: 48  IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMK-----GQAFIGLPNE 102

Query: 261 TGVRNAVE 268
                A++
Sbjct: 103 KAAAKALK 110

>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 = 43.9 bits (104), Expect = 4e-06
 Identities = 16/71 (22%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 200 SAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEF 257
           S ++D + IK +++  +P ++ E ++   F++FG++  E  V++ R   G+    AF+ +
Sbjct: 6   SGMKDHDAIK-LFIGQIPRNLDEKDLKPLFEEFGKI-YELTVLKDRFT-GMHKGCAFLTY 62

Query: 258 EDMTGVRNAVE 268
            +      A  
Sbjct: 63  CERESALKAQS 73

>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 = 43.4 bits (103), Expect = 4e-06
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 2/60 (3%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
            +V +R  P +V+E  + E       ++    ++R+       Y FV+F +   V+ A++
Sbjct: 11  HTVKLRGAPFNVTEKNVMEFLAPLKPVAI--RIVRNAHGNKTGYIFVDFSNEEEVKQALK 68

>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 = 43.5 bits (103), Expect = 5e-06
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 2/58 (3%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           V++R LP   +E++I   F     +     +    +  G   A VEF        A+ 
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTG--EADVEFATHEDAVAAMA 73

>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 = 45.3 bits (107), Expect = 5e-06
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 4/60 (6%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
            ++++ N+PPSVSE ++   F   G +       +  +      A ++   +     A+ 
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR----KMALIQMGSVEEAVQALI 176

>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 = 40.7 bits (95), Expect = 1e-04
 Identities = 11/59 (18%), Positives = 23/59 (38%), Gaps = 6/59 (10%)

Query: 211 VYVRNLPP-SVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           + V NL P  V+   +   F  +G++    ++   +       A V+  D    + A+ 
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK-----ENALVQMADGNQAQLAMS 59

>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 = 43.0 bits (102), Expect = 6e-06
 Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 12/75 (16%)

Query: 200 SAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGICYA 253
           S+     +   ++V  +P +  E+E+ E FKKFG + +E V+I      R R      + 
Sbjct: 2   SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVV-TEVVMIYDAEKQRPR-----GFG 55

Query: 254 FVEFEDMTGVRNAVE 268
           F+ FED   V  AV 
Sbjct: 56  FITFEDEQSVDQAVN 70

>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 = 45.1 bits (106), Expect = 6e-06
 Identities = 14/112 (12%), Positives = 35/112 (31%), Gaps = 13/112 (11%)

Query: 164 ISPVSDWNHVPQPTTQQETVSSYAYEKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSES 223
           ISP ++    P+     +T+     +         +      + I  +Y+ NL    ++ 
Sbjct: 25  ISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIA-LYIGNLTWWTTDE 83

Query: 224 EIAEEFKKFGELSSEGVVI-------RSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++ E     G      +         +S+      +A V        +  ++
Sbjct: 84  DLTEAVHSLGVNDILEIKFFENRANGQSK-----GFALVGVGSEASSKKLMD 130

>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 = 42.6 bits (101), Expect = 6e-06
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 12/76 (15%)

Query: 199 ISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGICY 252
           I+A ++EE+   ++V  L    S+ ++ + F KFGE+  +  +       RSR      +
Sbjct: 2   INASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEV-VDCTIKMDPNTGRSR-----GF 55

Query: 253 AFVEFEDMTGVRNAVE 268
            F+ F+D   V   ++
Sbjct: 56  GFILFKDAASVEKVLD 71

>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 = 45.0 bits (106), Expect = 7e-06
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 4/60 (6%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
            ++++ N+PPSVSE ++   F   G +       +  +      A ++   +     A+ 
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK----MALIQMGSVEEAVQALI 207

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 39.2 bits (91), Expect = 7e-04
 Identities = 11/59 (18%), Positives = 23/59 (38%), Gaps = 6/59 (10%)

Query: 211 VYVRNLPP-SVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           + V NL P  V+   +   F  +G++    ++   +       A V+  D    + A+ 
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK-----ENALVQMADGNQAQLAMS 90

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 43.2 bits (102), Expect = 7e-06
 Identities = 12/76 (15%), Positives = 26/76 (34%), Gaps = 4/76 (5%)

Query: 194 DTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-RSRKDVGICY 252
            +G     +    +   V V  +P S  E+++ + F     L  + V + +         
Sbjct: 2   SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFH---GLRVDAVHLLKDHVGRNNGN 58

Query: 253 AFVEFEDMTGVRNAVE 268
             V+F        A++
Sbjct: 59  GLVKFLSPQDTFEALK 74

>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 = 42.6 bits (100), Expect = 1e-05
 Identities = 16/67 (23%), Positives = 23/67 (34%), Gaps = 2/67 (2%)

Query: 204 DEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMT 261
           +  E   V +R LP S S  ++               V       G     AFVE E   
Sbjct: 13  EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESED 72

Query: 262 GVRNAVE 268
            V+ A++
Sbjct: 73  DVKLALK 79

>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 = 41.4 bits (98), Expect = 2e-05
 Identities = 9/66 (13%), Positives = 23/66 (34%), Gaps = 12/66 (18%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-------RSRKDVGICYAFVEFEDMTG 262
           ++Y+ NL    ++ ++ E     G      +         +S+   G  +A V       
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSK---G--FALVGVGSEAS 57

Query: 263 VRNAVE 268
            +  ++
Sbjct: 58  SKKLMD 63

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 43.0 bits (101), Expect = 2e-05
 Identities = 11/67 (16%), Positives = 23/67 (34%), Gaps = 12/67 (17%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-------RSRKDVGICYAFVEFEDMT 261
            +VYV +     ++ ++ +  +  G      +         +S+   G  YA V      
Sbjct: 56  AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSK---G--YAEVVVASEN 110

Query: 262 GVRNAVE 268
            V   +E
Sbjct: 111 SVHKLLE 117

>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 = 41.7 bits (98), Expect = 2e-05
 Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 7/58 (12%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           V V  LPPS S  ++ +  ++ G++    V    R   G     VEF     +  AV 
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVY---RDGTG----VVEFVRKEDMTYAVR 69

>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 = 41.8 bits (98), Expect = 2e-05
 Identities = 13/63 (20%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 209 KSVYVRNLP-PSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
           + +++ NLP    S+S + +  + +G++    +++R +       AF+E E        V
Sbjct: 26  RVIHLSNLPHSGYSDSAVLKLAEPYGKI-KNYILMRMK-----SQAFIEMETREDAMAMV 79

Query: 268 EVC 270
           + C
Sbjct: 80  DHC 82

>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 = 41.1 bits (97), Expect = 3e-05
 Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 13/71 (18%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-----RSRKDVGICYAFVEF 257
              +  K+++V+ L    +E  + E    F       +V       S+   G  + FV+F
Sbjct: 10  ARSQPSKTLFVKGLSEDTTEETLKES---FDGSVRARIVTDRETGSSK---G--FGFVDF 61

Query: 258 EDMTGVRNAVE 268
                 + A E
Sbjct: 62  NSEEDAKAAKE 72

>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 = 42.9 bits (100), Expect = 3e-05
 Identities = 18/131 (13%), Positives = 45/131 (34%), Gaps = 8/131 (6%)

Query: 139 YASILRVAKGQSTPSVTPQPSVSKNISPVSDWNHVPQPTTQQETVSSYAYEKSWADTGEE 198
           +  +  + K      +T   +V       S    +     + +   S +          +
Sbjct: 45  WVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYK 104

Query: 199 ISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC-YAFVEF 257
                ++ + +SVY++  P   +  +I E  +  G++ +  + +R           FV F
Sbjct: 105 -----NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLN--IQMRRTLHKAFKGSIFVVF 157

Query: 258 EDMTGVRNAVE 268
           + +   +  VE
Sbjct: 158 DSIESAKKFVE 168

>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 = 41.5 bits (97), Expect = 5e-05
 Identities = 15/68 (22%), Positives = 22/68 (32%), Gaps = 2/68 (2%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDM 260
            +  E   V +R LP S S  ++               V       G     AFVE    
Sbjct: 39  PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSE 98

Query: 261 TGVRNAVE 268
             V+ A++
Sbjct: 99  DDVKMALK 106

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 40.6 bits (95), Expect = 6e-05
 Identities = 9/60 (15%), Positives = 21/60 (35%), Gaps = 7/60 (11%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMTGVRNAVE 268
           + ++NLP   S  ++ +  ++            S  +         +EF     +  A+E
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENS-----LETTFSSVNTRDFDGTGALEFPSEEILVEALE 85

>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 = 40.0 bits (94), Expect = 7e-05
 Identities = 12/66 (18%), Positives = 24/66 (36%), Gaps = 8/66 (12%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
               +  ++YV      ++ + +   F  FG +    + +   +      AFV +E M  
Sbjct: 10  RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIID--LSMDPPR----NCAFVTYEKMES 61

Query: 263 VRNAVE 268
              AV 
Sbjct: 62  ADQAVA 67

>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 = 39.9 bits (94), Expect = 7e-05
 Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 5/58 (8%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           V+V      ++E E+ E F ++G++    +    R      +AFV F D    ++   
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSLCG 60

>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 = 40.2 bits (94), Expect = 8e-05
 Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 10/66 (15%)

Query: 211 VYVRNLPPSVSESEI---AEEFKKFGELSSEGVVIRSRKDVGI-----CYAFVEFEDMTG 262
           V+V  L   +++ E+    E F KFG++    VVI +             A+V +     
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHK--VVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 263 VRNAVE 268
              A++
Sbjct: 76  ALRAIQ 81

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 39.0 bits (92), Expect = 1e-04
 Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 12/64 (18%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGICYAFVEFEDMTGVR 264
           ++V  L  + +  ++   F++FG++  + +++      R R      + FV FE    V 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKV-DDAMLMFDKTTNRHR-----GFGFVTFESEDIVE 55

Query: 265 NAVE 268
              E
Sbjct: 56  KVCE 59

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 16/50 (32%), Positives = 24/50 (48%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED 259
           S++V +L P V +  + E F K       G V+  +  V   Y FV+F D
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTD 60

>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 = 39.5 bits (93), Expect = 1e-04
 Identities = 14/72 (19%), Positives = 25/72 (34%), Gaps = 12/72 (16%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGICYAFVE 256
              ++   + V  LP   +E ++ E F  FGE+     V        S+      + FV 
Sbjct: 10  RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEV-LMVQVKKDLKTGHSK-----GFGFVR 63

Query: 257 FEDMTGVRNAVE 268
           F +       + 
Sbjct: 64  FTEYETQVKVMS 75

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 38.6 bits (91), Expect = 1e-04
 Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 12/64 (18%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGICYAFVEFEDMTGVR 264
           ++V  L P   E +I E F  FGE+     +       + R      + F+ F++   V+
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEV-ESIELPMDNKTNKRR-----GFCFITFKEEEPVK 55

Query: 265 NAVE 268
             +E
Sbjct: 56  KIME 59

>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 = 39.1 bits (92), Expect = 1e-04
 Identities = 12/69 (17%), Positives = 25/69 (36%), Gaps = 5/69 (7%)

Query: 200 SAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED 259
            +         V+V      ++  E+ + F ++GE+    +    R      +AFV F D
Sbjct: 3   GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR-----AFAFVTFAD 57

Query: 260 MTGVRNAVE 268
               ++   
Sbjct: 58  DKVAQSLCG 66

>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 = 39.5 bits (92), Expect = 1e-04
 Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 8/62 (12%)

Query: 209 KSVYVRN--LPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNA 266
           +S+ V N  L   VS +++    +K G +  + +++   K     Y+F  +      + A
Sbjct: 26  QSLVVANGGLGNGVSRNQLLPVLEKCGLV--DALLMPPNKP----YSFARYRTTEESKRA 79

Query: 267 VE 268
             
Sbjct: 80  YV 81

>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 = 39.6 bits (93), Expect = 1e-04
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 13/92 (14%)

Query: 184 SSYAYEKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI- 242
            S   EK+      E    E E+  K +++  L    +E  +   ++++G+L ++ VV+ 
Sbjct: 4   GSSGMEKTLETVPLERKKREKEQFRK-LFIGGLSFETTEESLRNYYEQWGKL-TDCVVMR 61

Query: 243 -----RSRKDVGICYAFVEFEDMTGVRNAVEV 269
                RSR      + FV F  M  V  A+  
Sbjct: 62  DPASKRSR-----GFGFVTFSSMAEVDAAMAA 88

>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 = 38.8 bits (91), Expect = 2e-04
 Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 12/82 (14%)

Query: 193 ADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRK 246
             +G         +EI  ++V  L  S ++  +   F ++GE+  + V++      +SR 
Sbjct: 1   GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEV-VDCVIMKDKTTNQSR- 58

Query: 247 DVGICYAFVEFEDMTGVRNAVE 268
                + FV+F+D   V   + 
Sbjct: 59  ----GFGFVKFKDPNCVGTVLA 76

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 37.5 bits (88), Expect = 3e-04
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 12/64 (18%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVI------RSRKDVGICYAFVEFEDMTGVR 264
           +++  L    ++  + E F +FGE+  E +V+      RSR      + FV F D  GV 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEV-KECLVMRDPLTKRSR-----GFGFVTFMDQAGVD 56

Query: 265 NAVE 268
             + 
Sbjct: 57  KVLA 60

>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 = 39.3 bits (91), Expect = 3e-04
 Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 4/60 (6%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC 270
           + V NL   V+   + + F KFG +        +        A +++ D    ++A    
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLKI----ITFTKNNQFQALLQYADPVSAQHAKLSL 104

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 37.9 bits (88), Expect = 4e-04
 Identities = 9/63 (14%), Positives = 26/63 (41%), Gaps = 7/63 (11%)

Query: 209 KSVYVRNLPPSVS-ESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
           + V++ +     +   ++ +  + FG +S+  +++          AF+E       + AV
Sbjct: 16  RVVHIMDFQRGKNLRYQLLQLVEPFGVISNH-LILNKI-----NEAFIEMATTEDAQAAV 69

Query: 268 EVC 270
           +  
Sbjct: 70  DYY 72

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 5/62 (8%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMTGVRNA 266
            + YV NLP +  + +I   FK     S   V +   KD      + +VEF+++  ++ A
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLSIRS---VRLVRDKDTDKFKGFCYVEFDEVDSLKEA 72

Query: 267 VE 268
           + 
Sbjct: 73  LT 74

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	275
3ujm_A	120	Rasputin; NTF2-like fold, RAS signaling, signaling	99.73
3q90_A	140	RAS GTPase-activating protein-binding protein 1; s	99.71
1zo2_A	129	NTF2, nuclear transport factor 2; structural genom	99.67
1gy7_A	125	Nuclear transport factor 2; protein transport; 1.6	99.64
1gy6_A	127	Nuclear transport factor 2; 1.6A {Rattus norvegicu	99.64
3nv0_B	154	NTF2-related export protein; NTF2-like domain, bet	99.62
2qiy_A	154	UBP3-associated protein BRE5; deubiquitylation, ub	99.61
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.58
1jkg_A	140	P15; NTF2-like domain, transport protein; 1.90A {H	99.56
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.55
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.54
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.52
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.52
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.52
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.51
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.5
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.5
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.5
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.5
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.49
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.49
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.48
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.47
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.47
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.47
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.47
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.47
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.47
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.47
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.47
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.47
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.47
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.46
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.46
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.46
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.46
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.46
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.46
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.46
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.46
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.46
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.46
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.46
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.46
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.46
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.45
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.45
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.45
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.45
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.45
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.45
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.45
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.45
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.45
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.45
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.44
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.44
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.44
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.44
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.44
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.44
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.43
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.43
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.43
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.42
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.42
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.42
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.42
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.42
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.42
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.42
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.42
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.42
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.42
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.42
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.42
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.42
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.42
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.41
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.41
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.41
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.41
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.41
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.41
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.4
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.4
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.4
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.4
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.4
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.4
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.4
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.4
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.4
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.4
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.39
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.38
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.38
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.38
2div_A	99	TRNA selenocysteine associated protein; structural	99.38
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.38
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.38
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.38
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.38
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.38
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.38
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.37
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.37
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.37
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.37
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.37
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.37
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.36
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.35
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.35
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.35
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.35
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.35
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.34
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.34
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.34
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.34
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.34
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.34
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.34
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.34
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.33
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.33
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.33
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.33
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.32
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.32
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.32
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.31
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.31
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.31
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.31
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.31
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.31
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.31
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.31
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.3
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.3
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.29
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.29
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.28
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.28
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.28
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.27
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.27
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.27
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.27
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.27
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.27
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.27
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.26
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.26
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.25
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.25
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.25
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.24
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.23
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.88
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.23
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.23
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.22
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.21
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.21
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.21
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.2
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.2
1x5p_A	97	Negative elongation factor E; structure genomics,	99.19
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.19
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.18
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.18
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.18
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.18
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.16
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.16
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.16
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.15
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.15
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.14
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.1
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.09
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.05
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.05
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.03
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.02
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.02
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.01
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.01
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.99
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.99
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.97
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.97
3nv0_A	205	Nuclear RNA export factor 2; NTF2-like domain, bet	98.95
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.94
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.93
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.93
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.92
1jkg_B	250	TAP; NTF2-like domain, transport protein; 1.90A {H	98.89
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.88
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.87
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.84
1of5_A	221	MRNA export factor MEX67; nuclear protein, repeat,	98.68
1q40_B	219	MEX67, mRNA export factor MEX67; NTF2-fold, nuclea	98.66
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.63
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.61
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.58
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.53
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.27
1q42_A	201	MTR2, mRNA transport regulator MTR2; NTF2-fold, nu	97.92
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	97.62
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	97.55
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.3
1of5_B	184	MTR2, YKL186C, mRNA transport regulator MTR2; nucl	97.18
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.41
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.35
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.79
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	95.77
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.45
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	95.44
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	94.89
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	92.71
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	85.99
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	80.07

>3ujm_A Rasputin; NTF2-like fold, RAS signaling, signaling protein; HET: EPE; 2.74A {Drosophila melanogaster}

Probab=99.73  E-value=1.1e-18  Score=138.78  Aligned_cols=63  Identities=25%  Similarity=0.390  Sum_probs=57.0

Q ss_pred             CCCCcc--ceEEeeeeecccCCCcEEEEEEeEEEecCccccccceeEEEeeecCCCCeEeecCccc
Q 023954            1 MSLNYS--GIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQ   64 (275)
Q Consensus         1 ~sl~f~--~~~i~t~D~q~s~~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~~   64 (275)
                      ++|||+  +|+|+++|||+++++||||+|+|.|+.++ ++.|+|+|+|+|+|++.+.|||.||.|+
T Consensus        54 ~~Lpf~~~~~~I~t~D~Qp~~~~gili~V~G~l~~~~-~~~r~F~QtF~L~p~~~~~y~V~nDifR  118 (120)
T 3ujm_A           54 QQLNFNDCHAKISQVDAQATLGNGVVVQVTGELSNDG-QPMRRFTQTFVLAAQSPKKYYVHNDIFR  118 (120)
T ss_dssp             HHHCCCSCEEEEEEEEEEEEGGGEEEEEEEEEEESTT-CCCEEEEEEEEEEECSTTCEEEEEEEEE
T ss_pred             HcCCCcceEEEEecccceEcCCCCEEEEEEEEEEeCC-CCCceEEEEEEEEEcCCCCEEEEEEEEe
Confidence            368998  89999999999999999999999999998 7889999999999997556799999863

>3q90_A RAS GTPase-activating protein-binding protein 1; structural genomics, structural genomics consortium, SGC, NT (A+B proteins); 1.70A {Homo sapiens} SCOP: d.17.4.0

Probab=99.71  E-value=4.4e-18  Score=138.78  Aligned_cols=63  Identities=30%  Similarity=0.449  Sum_probs=57.2

Q ss_pred             CCCCcc--ceEEeeeeecccCCCcEEEEEEeEEEecCccccccceeEEEeeecC--CCCeEeecCccc
Q 023954            1 MSLNYS--GIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQE--KVPNHLMGGEIQ   64 (275)
Q Consensus         1 ~sl~f~--~~~i~t~D~q~s~~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~--~g~~~v~~~~~~   64 (275)
                      ++|||+  +|+|+++|||+++++||||+|+|.|+.++ +++|+|+|+|+|+|++  .+.|||.||.|+
T Consensus        67 ~~Lp~~~~~~~I~tvD~Qps~~~gilI~V~G~l~~~~-~~~~~F~QtF~L~p~~~~~~~y~V~nDifR  133 (140)
T 3q90_A           67 MSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNN-QALRRFMQTFVLAPEGSVANKFYVHNDIFR  133 (140)
T ss_dssp             HHTCCCSCEEEEEEEEEEECGGGCEEEEEEEEEECTT-CCCEEEEEEEEEEECSSSTTCEEEEEEEEE
T ss_pred             HhCCCccceEEEEeEEEEEeCCCCEEEEEEEEEecCC-CCccEEEEEEEEeecCCCCCCEEEEEEEeE
Confidence            378996  89999999999999999999999999998 8899999999999997  355799999974

>1zo2_A NTF2, nuclear transport factor 2; structural genomics, structural genomics consortium, SGC, transport protein; 1.60A {Cryptosporidium parvum} SCOP: d.17.4.2

Probab=99.67  E-value=3.4e-17  Score=131.71  Aligned_cols=62  Identities=31%  Similarity=0.434  Sum_probs=56.5

Q ss_pred             CCCcc--ceEEeeeeecccCCCcEEEEEEeEEEecCccccccceeEEEeeecCCCCeEeecCccc
Q 023954            2 SLNYS--GIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQ   64 (275)
Q Consensus         2 sl~f~--~~~i~t~D~q~s~~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~~   64 (275)
                      +|||+  +|+|.++|||++++|||||+|+|.|+.++ +++|+|+|+|+|+|+++|.|||.||.++
T Consensus        62 ~Lp~~~~~h~i~t~D~qp~~~~gilI~V~G~~~~~~-~~~~~F~qtF~L~p~~~~~y~I~nD~fR  125 (129)
T 1zo2_A           62 SLNFQRVQFEITRVDCQPSPNNGSIVFVTGDVRIDD-GQPLKFSQVFNLMPSGNGGFMIFNDLFR  125 (129)
T ss_dssp             HHCCSCEEEEEEEEEEEECTBSSEEEEEEEEEEETT-CCCEEEEEEEEEEECSSSCEEEEEEEEE
T ss_pred             hCCCcceEEEEEEEEEEEeCCCcEEEEEEEEEEECC-CCcceEEEEEEEEEcCCCcEEEEeEEEE
Confidence            68896  79999999999999999999999999998 7999999999999998555799999863

>1gy7_A Nuclear transport factor 2; protein transport; 1.6A {Saccharomyces cerevisiae} SCOP: d.17.4.2 PDB: 1gyb_A

Probab=99.64  E-value=1.3e-16  Score=127.61  Aligned_cols=62  Identities=24%  Similarity=0.403  Sum_probs=55.4

Q ss_pred             CCCcc--ceEEeeeeecccC-CCcEEEEEEeEEEecCccccccceeEEEeeecCCCCeEeecCccc
Q 023954            2 SLNYS--GIEIKTAHSLESW-NGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQ   64 (275)
Q Consensus         2 sl~f~--~~~i~t~D~q~s~-~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~~   64 (275)
                      +|||+  +|+|+++|||+++ +|||||+|+|.|+.++..++|+|+|+|+|+|++++ |||.||.++
T Consensus        56 ~Lp~~~~~h~i~t~D~qp~~~~~gili~V~G~~~~~~~~~~~~F~qtF~L~p~~~~-~~I~nD~fr  120 (125)
T 1gy7_A           56 SLPFQKVQHRITTLDAQPASPYGDVLVMITGDLLIDEEQNPQRFSQVFHLIPDGNS-YYVFNDIFR  120 (125)
T ss_dssp             HSCCSCEEEEEEEEEEEESSTTSCEEEEEEEEEEETTCSSCEEEEEEEEEEEETTE-EEEEEEEEE
T ss_pred             hCCCcceEEEEEEEEEEEecCCCeEEEEEEEEEEECCCCCCccEeEEEEEEEeCCE-EEEEEEEEE
Confidence            68996  8999999999996 58999999999999883389999999999999875 599999863

>1gy6_A Nuclear transport factor 2; 1.6A {Rattus norvegicus} SCOP: d.17.4.2 PDB: 1a2k_A 1oun_A 1ar0_A 1u5o_A 1ask_A 1gy5_A 1jb5_A 1jb4_A 1jb2_A 1qma_A

Probab=99.64  E-value=1.8e-16  Score=127.12  Aligned_cols=61  Identities=16%  Similarity=0.219  Sum_probs=56.0

Q ss_pred             CCCcc--ceEEeeeeecccCCCcEEEEEEeEEEecCccccccceeEEEeeecCCCCeEeecCccc
Q 023954            2 SLNYS--GIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQ   64 (275)
Q Consensus         2 sl~f~--~~~i~t~D~q~s~~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~~   64 (275)
                      +|||+  +|+|+++|||+++++||||+|+|.|+.++ +++|+|+|+|+|+|+++ .|||.||.++
T Consensus        58 ~Lp~~~~~h~i~t~d~qp~~~~~ili~V~G~~~~~~-~~~~~F~qtF~L~p~~~-~~~I~nD~fr  120 (127)
T 1gy6_A           58 SLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADE-DPIMGFHQMFLLKNIND-AWVCTNDMFR  120 (127)
T ss_dssp             HCSCSCEEEEEEEEEEEECTTSCEEEEEEEEEEETT-SCCEEEEEEEEEEEETT-EEEEEEEEEE
T ss_pred             hCCCcceEEEEEEEEEEEeCCCcEEEEEEEEEEECC-CCcceEeEEEEEEEeCC-EEEEEEEEEE
Confidence            68996  89999999999999999999999999988 79999999999999984 4699999874

>3nv0_B NTF2-related export protein; NTF2-like domain, beta sheet heterodimer interface, nucleopo binding pocket, water mediated interface; 1.84A {Caenorhabditis elegans}

Probab=99.62  E-value=2.2e-16  Score=130.53  Aligned_cols=61  Identities=23%  Similarity=0.402  Sum_probs=55.4

Q ss_pred             CCCccceEEeeeeecccC-------CCcEEEEEEeEEEecCccccccceeEEEeeecCCCCeEeecCccc
Q 023954            2 SLNYSGIEIKTAHSLESW-------NGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQ   64 (275)
Q Consensus         2 sl~f~~~~i~t~D~q~s~-------~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~~   64 (275)
                      +|||.+|+|.++|||+++       ++||||+|+|.|+.++ +++|+|+|+|+|+|++++ |||.||.|+
T Consensus        84 ~Lp~~~h~I~s~D~qp~~~~~~~q~~~~ilI~V~G~l~~~~-~~~r~F~QtFvL~p~~~~-y~V~NDifR  151 (154)
T 3nv0_B           84 ALPSTQHDIQSLDAQRLPEGVTGDMSGGMLLNVAGAVTVDG-DSKRAFTQTLLLGVEDGK-YKVKSDRFR  151 (154)
T ss_dssp             HSCCEEEEEEEEEEEECCTTCCGGGTTCEEEEEEEEEEETT-SCCEEEEEEEEEEEETTE-EEEEEEEEE
T ss_pred             hCCCeEEEEEEEEEEEcCccccCCCCCeEEEEEEEEEEECC-CCceeEEEEEEEEEeCCE-EEEEeeEEE
Confidence            688889999999999999       6799999999999998 679999999999999855 699999864

>2qiy_A UBP3-associated protein BRE5; deubiquitylation, ubiquitin-specific processing proteases(UB NTF2, protein-protein recognition; 1.69A {Saccharomyces cerevisiae} SCOP: d.17.4.2 PDB: 1zx2_A

Probab=99.61  E-value=2.7e-16  Score=130.07  Aligned_cols=62  Identities=19%  Similarity=0.270  Sum_probs=55.1

Q ss_pred             CC--Ccc--ceEEeeeeecccCC--CcEEEEEEeEEEecCccccccceeEEEeeecCC-CCeEeecCccc
Q 023954            2 SL--NYS--GIEIKTAHSLESWN--GGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK-VPNHLMGGEIQ   64 (275)
Q Consensus         2 sl--~f~--~~~i~t~D~q~s~~--~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~-g~~~v~~~~~~   64 (275)
                      +|  ||+  +|+|.++|||++++  +||||+|+|.|+.++ +++|+|+|||+|+|+++ |.|||.||.++
T Consensus        77 ~L~~pf~~~~h~I~s~D~q~~~~~~~~ilI~V~G~~~~~~-~~~r~F~qtFvL~p~~~~~~y~I~ND~fr  145 (154)
T 2qiy_A           77 RNDAKVRSLKLKLDTIDFQYTGHLHKSILIMATGEMFWTG-TPVYKFCQTFILLPSSNGSTFDITNDIIR  145 (154)
T ss_dssp             HTHHHHTTEEEEEEEEEEEEESGGGCEEEEEEEEEEEETT-CCCEEEEEEEEEEECC---CEEEEEEEEE
T ss_pred             hccCCCCceEEEEEEEEEEEccCCCCEEEEEEEEEEEECC-CCCceEEEEEEEEEeCCCCcEEEEEEEEE
Confidence            57  886  89999999999987  999999999999988 79999999999999986 56799999964

>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=99.58  E-value=5.1e-15  Score=113.14  Aligned_cols=62  Identities=21%  Similarity=0.404  Sum_probs=56.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .++++|||+|||+++|+++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~--~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~   80 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVE--SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT   80 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEE--EEEEEECSSSCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EeEeeecCCCCcccccEEEEECCHHHHHHHHHH
Confidence            4678999999999999999999999999999  88888776655  89999999999999999986

>1jkg_A P15; NTF2-like domain, transport protein; 1.90A {Homo sapiens} SCOP: d.17.4.2 PDB: 1jn5_A

Probab=99.56  E-value=3.4e-15  Score=121.59  Aligned_cols=62  Identities=24%  Similarity=0.339  Sum_probs=55.3

Q ss_pred             CCCccceEEeeeeecccC------CCcEEEEEEeEEEecCccccccceeEEEeeecC---CCCeEeecCccc
Q 023954            2 SLNYSGIEIKTAHSLESW------NGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQE---KVPNHLMGGEIQ   64 (275)
Q Consensus         2 sl~f~~~~i~t~D~q~s~------~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~---~g~~~v~~~~~~   64 (275)
                      +|||++|+|.++|||+++      ++||||+|+|.|+.++ +++|+|+|+|+|+|++   +|.|||.||.++
T Consensus        64 ~Lp~~~h~i~s~d~q~~~~~~~~~~~~ilI~V~G~~~~~~-~~~r~F~qtF~L~p~~~p~~~~~~I~nD~fr  134 (140)
T 1jkg_A           64 MLPSSEFQISVVDCQPVHDEATPSQTTVLVVICGSVKFEG-NKQRDFNQNFILTAQASPSNTVWKIASDCFR  134 (140)
T ss_dssp             HSCCEEEEEEEEEEEECCTTTSTTCCEEEEEEEEEEEETT-SCCEEEEEEEEEEEECCSSSCEEEEEEEEEE
T ss_pred             hCCCceeEEEEEEEEEcCCcccCCCCeEEEEEEEEEEECC-CCceeeeEEEEEEecCCCCCCeEEEEeeEEE
Confidence            689999999999999997      5899999999999998 7899999999999974   245799999974

>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=99.55  E-value=1.1e-14  Score=114.06  Aligned_cols=60  Identities=22%  Similarity=0.466  Sum_probs=56.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..+|||+|||+++++++|+++|++||.|.  .++|..+++++||||||+|.+.++|++||+.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~--~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~   64 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNIL--SCKVVCDENGSKGYGFVHFETQEAAERAIEK   64 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEEETTEEEEEEEEEESCHHHHHHHHHH
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEE--EEEEeecCCCCCceEEEEECCHHHHHHHHHH
Confidence            46899999999999999999999999999  8888888776799999999999999999986

>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=99.54  E-value=1.9e-14  Score=106.40  Aligned_cols=68  Identities=24%  Similarity=0.429  Sum_probs=59.5

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ....++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.....|
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~   77 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVV--DCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRL   77 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEE--EEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEE--EEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEE
Confidence            34679999999999999999999999999999  88887776544  8999999999999999998765443

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=3.7e-14  Score=109.27  Aligned_cols=67  Identities=19%  Similarity=0.304  Sum_probs=59.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++|+++|+++|++||.|.  .|.|+.++. ..||||||+|.+.++|.+||+...+.|
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~--~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~~~~~~~   76 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVL--NIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKY   76 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEE--EEEEECCCTTSCCCEEEEEESSHHHHHHHHTSSCCCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEE--EEEEEECCCCCCccEEEEEECCHHHHHHHHHcCCCEE
Confidence            3568999999999999999999999999999  888887664 348999999999999999999666555

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=2.8e-14  Score=111.29  Aligned_cols=67  Identities=18%  Similarity=0.358  Sum_probs=59.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++++++|+++|.+||.|.  .|.|..++.++  +|||||+|.+.++|.+||+.....|
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~   93 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLT--DCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSI   93 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCS--EEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEE
Confidence            3569999999999999999999999999999  88888876544  8999999999999999998865444

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.52  E-value=9.7e-15  Score=109.75  Aligned_cols=60  Identities=27%  Similarity=0.450  Sum_probs=54.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccC-ceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFG-ELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG-~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +.|||+|||+++|+++|+++|++|| .|.  .|+|..++.++  ||||||+|.+.++|.+||++.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~--~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~   64 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAR--EVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEAN   64 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCS--BCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeE--EEEEEecCCCCCcCceEEEEecCHHHHHHHHHhc
Confidence            6899999999999999999999999 788  88888776554  899999999999999999864

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=8.6e-14  Score=105.40  Aligned_cols=67  Identities=28%  Similarity=0.478  Sum_probs=59.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|.+||+.....|
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~   76 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVT--EVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDI   76 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEE--EEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEE
Confidence            3579999999999999999999999999999  88888776544  8999999999999999998655444

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=5e-14  Score=107.84  Aligned_cols=68  Identities=24%  Similarity=0.364  Sum_probs=59.6

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ....++|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|.+||+.....|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~--~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~   82 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVV--DCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTL   82 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEE--EEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeE
Confidence            34679999999999999999999999999999  88888775544  8999999999999999998765443

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.50  E-value=3.5e-14  Score=110.08  Aligned_cols=68  Identities=18%  Similarity=0.268  Sum_probs=57.5

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ....++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.....|
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~--~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l   91 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVK--ECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHEL   91 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEE--EEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeE--EEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcC
Confidence            34679999999999999999999999999999  88888776444  8999999999999999998765433

>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=99.50  E-value=1.1e-13  Score=105.58  Aligned_cols=63  Identities=24%  Similarity=0.376  Sum_probs=58.3

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ....++|||+|||+++++++|+++|++||.|.  .|.|..++.+++|||||+|.+.++|.+||+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~   74 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCK--SCKMITEHTSNDPYCFVEFYEHRDAAAALAA   74 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEE--EEEEECCCCSSCCEEEEEESSHHHHHHHHHH
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEe--EEEEEecCCCCCCEEEEEECCHHHHHHHHHH
Confidence            34679999999999999999999999999999  8999888777799999999999999999984

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.50  E-value=2.8e-14  Score=108.52  Aligned_cols=65  Identities=14%  Similarity=0.349  Sum_probs=56.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..-.+|||+|||+++|+++|+++|++||.+....|++..++.++  ||||||+|.+.++|.+||++.
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~l   73 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQIL   73 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHH
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHh
Confidence            45789999999999999999999999996432278888776655  899999999999999999863

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.49  E-value=9.1e-14  Score=108.26  Aligned_cols=62  Identities=24%  Similarity=0.315  Sum_probs=56.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+||++++++++|+++|++||.|.  .+.|..++.++  ||||||+|.+.++|++||+..
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~--~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~l   68 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVE--EVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL   68 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCee--EEEEEECCCCCceeeEEEEEECCHHHHHHHHHHh
Confidence            468999999999999999999999999999  88888777655  899999999999999999853

>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=99.49  E-value=2e-13  Score=104.11  Aligned_cols=63  Identities=24%  Similarity=0.373  Sum_probs=58.0

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ....++|||+|||+++++++|+++|++||.|.  .+.|..++...+|||||+|.+.++|.+||+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~--~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~   74 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKIL--DVEIIFNERGSKGFGFVTFENSADADRAREK   74 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEE--EEEEECCTTTTCCEEEEEESCHHHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEecCCCCcEEEEEEECCHHHHHHHHHH
Confidence            34679999999999999999999999999999  8888887766799999999999999999985

>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=99.48  E-value=1.5e-13  Score=104.74  Aligned_cols=62  Identities=23%  Similarity=0.404  Sum_probs=56.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|.+||+.
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~   76 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVL--MVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ   76 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEE--EEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeE--EEEEEecCCCCCccceEEEEECCHHHHHHHHHc
Confidence            4578999999999999999999999999999  88888776544  89999999999999999985

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.47  E-value=1.1e-13  Score=114.47  Aligned_cols=62  Identities=16%  Similarity=0.268  Sum_probs=55.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccC--ceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFG--ELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG--~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|++||  .|.  .+.|..++.+|  +|||||+|.+.++|.+||+..
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~--~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~l  119 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVV--ELKFAENRANGQSKGYAEVVVASENSVHKLLELL  119 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEE--EEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEE--EEEEEecCCCCccceEEEEEECCHHHHHHHHHHc
Confidence            568999999999999999999999999  898  88888876555  899999999999999999983

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=1.1e-13  Score=107.18  Aligned_cols=58  Identities=21%  Similarity=0.330  Sum_probs=53.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.|..+    ||||||+|++.++|.+||+.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~--~v~i~~~----kGfaFVeF~~~~~A~~Ai~~   71 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVT--NLLMLKG----KNQAFIEMNTEEAANTMVNY   71 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEE--EEEEETT----TTEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEcC----CCEEEEEECCHHHHHHHHHH
Confidence            4579999999999999999999999999999  8888764    78999999999999999985

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=8.5e-14  Score=107.84  Aligned_cols=62  Identities=24%  Similarity=0.382  Sum_probs=57.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||.++++++|+++|++||.|.  .+.+..+++..+|||||+|.+.++|.+||+.
T Consensus        27 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~   88 (109)
T 2err_A           27 SQPKRLHVSNIPFRFRDPDLRQMFGQFGKIL--DVEIIFNERGSKGFGFVTFENSADADRAREK   88 (109)
T ss_dssp             TCCCEEEEESCCTTCCHHHHHHHGGGTCCCS--CEEECCBTTBCTTEEEEECCCSHHHHHHHHH
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCEE--EEEEEECCCCCceEEEEEECCHHHHHHHHHH
Confidence            4679999999999999999999999999999  8899887766799999999999999999985

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.47  E-value=2.5e-13  Score=105.56  Aligned_cols=64  Identities=25%  Similarity=0.444  Sum_probs=57.3

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ....++|||+|||+++++++|+++|++||.|.  .|.|..++.++  +|||||+|.+.++|++||+..
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l   77 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRIS--DARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM   77 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHT
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            34679999999999999999999999999999  88888775444  899999999999999999864

>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=99.47  E-value=2.1e-13  Score=104.20  Aligned_cols=62  Identities=27%  Similarity=0.378  Sum_probs=56.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~   76 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVV--NTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI   76 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEE--EEECCBCSSSCSBCSCEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEecCCCCcCCcEEEEEECCHHHHHHHHHH
Confidence            4679999999999999999999999999999  88888775444  89999999999999999996

>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=99.47  E-value=1.8e-13  Score=104.94  Aligned_cols=69  Identities=20%  Similarity=0.197  Sum_probs=57.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecC-CCCCccEEEEEeCCHHHHHHHHHhcCccCC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR-KDVGICYAFVEFEDMTGVRNAVEVCILMWH  275 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~-~~~grgfgFV~F~~~~~a~~Ai~a~pi~ig  275 (275)
                      ...++|||+|||+++++++|+++|++||.|.. .|.|..+ .+..+|||||+|.+.++|++||+.+...|+
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~-~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~   82 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPN-GMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIG   82 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEE-EEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcce-eEEEEECCCCCcceEEEEEECCHHHHHHHHHhCcchhC
Confidence            45799999999999999999999999999982 3777655 333489999999999999999998655543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.47  E-value=6.6e-14  Score=100.57  Aligned_cols=63  Identities=19%  Similarity=0.358  Sum_probs=55.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC--CccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV--GICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       210 ~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~--grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      +|||+|||+++++++|+++|++||.|.  .+.+..++.+  .+|||||+|.+.++|++||+.....|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~   65 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVD--DAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEI   65 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCS--EECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCS
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEE--EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEE
Confidence            589999999999999999999999999  8888776544  48999999999999999998665554

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=2.4e-13  Score=105.93  Aligned_cols=65  Identities=20%  Similarity=0.442  Sum_probs=58.3

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcC
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCI  271 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~p  271 (275)
                      ....++|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|++||+...
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~   80 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIE--EAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN   80 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEE--EEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCee--EEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCC
Confidence            34679999999999999999999999999999  88888776544  8999999999999999998764

>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=99.47  E-value=1e-13  Score=107.76  Aligned_cols=67  Identities=19%  Similarity=0.326  Sum_probs=58.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .|.|..++.++  +|||||+|.+.++|.+||......|
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~   91 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVR--DVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRL   91 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEE--EEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEe--EEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEe
Confidence            3579999999999999999999999999999  88888777544  8999999999999999995444443

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.47  E-value=2.3e-13  Score=106.23  Aligned_cols=63  Identities=21%  Similarity=0.489  Sum_probs=57.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+..
T Consensus        38 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l  102 (118)
T 2khc_A           38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVI--SAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM  102 (118)
T ss_dssp             CCSEEEEEECSCTTCCHHHHHHHTTTSCEEE--EEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHc
Confidence            4679999999999999999999999999999  88888775544  899999999999999999864

>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=99.46  E-value=1.9e-13  Score=105.37  Aligned_cols=63  Identities=25%  Similarity=0.398  Sum_probs=57.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .|.|..++.++  +|||||+|.+.++|.+||+..
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~   77 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLK--YVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA   77 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEE--EEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeE--EEEEEecCCCCCCccEEEEEECCHHHHHHHHHHh
Confidence            4578999999999999999999999999999  88888776544  899999999999999999865

>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=99.46  E-value=2.9e-13  Score=105.29  Aligned_cols=62  Identities=18%  Similarity=0.485  Sum_probs=56.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|.+||+.
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~   86 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVV--SAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS   86 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCS--EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEECCCCCCcCccEEEEECCHHHHHHHHHH
Confidence            3578999999999999999999999999999  88887776444  89999999999999999976

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.46  E-value=2.8e-13  Score=103.74  Aligned_cols=63  Identities=27%  Similarity=0.470  Sum_probs=56.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecC-C--CCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR-K--DVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~-~--~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .|.|..+ +  +..+|||||+|.+.++|.+||+..
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l   78 (107)
T 2cph_A           13 QTTSKILVRNIPFQANQREIRELFSTFGELK--TVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNAL   78 (107)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEE--EEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHccCCeE--EEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHh
Confidence            4679999999999999999999999999999  8888776 3  344899999999999999999873

>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=99.46  E-value=4.6e-14  Score=101.29  Aligned_cols=63  Identities=22%  Similarity=0.417  Sum_probs=56.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       210 ~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      +|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.....|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~   65 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVE--SIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNV   65 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCS--EECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCB
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeE
Confidence            589999999999999999999999999  88887765544  8999999999999999999876554

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.46  E-value=7.7e-13  Score=106.18  Aligned_cols=63  Identities=21%  Similarity=0.487  Sum_probs=57.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||.++++++|+++|++||.|.  .|.|..++.++  +|||||+|.+.++|.+||+..
T Consensus        40 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l  104 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIE--SVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL  104 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEE--EEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            4679999999999999999999999999999  88888776655  899999999999999999863

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=3.4e-13  Score=103.18  Aligned_cols=62  Identities=23%  Similarity=0.441  Sum_probs=56.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~   84 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIK--NIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG   84 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTSSEEEEEEEEESCHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeE--EEEEEecCCCCceeeEEEEEECCHHHHHHHHHH
Confidence            3578999999999999999999999999999  88888776655  89999999999999999985

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=2.8e-13  Score=101.41  Aligned_cols=62  Identities=26%  Similarity=0.357  Sum_probs=56.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~   76 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIA--DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER   76 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEE--EEEEEECSSSSSEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCee--EEEEEEcCCCCCcccEEEEEECCHHHHHHHHHH
Confidence            4579999999999999999999999999999  88888776544  89999999999999999986

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.46  E-value=1.4e-13  Score=100.68  Aligned_cols=61  Identities=21%  Similarity=0.307  Sum_probs=53.8

Q ss_pred             CcEEEEcCCCCCC------CHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSV------SESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~------te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++|||+|||..+      ++++|+++|++||.|.  .+.+....+..+|||||+|.+.++|.+||+..
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~--~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~l   67 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASPAHAVDAVKNA   67 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEE--EEECCCBTTBCCCEEEEEESSHHHHHHHHTTS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeE--EEEecCCCCcEeEEEEEEECCHHHHHHHHHHh
Confidence            3689999999999      6799999999999999  77777555556999999999999999999863

>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=99.46  E-value=2.4e-13  Score=100.11  Aligned_cols=61  Identities=28%  Similarity=0.471  Sum_probs=55.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~   67 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRIS--DARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ   67 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEe--EEEEEecCCCCccceEEEEEECCHHHHHHHHHH
Confidence            568999999999999999999999999999  88887775444  89999999999999999986

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.46  E-value=2.5e-13  Score=99.20  Aligned_cols=60  Identities=22%  Similarity=0.367  Sum_probs=54.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~--~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~   62 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYL--SGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS   62 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEE--EEEEEECTTTCCEEEEEEEEESCHHHHHHHHHH
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCee--EEEEEEcCCCCCccceEEEEECCHHHHHHHHHH
Confidence            36899999999999999999999999999  88887775544  89999999999999999986

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.46  E-value=7.6e-14  Score=100.52  Aligned_cols=63  Identities=19%  Similarity=0.319  Sum_probs=56.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCcc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILM  273 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~  273 (275)
                      ++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.....
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~   65 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVK--ECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHE   65 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCC--CEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCc
Confidence            4799999999999999999999999999  88888776544  899999999999999999876533

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.46  E-value=3.3e-13  Score=100.56  Aligned_cols=61  Identities=20%  Similarity=0.277  Sum_probs=56.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..+.+..+|||||+|.+.++|.+||+.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~--~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~   67 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVL--YADIKMENGKSKGCGVVKFESPEVAERACRM   67 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEE--EEEEEESSSCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEccCCCcceEEEEEECCHHHHHHHHHH
Confidence            579999999999999999999999999999  8888776655699999999999999999985

>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=99.46  E-value=4.3e-13  Score=103.56  Aligned_cols=58  Identities=31%  Similarity=0.415  Sum_probs=52.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .|.+..    +||||||+|++.++|.+||+.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~--~v~i~~----~kg~aFVef~~~~~A~~Ai~~   70 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTIC--YVMMMP----FKRQALVEFENIDSAKECVTF   70 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEE--EEEEET----TTTEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEE--EEEEEC----CCCEEEEEECCHHHHHHHHHH
Confidence            3568999999999999999999999999999  777765    378999999999999999985

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.45  E-value=3.7e-13  Score=101.92  Aligned_cols=61  Identities=21%  Similarity=0.426  Sum_probs=55.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEce--------EEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEG--------VVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~--------v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .        +.+..++.++  +|||||+|.+.++|.+||+.
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~   82 (99)
T 2la6_A           12 DNNTIFVQGLGENVTIESVADYFKQIGIIK--TNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW   82 (99)
T ss_dssp             CCSEEEEECCCSSCCHHHHHHHHTTTSCBC--EETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCEe--eccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHH
Confidence            479999999999999999999999999999  6        8888776554  89999999999999999985

>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=99.45  E-value=9.2e-14  Score=103.71  Aligned_cols=60  Identities=13%  Similarity=0.310  Sum_probs=52.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccC--ceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFG--ELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG--~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+|||+|||+++++++|+++|++||  .|.  .+.+..++.+|  +|||||+|.+.++|.+||+..
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~--~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l   65 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDIL--EIKFFENRANGQSKGFALVGVGSEASSKKLMDLL   65 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCC--CEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHG
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceE--EEEEEecCCCCccCcEEEEEECCHHHHHHHHHHc
Confidence            5799999999999999999999999  998  88888876555  899999999999999999754

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=4.3e-13  Score=101.66  Aligned_cols=62  Identities=23%  Similarity=0.349  Sum_probs=55.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++ +..+|||||+|.+.++|.+||+.
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~   77 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVK--DLRLVTNRAGKPKGLAYVEYENESQASQAVMK   77 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEE--EEEEEECTTSCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeE--EEEEEECCCCCEEeEEEEEECCHHHHHHHHHH
Confidence            4578999999999999999999999999999  88887776 22389999999999999999976

>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=99.45  E-value=1.5e-13  Score=107.23  Aligned_cols=67  Identities=13%  Similarity=0.186  Sum_probs=58.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCce-eEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGEL-SSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I-~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++++++|+++|++||.| .  .|.|..++ +..+|||||+|.+.++|.+||+.....|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~--~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~   81 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDEN--AVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKL   81 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCST--TEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCC--eEEEEECCCCCcceEEEEEECCHHHHHHHHHhCCCcc
Confidence            457899999999999999999999999999 7  78887776 2238999999999999999998765544

>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=99.45  E-value=3e-13  Score=103.99  Aligned_cols=58  Identities=21%  Similarity=0.324  Sum_probs=52.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..+    ||||||+|++.++|.+||+.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~--~v~i~~~----kg~aFVef~~~~~A~~Ai~~   70 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVT--NILMLKG----KNQAFLELATEEAAITMVNY   70 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEE--EEEEETT----TTEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEECC----CCEEEEEECCHHHHHHHHHH
Confidence            4578999999999999999999999999999  7777653    78999999999999999985

>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=99.45  E-value=2.2e-13  Score=104.23  Aligned_cols=63  Identities=14%  Similarity=0.362  Sum_probs=56.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .|.|..++.++  +|||||+|.+.++|.+||++.
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l   75 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIY--ELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL   75 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHHSCCC--EEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCee--EEEEEecCCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            4579999999999999999999999999999  88888776544  899999999999999999853

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=2e-13  Score=100.33  Aligned_cols=61  Identities=20%  Similarity=0.453  Sum_probs=55.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~--~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~   66 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIV--STKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA   66 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEE--EEEEECCSSSCSCCSEEEEEESCHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHH
Confidence            578999999999999999999999999999  88887775444  89999999999999999985

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=2.9e-13  Score=103.20  Aligned_cols=64  Identities=23%  Similarity=0.466  Sum_probs=57.4

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ....++|||+|||+++++++|+++|++||.|.  .|.|..++.++  +|||||+|.+.++|.+||+..
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l   77 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSIS--RIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV   77 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEE--EEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeE--EEEEeecCCCCceeeEEEEEECCHHHHHHHHHHc
Confidence            34679999999999999999999999999999  88888775544  899999999999999999854

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.45  E-value=3.9e-13  Score=102.56  Aligned_cols=66  Identities=24%  Similarity=0.420  Sum_probs=57.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++++++|+++|++|| |.  .|.|..++.++  +|||||+|.+.++|.+||+.+...|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~--~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~   80 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IR--SVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALL   80 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EE--EEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEE
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ce--EEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeE
Confidence            3579999999999999999999999997 88  88888776554  8999999999999999995444443

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=3.5e-13  Score=102.74  Aligned_cols=63  Identities=19%  Similarity=0.389  Sum_probs=56.8

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ....++|||+|||+++++++|+++|++||.|.  .+.+..+.+..+|||||+|.+.++|.+||+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~   74 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTIT--SAKVMMEGGRSKGFGFVCFSSPEEATKAVTE   74 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEE--EEEEEECSSSEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEcCCCCcCEEEEEEECCHHHHHHHHHH
Confidence            34689999999999999999999999999999  8888777444589999999999999999985

>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=99.44  E-value=4.9e-13  Score=102.12  Aligned_cols=62  Identities=23%  Similarity=0.352  Sum_probs=55.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.|..++. ..+|||||+|.+.++|.+||+.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~   75 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVID--ECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHA   75 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEE--EEEEEECSSSCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEECCCCCcCcEEEEEeCCHHHHHHHHHH
Confidence            3579999999999999999999999999999  888877652 2389999999999999999985

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.44  E-value=3.5e-13  Score=101.85  Aligned_cols=63  Identities=24%  Similarity=0.265  Sum_probs=56.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+..
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l   70 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLS--ELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV   70 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEE--EEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEe--EEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHh
Confidence            3579999999999999999999999999999  88887776444  899999999999999999653

>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=99.44  E-value=8e-13  Score=102.27  Aligned_cols=62  Identities=23%  Similarity=0.438  Sum_probs=56.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus        24 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~   87 (108)
T 2jrs_A           24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIE--SIQLMMDSETGRSKGYGFITFSDSECAKKALEQ   87 (108)
T ss_dssp             SSCEEEEEECCCSSCCHHHHHHHHTTTSCEE--EEEEEEETTTTEEEEEEEEEESCHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEEcCCCCccceEEEEEECCHHHHHHHHHH
Confidence            4579999999999999999999999999999  88887776555  89999999999999999974

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=5.5e-13  Score=99.89  Aligned_cols=61  Identities=28%  Similarity=0.520  Sum_probs=55.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~   66 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKID--NIVLMKDSDTGRSKGYGFITFSDSECARRALEQ   66 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEE--EEEEECCSSSCCCCSEEEEEESCHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEe--EEEEeecCCCCceeeEEEEEECCHHHHHHHHHH
Confidence            468999999999999999999999999999  88888776444  89999999999999999984

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=4e-13  Score=100.51  Aligned_cols=63  Identities=30%  Similarity=0.459  Sum_probs=56.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+..
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l   78 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVV--KVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI   78 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEE--EEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeE--EEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHc
Confidence            3578999999999999999999999999999  88888776544  899999999999999999753

>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=99.44  E-value=3e-13  Score=100.06  Aligned_cols=66  Identities=26%  Similarity=0.466  Sum_probs=57.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||..+...|
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~   72 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVN--RVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLF   72 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEE--EEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEE
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEE--EEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEE
Confidence            468999999999999999999999999999  88887775444  8999999999999999995444433

>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=99.43  E-value=3.9e-13  Score=98.58  Aligned_cols=62  Identities=24%  Similarity=0.420  Sum_probs=55.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~   68 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN   68 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEE--EEECCEETTTTEECSEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEE--EEEEEECCCCCccccEEEEEECCHHHHHHHHHH
Confidence            3579999999999999999999999999999  88887665554  89999999999999999965

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.43  E-value=1.3e-13  Score=105.19  Aligned_cols=61  Identities=18%  Similarity=0.310  Sum_probs=56.1

Q ss_pred             CCcEEEEcCCCC------CCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPP------SVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~------~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+      ++++++|+++|++||.|.  .+.|..++.++  ||||||+|.+.++|.+||+.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~--~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~   73 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVV--NMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS   73 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEE--EEECCEETTTTEECSEEEEEESSHHHHHHHHHH
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEe--EEEEEEcCCCCccceEEEEEECCHHHHHHHHHH
Confidence            468999999999      999999999999999999  88888777655  89999999999999999975

>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=99.43  E-value=3.8e-13  Score=101.58  Aligned_cols=62  Identities=24%  Similarity=0.326  Sum_probs=56.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHH----HHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIA----EEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~----~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+    ++|++||.|.  .+.|..++.+ ||||||+|.+.++|++||+..
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~--~v~i~~~~~~-rg~afV~f~~~~~A~~Ai~~l   72 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVK--SVELSPHTDY-QLKAVVQMENLQDAIGAVNSL   72 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEE--EEEECSCCST-TCCEEEEESSHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEE--EEEEEeCCCC-CeEEEEEECCHHHHHHHHHHh
Confidence            357899999999999999999    9999999999  8999887766 999999999999999999853

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=2.3e-13  Score=103.43  Aligned_cols=62  Identities=24%  Similarity=0.420  Sum_probs=56.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|.+||+.
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~   73 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN   73 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCC--CEECCCCSSSCCCSSEEEECCSSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEE--EEEEEecCCCCCcceEEEEEECCHHHHHHHHHH
Confidence            3579999999999999999999999999999  88887765544  89999999999999999975

>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=99.42  E-value=2.6e-13  Score=104.60  Aligned_cols=67  Identities=18%  Similarity=0.223  Sum_probs=58.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCc---eeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGE---LSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~---I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++|+++|+++|+.||.   |.  .|.|..++. ..+|||||+|.+.++|.+||+.+...|
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~--~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~~~~~   79 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGEN--GIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYM   79 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTT--TEECCCCTTSTTCSEEEEEBSSHHHHHHHHTTTTCCS
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcc--eEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCccee
Confidence            46899999999999999999999999998   78  788876654 348999999999999999998655544

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.42  E-value=3.4e-13  Score=102.76  Aligned_cols=62  Identities=24%  Similarity=0.394  Sum_probs=56.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|.+||+.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~   74 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVG--DVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA   74 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEE--EEECCBCSSSCSBCSCEEEEESSSSHHHHHHHH
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHH
Confidence            4579999999999999999999999999999  88888776544  89999999999999999985

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=6.1e-13  Score=101.06  Aligned_cols=62  Identities=23%  Similarity=0.493  Sum_probs=56.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~   73 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQIS--EVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA   73 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCC--EEEECCCSSSCSCCSEEEEECSSHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeE--EEEEEeCCCCCCcccEEEEEECCHHHHHHHHHH
Confidence            3579999999999999999999999999999  88888765444  89999999999999999965

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.42  E-value=6.1e-13  Score=102.18  Aligned_cols=58  Identities=36%  Similarity=0.484  Sum_probs=52.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...+.|||+|||.++|+++|+++|++||.|.  .+.+..    +||||||+|++.++|.+||+.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~--~v~i~~----~kg~AFVef~~~~~A~~Av~~   76 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPIS--YVVVMP----KKRQALVEFEDVLGACNAVNY   76 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEET----TTTEEEEEESSHHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEE--EEEEEc----CCCEEEEEECCHHHHHHHHHH
Confidence            4678999999999999999999999999999  777764    478999999999999999985

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.42  E-value=2.9e-13  Score=108.06  Aligned_cols=64  Identities=19%  Similarity=0.346  Sum_probs=55.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|....|+|+.++.++  ||||||+|.+. +|.+||+..
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l   86 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQIL   86 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHh
Confidence            35689999999999999999999999999971138888887555  89999999999 999998764

>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=99.42  E-value=5e-13  Score=100.68  Aligned_cols=60  Identities=25%  Similarity=0.437  Sum_probs=54.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~   63 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVI--NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN   63 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEE--EEECCBCTTTCCBCSEEEEEESSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEE--EEEEEeCCCCCccceEEEEEECCHHHHHHHHHH
Confidence            47999999999999999999999999999  88888776444  89999999999999999975

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=4.1e-13  Score=100.78  Aligned_cols=62  Identities=26%  Similarity=0.501  Sum_probs=55.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceE-EEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGV-VIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v-~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+ .+..++.++  +|||||+|.+.++|.+||+..
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l   68 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVIL--QTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAM   68 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBS--SCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCee--EEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHc
Confidence            478999999999999999999999999999  77 887765444  899999999999999999853

>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=99.42  E-value=5.7e-13  Score=106.54  Aligned_cols=62  Identities=26%  Similarity=0.357  Sum_probs=56.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .|.+..++.++  +|||||+|.+.++|++||+.
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~--~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~  107 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIA--DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER  107 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEE--EEEEECCSSSSCCCCEEEEEESCHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEecCCCCccceEEEEEECCHHHHHHHHHH
Confidence            4578999999999999999999999999999  88888776544  89999999999999999985

>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=99.42  E-value=5.2e-13  Score=105.74  Aligned_cols=59  Identities=20%  Similarity=0.321  Sum_probs=53.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .|.|..+    ||||||+|++.++|.+||+..
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~--~v~i~~~----kG~AFVeF~~~e~A~~Ai~~l   87 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVT--NLLMLKG----KNQAFIEMNTEEAANTMVNYY   87 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCC--EEEEEGG----GTEEEEECSCHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEeCC----CCEEEEEECCHHHHHHHHHHh
Confidence            4578999999999999999999999999999  8888764    789999999999999999853

>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=99.42  E-value=6.3e-13  Score=101.55  Aligned_cols=65  Identities=23%  Similarity=0.348  Sum_probs=56.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC---CccEEEEEeCCHHHHHHHHHhcCcc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV---GICYAFVEFEDMTGVRNAVEVCILM  273 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~---grgfgFV~F~~~~~a~~Ai~a~pi~  273 (275)
                      ...++|||+|||+++++++|+++|++|| |.  .|.|..++.+   .+|||||+|.+.++|.+||......
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~--~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~   80 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-IS--AVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEES   80 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EE--EEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ce--EEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCE
Confidence            3569999999999999999999999999 98  8888877644   4899999999999999999444443

>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=99.42  E-value=4.1e-13  Score=103.03  Aligned_cols=66  Identities=21%  Similarity=0.088  Sum_probs=55.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++++++|+++|++|| +.  .|.|..++ +..+|||||+|.+.++|++||+.+...|
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~--~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~   79 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PM--RVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANM   79 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CS--EEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-ce--EEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeE
Confidence            4578999999999999999999999999 55  66776655 2338999999999999999997665544

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.42  E-value=4.5e-13  Score=105.50  Aligned_cols=67  Identities=24%  Similarity=0.384  Sum_probs=57.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC--CccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV--GICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~--grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++.+  .+|||||+|.+.++|.+||+.....|
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~  102 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSIN--RITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVF  102 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEE--EEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeE
Confidence            3578999999999999999999999999999  8888776544  48999999999999999995444433

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.42  E-value=3.6e-13  Score=101.65  Aligned_cols=61  Identities=21%  Similarity=0.465  Sum_probs=55.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-----CCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-----VGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-----~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..++.     ..+|||||+|.+.++|.+||+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~   69 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIK--SCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ   69 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEE--EEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHH
Confidence            568999999999999999999999999999  888876544     3389999999999999999996

>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=99.41  E-value=6.5e-13  Score=99.52  Aligned_cols=62  Identities=29%  Similarity=0.411  Sum_probs=55.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++. ..+|||||+|.+.++|.+||+.
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~--~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~   76 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLT--KVTICKDREGKPKSFGFVCFKHPESVSYAIAL   76 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTSCEEEEEEEEESSTHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEE--EEEEEECCCCCCceEEEEEECCHHHHHHHHHH
Confidence            4579999999999999999999999999999  888877654 3389999999999999999985

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.41  E-value=9.6e-13  Score=100.31  Aligned_cols=62  Identities=27%  Similarity=0.445  Sum_probs=56.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhc-cCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKK-FGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~-fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++ ||.|.  .+.|..++ ++  +|||||+|.+.++|.+||+..
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~--~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l   71 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCR--GGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTEC   71 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEE--EEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeE--EEEEEECC-CCCccceEEEEECCHHHHHHHHHHc
Confidence            45799999999999999999999999 99999  88887775 44  899999999999999999864

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.41  E-value=5.7e-13  Score=104.71  Aligned_cols=67  Identities=24%  Similarity=0.163  Sum_probs=57.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCc---eeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGE---LSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~---I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++|+++|+++|++||.   |.  .|.|..++. ..+|||||+|.+.++|++||+.....|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~--~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~   85 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVA--GVHFIYTREGRQSGEAFVELESEDDVKLALKKDRESM   85 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGG--GEEEEECSSSCEEEEEEEEBSSHHHHHHHGGGTTEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCce--eEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeE
Confidence            45799999999999999999999999999   77  788776654 338999999999999999998655544

>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=99.41  E-value=1.4e-12  Score=100.45  Aligned_cols=62  Identities=34%  Similarity=0.597  Sum_probs=54.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.|..++ ..+|||||+|.+.++|++||+..
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~--~~~i~~~~-~~~g~afV~f~~~~~A~~A~~~l   81 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIR--DIDLKNRR-GGPPFAFVEFEDPRDAEDAVYGR   81 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEECCSS-SSSCCEEEEESCHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEECC-CCCcEEEEEECCHHHHHHHHHHc
Confidence            4579999999999999999999999999999  78886543 35899999999999999999653

>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=99.41  E-value=3.6e-13  Score=106.42  Aligned_cols=67  Identities=21%  Similarity=0.259  Sum_probs=55.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEce-EEEec-CCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEG-VVIRS-RKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~-v~v~~-~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++++++|+++|++||.|.  . +.+.. ..+..+|||||+|.+.++|.+||+.+...|
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~--~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~   91 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVE--DSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYM   91 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCT--TTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCcc--ceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeE
Confidence            3568999999999999999999999999998  4 33332 233348999999999999999998555554

>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=99.41  E-value=8.2e-13  Score=101.82  Aligned_cols=62  Identities=27%  Similarity=0.424  Sum_probs=56.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~   87 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIK--NIHLNLDRRTGFSKGYALVEYETHKQALAAKEA   87 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEE--EEECCBCTTTSSBCSEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEecCCCCCcceEEEEEECCHHHHHHHHHH
Confidence            4579999999999999999999999999999  88887776544  89999999999999999985

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.40  E-value=2e-13  Score=103.86  Aligned_cols=59  Identities=29%  Similarity=0.487  Sum_probs=54.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHH
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~  268 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..++ ++  +|||||+|.+.++|.+||+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~   68 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVK--EVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE   68 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEE--EEEEEECT-TSCEEEEEEEEESSCCCHHHHTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeE--EEEEEECC-CCCccceEEEEECCHHHHHHHHh
Confidence            568999999999999999999999999999  88887776 44  8999999999999999998

>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=99.40  E-value=3.4e-13  Score=102.64  Aligned_cols=65  Identities=23%  Similarity=0.356  Sum_probs=55.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC---CCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK---DVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~---~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++|| |.  .+.+..++   +..+|||||+|.+.++|.+||......|
T Consensus        18 ~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~--~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~   85 (100)
T 2j76_E           18 PPYTAFLGNLPYDVTEESIKEFFRGLN-IS--AVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESL   85 (100)
T ss_dssp             --CEEEESCCSSCCSSSHHHHHSCSSC-EE--EEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCB
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcC-Ce--EEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEE
Confidence            579999999999999999999999999 98  88887765   3348999999999999999995455444

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.40  E-value=1.3e-12  Score=104.39  Aligned_cols=63  Identities=24%  Similarity=0.409  Sum_probs=56.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+..
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l  125 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM  125 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEE--EEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHS
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEE--EEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHh
Confidence            4579999999999999999999999999999  88887765444  899999999999999999753

>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=99.40  E-value=5.1e-13  Score=98.46  Aligned_cols=61  Identities=23%  Similarity=0.378  Sum_probs=54.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC---CccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV---GICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~---grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+.+..++.+   .+|||||+|.+.++|.+||+.
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~   66 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIK--MIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH   66 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEE--EEECCEETTEEEEECSEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEE--EEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHH
Confidence            468999999999999999999999999999  8888766543   489999999999999999985

>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=99.40  E-value=4.9e-13  Score=103.05  Aligned_cols=58  Identities=21%  Similarity=0.308  Sum_probs=52.9

Q ss_pred             CCCcEEEEcCCCC-CCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPP-SVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~-~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+ ++++++|+++|++||.|.  .+.|..+    ||||||+|++.++|.+||+.
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~--~v~i~~~----kg~aFVef~~~~~A~~Ai~~   71 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVIS--NHLILNK----INEAFIEMATTEDAQAAVDY   71 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEE--EEEECSS----SSCEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEE--EEEEEcC----CCEEEEEECCHHHHHHHHHH
Confidence            3578999999999 999999999999999999  8887654    57999999999999999985

>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=99.40  E-value=1.6e-12  Score=100.79  Aligned_cols=61  Identities=23%  Similarity=0.406  Sum_probs=55.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.|..++ ++  +|||||+|.+.++|.+||+.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~   85 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVI--STRILRDS-SGTSRGVGFARMESTEKCEAVIGH   85 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEE--EEEEEECS-SSCEEEEEEEEESCHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEECC-CCCcceEEEEEECCHHHHHHHHHH
Confidence            4578999999999999999999999999999  88887765 44  89999999999999999984

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=5.1e-13  Score=104.05  Aligned_cols=65  Identities=15%  Similarity=0.162  Sum_probs=56.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      +.++|||+|||+++++++|+++|+.| .|.  .|.|..++. ..+|||||+|.+.++|++||+.+...|
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~--~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~   80 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVD--AVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLM   80 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCC--EEEECCCTTCCCCSEEEEECSSHHHHHHHHHTTTEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-Cee--EEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeE
Confidence            46899999999999999999999999 888  888876654 348999999999999999997655444

>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=99.40  E-value=1.1e-12  Score=102.88  Aligned_cols=63  Identities=21%  Similarity=0.381  Sum_probs=56.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .|.+..++ +..+|||||+|.+.++|++||+..
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l   68 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPIS--EVLLIKDRTSKSRGFAFITFENPADAKNAAKDM   68 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCS--EEEEECSTTTTCCCEEEEECSSHHHHHHHHHHC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEECCCCCcccEEEEEECCHHHHHHHHHHh
Confidence            3578999999999999999999999999999  88887776 233899999999999999999863

>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=99.40  E-value=1.3e-12  Score=100.18  Aligned_cols=62  Identities=27%  Similarity=0.341  Sum_probs=55.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.|..++ +..+|||||+|.+.++|.+||+.
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~   89 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLK--KAAVHYDRSGRSLGTADVHFERKADALKAMKQ   89 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEE--EEEEEECTTSCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEECCCCCcceEEEEEECCHHHHHHHHHH
Confidence            4579999999999999999999999999999  88887765 22389999999999999999996

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.40  E-value=5.1e-13  Score=102.63  Aligned_cols=62  Identities=21%  Similarity=0.281  Sum_probs=54.9

Q ss_pred             CCCcEEEEcCCCCCC------CHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSV------SESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~------te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+.+      ++++|+.+|++||.|.  .+.+....+..+|||||+|.+.++|.+||+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~--~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~   80 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASPAHAVDAVKN   80 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEE--EEECCCBTTBSCCEEEEEECSSSHHHHHHHH
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEE--EEEeeCCCCCeeeEEEEEECCHHHHHHHHHH
Confidence            346899999999999      7899999999999999  7877755555599999999999999999996

>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=99.39  E-value=6e-13  Score=100.39  Aligned_cols=63  Identities=25%  Similarity=0.230  Sum_probs=53.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC--CccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV--GICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~--grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|.+||.|.  .+.+..++.+  .+|||||+|.+.++|++||+..
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~--~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l   77 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIP--GSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL   77 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCT--TTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcc--ceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHh
Confidence            3568999999999999999999999999998  5555444444  4899999999999999999764

>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=99.38  E-value=1e-12  Score=100.98  Aligned_cols=62  Identities=26%  Similarity=0.317  Sum_probs=55.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCc-eeEceEEEe-cCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGE-LSSEGVVIR-SRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~-I~~~~v~v~-~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|.+||. |.  .+.+. .++.++  +|||||+|.+.++|.+||+..
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~--~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l   72 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVL--DVIVYASAADKMKNRGFAFVEYESHRAAAMARRKL   72 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEE--EEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCce--EEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHh
Confidence            5689999999999999999999999998 99  77776 566543  899999999999999999974

>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=99.38  E-value=9.3e-13  Score=100.29  Aligned_cols=62  Identities=23%  Similarity=0.472  Sum_probs=56.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+..
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~--~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l   70 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVV--SFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL   70 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCS--EEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHS
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCee--EEEEEeCCCCCccceEEEEEECCHHHHHHHHHHh
Confidence            568999999999999999999999999999  88887775555  899999999999999999753

>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=99.38  E-value=1.2e-12  Score=109.77  Aligned_cols=67  Identities=15%  Similarity=0.365  Sum_probs=59.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.++.++.++  +|||||+|.+.++|.+||+.....|
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~   79 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLT--DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKV   79 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEE--EEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEE
Confidence            4679999999999999999999999999999  88888776554  8999999999999999999865544

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=1.4e-12  Score=98.51  Aligned_cols=64  Identities=27%  Similarity=0.433  Sum_probs=54.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.. .+.+..++.++  +|||||+|.+.++|++||+..
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~-~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l   72 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVM-SVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKI   72 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCC-EEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTT
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHH
Confidence            35799999999999999999999999999872 45666665444  899999999999999999853

>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=99.38  E-value=1.1e-12  Score=102.71  Aligned_cols=58  Identities=22%  Similarity=0.315  Sum_probs=52.8

Q ss_pred             CCCcEEEEcCCCCC-CCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPS-VSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~-~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||++ +++++|+++|++||.|.  .+.|..    +||||||+|++.++|.+||+.
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~--~v~i~~----~kg~aFVef~~~~~A~~Ai~~   81 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIK--NYILMR----MKSQAFIEMETREDAMAMVDH   81 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCS--EEEEET----TTTEEEEECSSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEE--EEEEec----CCCEEEEEECCHHHHHHHHHH
Confidence            45789999999998 99999999999999999  787764    478999999999999999985

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=7.5e-13  Score=105.31  Aligned_cols=67  Identities=21%  Similarity=0.204  Sum_probs=56.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCce----eEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGEL----SSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I----~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++|+++|+++|++||.|    .  .|.|..++ +..+|||||+|.+.++|++||+.+...|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~--~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l   92 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKE--GILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLL   92 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGG--GEEEEECTTSCEEEEEEECCSSHHHHHHHHTTTTEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcc--eEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCee
Confidence            467899999999999999999999999976    4  67776653 3338999999999999999998765544

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.38  E-value=1.2e-12  Score=101.43  Aligned_cols=64  Identities=30%  Similarity=0.389  Sum_probs=55.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEc------eEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSE------GVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~------~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|..+      .+.|..++.++  +|||||+|.+.++|.+||+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~   84 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEW   84 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHH
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHH
Confidence            467999999999999999999999999999721      27777765444  89999999999999999985

>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=99.38  E-value=2.1e-12  Score=94.72  Aligned_cols=58  Identities=26%  Similarity=0.520  Sum_probs=53.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||.++++++|+++|++||.|.  .+.+..+    +|||||+|.+.++|.+||+.
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~--~~~~~~~----kg~afV~f~~~~~A~~a~~~   67 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIR--TITVVQR----QQCAFIQFATRQAAEVAAEK   67 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEE--EEEEEGG----GTEEEEEESSHHHHHHHHHT
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEe--EEEEECC----CCEEEEEECCHHHHHHHHHH
Confidence            4578999999999999999999999999999  8888753    78999999999999999986

>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=99.38  E-value=5.7e-13  Score=99.83  Aligned_cols=61  Identities=28%  Similarity=0.298  Sum_probs=53.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.++.++.++  +|||||+|.+.++|++||+.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~   76 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIP--GSVCLKYNEKGMPTGEAMVAFESRDEATAAVID   76 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCT--TCCEEEECTTSCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCcc--ceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHH
Confidence            458999999999999999999999999998  55665554444  89999999999999999985

>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=99.38  E-value=1.7e-12  Score=102.39  Aligned_cols=62  Identities=23%  Similarity=0.441  Sum_probs=56.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .|.|..++.++  +|||||+|.+.++|.+||+.
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~   83 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIK--NIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG   83 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEE--EEECCBCTTTSSBCSCEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEecCCCCccceEEEEEECCHHHHHHHHHH
Confidence            3578999999999999999999999999999  88887775444  89999999999999999975

>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=99.37  E-value=1e-12  Score=98.22  Aligned_cols=57  Identities=23%  Similarity=0.345  Sum_probs=50.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHH
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV  267 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai  267 (275)
                      ....+|||+|||+++|+++|+++|++||.|.  .+.|..+   +||||||+|.+.++|+++.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~--~v~i~~~---srGfaFV~F~~~~~A~~~~   65 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVV--DVFIPKP---FRAFAFVTFADDKVAQSLC   65 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEE--EEECCSS---CCSEEEEEESCHHHHHHHT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEE--EEEEeeC---CCCEEEEEECCHHHHHHHc
Confidence            4579999999999999999999999999999  7887764   6899999999999998543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.37  E-value=1.8e-12  Score=96.58  Aligned_cols=66  Identities=20%  Similarity=0.275  Sum_probs=55.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecC-CCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR-KDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~-~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++++++|+++|++| .|.  .+.+..+ .+..+|||||+|.+.++|.+||+.....|
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~--~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~~g~~~   74 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPV--AIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYM   74 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCS--EEEEEECTTSCEEEEEEEECSSHHHHHHHHHSCSEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-Cce--EEEEEECCCCCCceEEEEEECCHHHHHHHHHhCCcee
Confidence            457999999999999999999999999 888  7887766 23338999999999999999998444433

>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=99.37  E-value=1.1e-12  Score=104.88  Aligned_cols=68  Identities=21%  Similarity=0.216  Sum_probs=55.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++|+++|+++|++| .|..+.|.|..++. ..+|||||+|.+.++|++||+.....|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~~~~~l  108 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERI  108 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTTTTCCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHHCCCEE
Confidence            456889999999999999999999999 45533566665544 348999999999999999998765544

>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=99.37  E-value=8e-13  Score=106.96  Aligned_cols=67  Identities=22%  Similarity=0.129  Sum_probs=57.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCc---eeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGE---LSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~---I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++|+++|+++|++||.   |.  .|.|..++. ..+|||||+|.+.++|++||+.+...|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~--~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~~~g~~l  112 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAA--GVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESM  112 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSST--TEEEEECSSSCEEEEEEEECSSHHHHHHHHTTTEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCcee--EEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCEE
Confidence            45799999999999999999999999999   77  778776654 348999999999999999998544433

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.37  E-value=2.8e-12  Score=99.27  Aligned_cols=62  Identities=24%  Similarity=0.215  Sum_probs=55.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|.+||.|.  .+.|..++. ..+|||||+|.+.++|.+||+.
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~--~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~   75 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVV--RADILEDKDGKSRGIGTVTFEQSIEAVQAISM   75 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEE--EEEEEECTTCSEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEECCCCCeeeEEEEEECCHHHHHHHHHH
Confidence            4578999999999999999999999999999  888876653 2389999999999999999985

>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=99.37  E-value=9.2e-13  Score=102.18  Aligned_cols=62  Identities=24%  Similarity=0.388  Sum_probs=55.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHH---HHHhccCceeEceEEEecCCCC-----CccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIA---EEFKKFGELSSEGVVIRSRKDV-----GICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~---~~F~~fG~I~~~~v~v~~~~~~-----grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+   ++|++||.|.  .+.|..++.+     .+|||||+|.+.++|++||+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~--~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~   82 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIH--KVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQC   82 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEE--EEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEE--EEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHH
Confidence            356899999999999999999   9999999999  8888877653     369999999999999999997

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.36  E-value=1.4e-12  Score=97.75  Aligned_cols=58  Identities=10%  Similarity=0.083  Sum_probs=52.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ....||||||++.+|+++|+++|.+||+|.  .+.+..    .||||||+|.+.++|.+||++.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~--~~~l~~----~kGfaFVey~~~~eA~~Ai~~L   63 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLV--SFHPYL----NQGIALCKYTTREEANKAQMAL   63 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEE--EEEEET----TTTEEEEEESSHHHHHHHHHHH
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEE--EEEEcC----CCcEEEEEECCHHHHHHHHHHh
Confidence            367899999999999999999999999999  777755    5799999999999999999874

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.35  E-value=2.9e-12  Score=100.99  Aligned_cols=62  Identities=27%  Similarity=0.339  Sum_probs=55.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||.++++++|+++|++||.|.  .+.+..++ +..+|||||+|.+.++|.+||+.
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~--~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~   95 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLK--KAAVDYDRSGRSLGTADVHFERRADALKAMKQ   95 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCS--EEEEECCSSSSCCSEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCee--EEEEEECCCCCEeeEEEEEECCHHHHHHHHHH
Confidence            4679999999999999999999999999999  88887766 22389999999999999999984

>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=99.35  E-value=5.9e-13  Score=98.86  Aligned_cols=59  Identities=25%  Similarity=0.473  Sum_probs=53.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.+ |.+||+..
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l   62 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVF--NVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKL   62 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCS--EEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTS
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEE--EEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHh
Confidence            6899999999999999999999999999  88888776544  899999999999 99999863

>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=99.35  E-value=2.4e-12  Score=105.32  Aligned_cols=62  Identities=27%  Similarity=0.446  Sum_probs=56.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC--CccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV--GICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~--grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.|..++.+  .+|||||+|.+.++|.+||+.
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~--~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~  131 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG--DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA  131 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEE--EEECCCCSSCTTSCCEEEEEESBHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEeecCCCCccceEEEEEECCHHHHHHHHHH
Confidence            3578999999999999999999999999999  8888877544  489999999999999999986

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.35  E-value=1.5e-12  Score=98.83  Aligned_cols=57  Identities=14%  Similarity=0.344  Sum_probs=52.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+.+..    .+|||||+|.+.++|.+||+.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~--~~~~~~----~~g~afV~f~~~~~A~~Ai~~   82 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFIL--DFKHYP----EKGCCFIKYDTHEQAAVCIVA   82 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCS--EEEEET----TTTEEEEECSSHHHHHHHHHH
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEE--EEEEec----CCCEEEEEECCHHHHHHHHHH
Confidence            468999999999999999999999999999  777763    478999999999999999976

>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=99.35  E-value=3.3e-12  Score=104.59  Aligned_cols=63  Identities=25%  Similarity=0.370  Sum_probs=57.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .|.|..++.++  +|||||+|.+.++|.+||+..
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l  101 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIK--KIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI  101 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEecCCCCccceEEEEEECCHHHHHHHHHHh
Confidence            3579999999999999999999999999999  88888776554  899999999999999999963

>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=99.34  E-value=4.1e-12  Score=98.60  Aligned_cols=60  Identities=27%  Similarity=0.481  Sum_probs=54.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..+. .++|||||+|.+.++|.+||+.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~--~v~i~~~~-~~~g~afV~f~~~~~A~~A~~~   66 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIR--QIRVGNTP-ETRGTAYVVYEDIFDAKNAVDH   66 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEE--EEEEECST-TTTTCEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEeeCC-CCCcEEEEEECCHHHHHHHHHH
Confidence            468999999999999999999999999999  88887653 3489999999999999999985

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.34  E-value=2.5e-12  Score=110.52  Aligned_cols=62  Identities=24%  Similarity=0.452  Sum_probs=56.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++|+++|+++|++||.|.  .|+|+.++.++  +|||||+|.+.++|.+||+..
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~--~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~   77 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPIL--SIRVCRDMITRRSLGYAYVNFQQPADAERALDTM   77 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEE--EEEEecccCCCCccccccceeCCHHHHHHHHHHh
Confidence            457999999999999999999999999999  88888876655  899999999999999999864

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.34  E-value=5.9e-13  Score=101.07  Aligned_cols=65  Identities=17%  Similarity=0.253  Sum_probs=53.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecC--CCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR--KDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~--~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  . .++.+  .+..+|||||+|.+.++|.+||+.....|
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~--~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~   82 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKN--D-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKV   82 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHH--T-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCB
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcc--e-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEE
Confidence            578999999999999999999999999998  4 33333  23458999999999999999998444433

>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=99.34  E-value=1.9e-12  Score=105.79  Aligned_cols=62  Identities=23%  Similarity=0.408  Sum_probs=56.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +.++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+..
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~   65 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVT--DLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ   65 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEE--EEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEE--EEEEEECCCCCCccceEEEEEccHHHHHHHHhcc
Confidence            468999999999999999999999999999  88888775444  899999999999999999964

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.34  E-value=4.1e-12  Score=95.29  Aligned_cols=63  Identities=27%  Similarity=0.483  Sum_probs=53.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .|  ..++.+++ ||||+|.+.++|.+||+.....|
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~--~v--~~~~~~g~-~afV~f~~~~~a~~ai~l~g~~~   69 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVA--SV--VMDKDKGV-FAIVEMGDVGAREAVLSQSQHSL   69 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEE--EE--EECSSSCC-EEEEEESSHHHHHHHHTCSCCEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeE--EE--EEcCCCCc-EEEEEECCHHHHHHHHhcCCeEE
Confidence            468999999999999999999999999999  55  44555556 99999999999999998545443

>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=99.34  E-value=3.9e-12  Score=96.24  Aligned_cols=58  Identities=28%  Similarity=0.480  Sum_probs=52.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..+    +|||||+|.+.++|.+||+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~~~~~----kg~afV~f~~~~~a~~a~~~   70 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAG--EVFIHKD----KGFGFIRLETRTLAEIAKVE   70 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCS--EEEEETT----TTEEEEECSSSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeE--EEEEecC----CCEEEEEECCHHHHHHHHHH
Confidence            4578999999999999999999999999999  8887753    68999999999999999976

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.34  E-value=2.5e-12  Score=97.57  Aligned_cols=61  Identities=28%  Similarity=0.462  Sum_probs=51.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.    .++...+..+|||||+|.+.++|++||+..
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~----~~~~~~g~~~g~afV~f~~~~~A~~A~~~l   73 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEALNSC   73 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEEE----CCBCSSSCBCSEEEEECSSHHHHHHHHHHT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEEE----EEECCCCCEeeEEEEEECCHHHHHHHHHHh
Confidence            4679999999999999999999999999885    223334445899999999999999999853

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.34  E-value=1.1e-12  Score=102.15  Aligned_cols=61  Identities=30%  Similarity=0.576  Sum_probs=52.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-----CCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-----DVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-----~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|++||.|.  . .+..++     +..||||||+|.+.++|++||++.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~--~-~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~   72 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV--V-DWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC   72 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC--E-ECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE--E-EEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh
Confidence            568999999999999999999999999997  3 344433     344899999999999999999875

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

Probab=99.33  E-value=4.8e-12  Score=94.09  Aligned_cols=57  Identities=28%  Similarity=0.498  Sum_probs=52.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||.++++++|+++|++||.|.  .+.+.      +|||||+|.+.++|.+||+..
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~v~~~------~g~afV~f~~~~~A~~A~~~l   62 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVL--ECDII------KNYGFVHIEDKTAAEDAIRNL   62 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEE--EEEEE------TTEEEEEESSHHHHHHHHHHH
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEE--EEEEE------CCEEEEEECCHHHHHHHHHHh
Confidence            3579999999999999999999999999999  77776      579999999999999999754

>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=99.33  E-value=3.9e-12  Score=98.04  Aligned_cols=58  Identities=17%  Similarity=0.388  Sum_probs=53.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||.++++++|+++|++||.|.  .+.+..+    +|||||+|.+.++|.+||+.
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~--~v~i~~~----~g~afV~f~~~~~a~~A~~~   80 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIM--EIRVFPE----KGYSFVRFSTHESAAHAIVS   80 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEE--EEEEETT----TTEEEEEESSHHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEeCC----CCEEEEEECCHHHHHHHHHH
Confidence            4578999999999999999999999999999  8888765    68999999999999999975

>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=99.33  E-value=2.2e-12  Score=112.92  Aligned_cols=62  Identities=13%  Similarity=0.294  Sum_probs=55.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccC--ceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFG--ELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG--~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+||++++|+++|+++|++||  .|.  .|.|+.++.++  ||||||+|.+.++|++||+..
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~--~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~l  132 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDIL--EIKFFENRANGQSKGFALVGVGSEASSKKLMDLL  132 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEE--EEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTS
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceE--EEEEEecCCCCccceEEEEEECCHHHHHHHHHHc
Confidence            568999999999999999999999999  999  88888886555  899999999999999999864

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.33  E-value=3.4e-12  Score=98.80  Aligned_cols=56  Identities=38%  Similarity=0.560  Sum_probs=52.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+.      +|||||+|.+.++|.+||+.
T Consensus        29 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~--~v~i~------kg~afV~f~~~~~A~~Ai~~   84 (108)
T 2jvo_A           29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMK--EVKIL------NGFAFVEFEEAESAAKAIEE   84 (108)
T ss_dssp             CSCSEEEECSSCTTCCHHHHHHHHTTTSCCC--EEEEE------TTEEEEECSSHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEE--EEEEE------CCEEEEEECCHHHHHHHHHH
Confidence            4579999999999999999999999999999  77776      68999999999999999985

>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=99.32  E-value=7.7e-12  Score=96.35  Aligned_cols=57  Identities=23%  Similarity=0.276  Sum_probs=52.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.|..+     |||||+|.+.++|++||+..
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~~~i~~~-----g~afV~f~~~~~a~~Ai~~l   70 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVC--YADVYRD-----GTGVVEFVRKEDMTYAVRKL   70 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEE--EEEEETT-----TEEEEEESSHHHHHHHHHHS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEe--EEEEecC-----CEEEEEECCHHHHHHHHHHH
Confidence            578999999999999999999999999999  8888765     79999999999999999853

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.32  E-value=2.3e-12  Score=100.64  Aligned_cols=59  Identities=17%  Similarity=0.116  Sum_probs=52.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccC-ceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFG-ELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG-~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++|| .|.  .+.+..+  ..+|||||+|.+.++|++||+.
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~--~v~i~~~--~~rGfaFV~F~~~e~A~~Ai~~   86 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETT--FSSVNTR--DFDGTGALEFPSEEILVEALER   86 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCS--EEECSSC--SSSCCEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeE--EEEEEcC--CCCCEEEEEECCHHHHHHHHHH
Confidence            468999999999999999999999999 898  7776433  3689999999999999999975

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

Probab=99.32  E-value=3.3e-12  Score=96.87  Aligned_cols=56  Identities=36%  Similarity=0.506  Sum_probs=52.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ++|||+|||.++++++|+++|++||.|.  .+.+..+   .+|||||+|.+.++|.+||++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~---~~g~afV~f~~~~~a~~A~~~   56 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLR--TVWIARN---PPGFAFVEFEDPRDAEDAVRG   56 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCS--EEEEESS---SSSEEEEECSSHHHHHHHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEeeC---CCCEEEEEECCHHHHHHHHHH
Confidence            4899999999999999999999999999  8888776   688999999999999999985

>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=99.31  E-value=6.2e-12  Score=104.18  Aligned_cols=62  Identities=27%  Similarity=0.426  Sum_probs=56.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+.+|++||.|.  .|.|..++.++  +|||||+|.+.++|.+||++.
T Consensus        71 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l  134 (165)
T 1rk8_A           71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIK--NIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL  134 (165)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcCCCEE--EEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHh
Confidence            578999999999999999999999999999  88888776555  899999999999999999863

>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=99.31  E-value=3.2e-12  Score=99.30  Aligned_cols=58  Identities=31%  Similarity=0.462  Sum_probs=52.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .|.|..    .+|||||+|.+.++|.+||+..
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~--~v~i~~----~~g~afV~f~~~~~A~~Ai~~l   66 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLG--RVLLPE----GGITAIVEFLEPLEARKAFRHL   66 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEE--EEECCS----SSSCEEEEESCHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEeC----CCCEEEEEeCCHHHHHHHHHHh
Confidence            468999999999999999999999999999  777653    5789999999999999999853

>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=99.31  E-value=9.6e-12  Score=93.70  Aligned_cols=58  Identities=21%  Similarity=0.448  Sum_probs=52.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||.++++++|+++|++||.|.  .+.+..+    +|||||+|.+.++|++||+.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~--~v~~~~~----~g~afV~f~~~~~A~~A~~~   72 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIR--TIDHVKG----DSFAYIQYESLDAAQAACAK   72 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEE--EEEECSS----SCCEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCee--EEEEeCC----CCEEEEEECCHHHHHHHHHH
Confidence            3568999999999999999999999999999  7777643    78999999999999999985

>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=99.31  E-value=4.9e-12  Score=98.08  Aligned_cols=65  Identities=25%  Similarity=0.372  Sum_probs=52.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|....+.+....+..+|||||+|.+.++|.+||+..
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l   87 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV   87 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHh
Confidence            35789999999999999999999999999941112222224455899999999999999999863

>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=99.31  E-value=9.9e-13  Score=97.44  Aligned_cols=58  Identities=24%  Similarity=0.358  Sum_probs=51.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..+   .+|||||+|.+.++|++|+..
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--~v~i~~~---~~g~afV~f~~~~~a~~~~~~   61 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVM--DVFIPKP---FRAFAFVTFADDQIAQSLCGE   61 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCC--EEECCSS---CCSCCEEECSCHHHHHHTTTC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCee--EEEEecC---CCCEEEEEECCHHHHHHHhcC
Confidence            469999999999999999999999999999  7777654   589999999999999876543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.31  E-value=2.2e-12  Score=103.85  Aligned_cols=62  Identities=27%  Similarity=0.446  Sum_probs=55.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC--CccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV--GICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~--grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .|.|..++.+  .+|||||+|.+.++|++||+.
T Consensus        45 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~--~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~  108 (135)
T 2lea_A           45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG--DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA  108 (135)
T ss_dssp             GGCCCEEEECCCSSCHHHHHHHHHGGGSCCS--EEECCCCSSSSSCCSCCEEECSCHHHHHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEEecCCCCccceEEEEEECCHHHHHHHHHH
Confidence            3578999999999999999999999999999  8888776544  489999999999999999986

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.31  E-value=5.7e-12  Score=100.71  Aligned_cols=61  Identities=18%  Similarity=0.294  Sum_probs=52.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHH----HHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIA----EEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~----~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+||++++++++|+    ++|++||.|.  .|.+.. .+..||||||+|.+.++|.+||+..
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~--~v~i~~-~~~~rG~aFV~F~~~~~A~~Ai~~l   92 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQGDIL--DIVVDL-SDDNSGKAYIVFATQESAQAFVEAF   92 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEE--EEEECC-CCSSCCCEEEEESSHHHHHHHHHHS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeE--EEEecc-CCCcCCEEEEEECCHHHHHHHHHHH
Confidence            46899999999999999876    6999999999  777653 3445999999999999999999764

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=1.3e-11  Score=93.14  Aligned_cols=59  Identities=22%  Similarity=0.336  Sum_probs=50.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  . .+..+  ..+|||||+|.+.++|.+||+.
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~--~-~~~~~--~~~g~afV~f~~~~~a~~A~~~   75 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP--L-RLTWQ--GPRRRAFLHYPDSAAAQQAVSC   75 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC--S-EEEEE--TTTTEEEEECSSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE--E-EEEcC--CCCcEEEEEECCHHHHHHHHHH
Confidence            3568999999999999999999999999996  3 33332  3588999999999999999976

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

Probab=99.30  E-value=6.8e-12  Score=94.56  Aligned_cols=56  Identities=25%  Similarity=0.588  Sum_probs=51.3

Q ss_pred             CCCcEEEEcCCCC-CCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPP-SVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~-~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+ ++++++|+++|++||.|.  .+.+.      +|||||+|.+.++|.+||+.
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~--~v~i~------~g~afV~f~~~~~A~~A~~~   64 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIM--QINIK------NAFGFIQFDNPQSVRDAIEC   64 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCC--EEEEE------TTEEEEEESCHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEE--EEEEe------CCEEEEEECCHHHHHHHHHH
Confidence            4679999999998 999999999999999999  77774      68999999999999999986

>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=99.30  E-value=8.7e-12  Score=94.46  Aligned_cols=57  Identities=25%  Similarity=0.558  Sum_probs=51.6

Q ss_pred             CCCcEEEEcCCCC-CCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPP-SVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~-~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+ ++++++|+++|++||.|.  .+.+.      +|||||+|.+.++|.+||+..
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~--~v~i~------~g~afV~f~~~~~A~~Ai~~l   77 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIM--QINIK------NAFGFIQFDNPQSVRDAIEXE   77 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEE--EEEEC------SSEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEE--EEEEe------CCEEEEEECCHHHHHHHHHHc
Confidence            3579999999998 999999999999999999  77773      689999999999999999853

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

Probab=99.29  E-value=9.3e-12  Score=92.87  Aligned_cols=56  Identities=23%  Similarity=0.404  Sum_probs=51.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+.      ++||||+|.+.++|.+||+.
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~--~v~~~------~~~afV~f~~~~~a~~A~~~   63 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVI--ECDIV------KDYAFVHMERAEDAVEAIRG   63 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCC--EEEEC------SSEEEEEESCHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEE------CCEEEEEECCHHHHHHHHHH
Confidence            4679999999999999999999999999999  77775      34999999999999999975

>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=99.29  E-value=1.6e-12  Score=105.52  Aligned_cols=66  Identities=23%  Similarity=0.109  Sum_probs=55.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++|+++|+++|++|| |.  .|.|..++. ..+|||||+|.+.++|++||+.+...|
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~--~v~i~~d~~g~srGfaFV~F~~~e~A~~Al~~~g~~l  110 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PV--RVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRANM  110 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CS--EEECCCSSSSCSSCCCEEECSHHHHHHHHTTCCSCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-Ce--EEEEEECCCCCCceEEEEEeCCHHHHHHHHhhCCCEE
Confidence            4578999999999999999999999999 76  777776654 348999999999999999996555444

>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=99.28  E-value=2.5e-12  Score=96.67  Aligned_cols=61  Identities=21%  Similarity=0.429  Sum_probs=53.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHH----HHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIA----EEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~----~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||.++++++|+    ++|++||.|.  .+.+.. .+..+|||||+|.+.++|.+||+.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~--~v~i~~-~~~~~g~afV~f~~~~~A~~A~~~   70 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQIL--DILVSR-SLKMRGQAFVIFKEVSSATNALRS   70 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEE--EEECCH-HHHHTTCEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEE--EEEEEc-CCCcCcEEEEEeCCHHHHHHHHHH
Confidence            357899999999999999999    9999999999  777753 223489999999999999999985

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

Probab=99.28  E-value=1.9e-11  Score=92.39  Aligned_cols=56  Identities=36%  Similarity=0.492  Sum_probs=50.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhcc--CceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKF--GELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~f--G~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++|  |.|.  .+.+.      +|||||+|.+.++|.+||+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~--~~~~~------~g~afV~f~~~~~A~~A~~~   70 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVE--RVKKI------RDYAFVHFSNREDAVEAMKA   70 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEE--EEEEC------SSEEEEEESSHHHHHHHHHH
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceE--EEEEe------CCeEEEEeCCHHHHHHHHHH
Confidence            457999999999999999999999999  8888  66553      57999999999999999984

>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=99.28  E-value=1.5e-11  Score=99.98  Aligned_cols=59  Identities=32%  Similarity=0.418  Sum_probs=54.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..+   .+|||||+|.+.++|.+||+.
T Consensus        71 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~--~v~i~~~---~~g~afV~f~~~~~a~~A~~~  129 (150)
T 2i2y_A           71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLR--SVWVARN---PPGFAFVEFEDPRDAADAVRE  129 (150)
T ss_dssp             TTSCEEEEESCCSCCSCHHHHHHHHHHSCEE--EEEECSS---SCSEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEE--EEEEeeC---CCcEEEEEECCHHHHHHHHHH
Confidence            4579999999999999999999999999999  8888765   578999999999999999985

>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=99.27  E-value=5.2e-12  Score=99.23  Aligned_cols=58  Identities=17%  Similarity=0.287  Sum_probs=51.5

Q ss_pred             CCcEEEE--cCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYV--RNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV--~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||  +||++++++++|+++|++||.|.  .|.+..    +||||||+|.+.++|++||++.
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~--~v~i~~----~rgfaFV~f~~~~~A~~Ai~~l   83 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVD--ALLMPP----NKPYSFARYRTTEESKRAYVTL   83 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEE--EEECCT----TCSCEEEEESSHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeE--EEEEeC----CCCEEEEEECCHHHHHHHHHHh
Confidence            4688999  77999999999999999999998  776653    4789999999999999999864

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.27  E-value=4.8e-12  Score=94.97  Aligned_cols=60  Identities=22%  Similarity=0.328  Sum_probs=52.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+   ...+..+|||||+|.+.++|.+||+..
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~--~~---~~~~~~~g~afV~f~~~~~a~~A~~~l   73 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIR--LV---SQDGKSKGIAYIEFKSEADAEKNLEEK   73 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEEC--CE---EETTEEEEEEEEEESSHHHHHHHHHHT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEE--Ee---CCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            3579999999999999999999999999998  55   333445899999999999999999853

>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=99.27  E-value=1.1e-11  Score=91.06  Aligned_cols=61  Identities=23%  Similarity=0.426  Sum_probs=52.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcc----C-------ceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCcc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKF----G-------ELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILM  273 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~f----G-------~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~  273 (275)
                      ..++|||+|||+++++++|+++|++|    |       .|.  .+.+..+    +|||||+|.+.++|.+||..+...
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~--~~~~~~~----kg~afV~f~~~~~a~~A~~l~g~~   76 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVL--AVQINQD----KNFAFLEFRSVDETTQAMAFDGII   76 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEE--EEEECSS----SSEEEEEESSHHHHHHHGGGTTCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcce--EEEecCC----CcEEEEEcCCHHHHHHHHhcCCCE
Confidence            57999999999999999999999999    8       888  7777643    789999999999999999444443

>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=99.27  E-value=1.3e-11  Score=101.25  Aligned_cols=62  Identities=18%  Similarity=0.330  Sum_probs=55.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC----CccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV----GICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~----grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +.++|||+|||+++++++|+++|++||.|.  .+.+..++.+    .+|||||+|.+.++|.+||+..
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l   67 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVY--EINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNAL   67 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEE--EEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEE--EEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            468999999999999999999999999999  8888776654    3899999999999999999754

>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=99.27  E-value=1.8e-11  Score=94.33  Aligned_cols=55  Identities=29%  Similarity=0.497  Sum_probs=50.7

Q ss_pred             CCcEEEEcCCCCC-CCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPS-VSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~-~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||++ +++++|+++|++||.|.  .+.+      .+|||||+|.+.++|.+||+.
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~--~v~i------~~g~afV~f~~~~~A~~A~~~   81 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVA--GCSV------HKGYAFVQYSNERHARAAVLG   81 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCS--EEEE------ETTEEEEECSSSHHHHHHHHH
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeE--EEEE------eCCEEEEEECCHHHHHHHHHH
Confidence            4689999999999 99999999999999999  7777      468999999999999999965

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

Probab=99.27  E-value=1.1e-11  Score=92.12  Aligned_cols=56  Identities=20%  Similarity=0.346  Sum_probs=51.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+.      ++||||+|.+.++|.+||+.
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~--~~~~~------~~~afV~f~~~~~a~~A~~~   62 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVI--ECDVV------KDYAFVHMEKEADAKAAIAQ   62 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEE--EEEEC------SSCEEEEESCHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEE--EEEEE------CCEEEEEECCHHHHHHHHHH
Confidence            4679999999999999999999999999999  77775      34999999999999999985

>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=99.27  E-value=1e-11  Score=94.69  Aligned_cols=55  Identities=35%  Similarity=0.616  Sum_probs=50.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+.      +|||||+|.+.++|.+||+.
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~--~v~~~------~~~afV~f~~~~~a~~A~~~   64 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLE--RVKKL------KDYAFIHFDERDGAVKAMEE   64 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEE--EEEEC------SSCEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEE--EEEEE------CCEEEEEeCCHHHHHHHHHH
Confidence            568999999999999999999999999999  77775      46999999999999999986

>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=99.26  E-value=8.8e-12  Score=97.35  Aligned_cols=57  Identities=23%  Similarity=0.276  Sum_probs=51.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.|..+     |||||+|.+.++|++||+..
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~--~~~i~~~-----g~afV~f~~~~~a~~Ai~~l   71 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVC--YADVYRD-----GTGVVEFVRKEDMTYAVRKL   71 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEE--EEEECTT-----SEEEEEESSHHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEecC-----CEEEEEECCHHHHHHHHHHh
Confidence            468999999999999999999999999999  8888665     79999999999999999853

>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=99.26  E-value=1.5e-11  Score=102.88  Aligned_cols=66  Identities=21%  Similarity=0.414  Sum_probs=58.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.....|
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~~~~  170 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIE--VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTV  170 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEE
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeE--EEEEeecCCCCCccceEEEEECCHHHHHHHHHhCCcEE
Confidence            358999999999999999999999999999  88888775444  8999999999999999998765443

>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=99.25  E-value=2.1e-11  Score=98.97  Aligned_cols=60  Identities=23%  Similarity=0.441  Sum_probs=54.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~--~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~   63 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIE--SCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT   63 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeE--EEEEEeCCCCCcceeEEEEEECCHHHHHHHHHH
Confidence            47999999999999999999999999999  88887776444  89999999999999999985

>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=99.25  E-value=1.7e-11  Score=104.56  Aligned_cols=66  Identities=20%  Similarity=0.318  Sum_probs=57.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .|.++.+.. ..+|||||+|++.++|.+||+.....|
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~--~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~~~  174 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVL--NIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKY  174 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEE--EEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTCEE
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEE--EEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCCeE
Confidence            468999999999999999999999999999  888876543 338999999999999999998765444

>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=99.25  E-value=1.5e-11  Score=100.29  Aligned_cols=61  Identities=25%  Similarity=0.443  Sum_probs=55.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~   64 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPIN--TCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV   64 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEE--EEECCEETTTTEECSEEEEEESSHHHHHHHHHH
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCee--EEEEEEeCCCCccceEEEEEECCHHHHHHHHHh
Confidence            368999999999999999999999999999  88887765554  89999999999999999974

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.24  E-value=1.4e-11  Score=105.79  Aligned_cols=61  Identities=21%  Similarity=0.481  Sum_probs=56.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.|..+++.++|||||+|.+.++|.+||+.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~--~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~  162 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNIL--SCKVVCDENGSKGYGFVHFETQEAAERAIEK  162 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEEETTEEEEEEEEEESSHHHHHHHHHH
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeE--EEEeeccCCCCceEEEEEeCCHHHHHHHHHH
Confidence            357899999999999999999999999999  8888877766799999999999999999986

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.23  E-value=2.6e-11  Score=90.96  Aligned_cols=59  Identities=15%  Similarity=0.376  Sum_probs=52.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceE-EEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGV-VIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v-~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+ .+..++.++  .|||+|.+.++|.+||+.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~--~~~~i~~~~~~~--~afV~f~~~~~a~~Ai~~   73 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVE--SCEQVNTDSETA--VVNVTYSSKDQARQALDK   73 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEE--EEEEECCSSSSE--EEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeE--EEEEeecCCCCC--EEEEEECCHHHHHHHHHH
Confidence            468999999999999999999999999999  77 477666544  499999999999999984

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.88  E-value=8.2e-13  Score=103.00  Aligned_cols=62  Identities=21%  Similarity=0.420  Sum_probs=55.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEce--------EEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEG--------VVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~--------v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .        +.+..++.++  +|||||+|.+.++|.+||+.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~   76 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIK--TNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW   76 (116)
Confidence            4678999999999999999999999999998  6        7777765444  89999999999999999985

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.23  E-value=2.6e-11  Score=102.96  Aligned_cols=62  Identities=24%  Similarity=0.353  Sum_probs=55.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC--CccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV--GICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~--grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++.+  .+|||||+|.+.++|.+||+.
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~   89 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIK--SIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ   89 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEE--EEEECCC-CC-CCCSEEEEEESSHHHHHHHHHH
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEE--EEEEeecCCCCccCceEEEEeCCHHHHHHHHHH
Confidence            3578999999999999999999999999999  8888776544  489999999999999999984

>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=99.23  E-value=1.2e-11  Score=100.82  Aligned_cols=66  Identities=18%  Similarity=0.388  Sum_probs=57.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC--CccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV--GICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~--grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+.+..++.+  .+|||||+|.+.++|.+||+.....|
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~  153 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTII--DAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDF  153 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCS--EEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECS
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEE--EEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEe
Confidence            357899999999999999999999999999  8888776544  48999999999999999998655444

>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=99.22  E-value=1.5e-11  Score=91.88  Aligned_cols=57  Identities=28%  Similarity=0.484  Sum_probs=50.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCc-eeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGE-LSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~-I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|++||. |.  .+.++     .+|||||+|.+.++|.+||+..
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~--~~~~~-----~~g~afV~f~~~~~A~~A~~~l   64 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLA--GQVLL-----KSGYAFVDYPDQNWAIRAIETL   64 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCS--SCEEE-----ETTEEEECCSCHHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceE--EEEEc-----CCCEEEEEECCHHHHHHHHHHc
Confidence            5689999999999999999999999999 55  55553     3689999999999999999854

>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=99.21  E-value=2.9e-11  Score=100.67  Aligned_cols=60  Identities=18%  Similarity=0.275  Sum_probs=53.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...+|||+||++.+++++|+++|++||.|.  .|.|..++  .+|||||+|.+.++|.+||++.
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~--~V~i~~k~--~rgfAFVeF~d~~~A~~Ai~~L  104 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVL--KIITFTKN--NQFQALLQYADPVSAQHAKLSL  104 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEE--EEEEEESS--SCEEEEEEESCHHHHHHHHHHS
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEE--EEEEEeCC--CCCEEEEEECCHHHHHHHHHHh
Confidence            467899999999999999999999999999  77775432  4789999999999999999864

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.21  E-value=3.4e-11  Score=91.25  Aligned_cols=59  Identities=20%  Similarity=0.374  Sum_probs=49.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC--CCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK--DVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~--~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|+.|+.+.     +..++  +..+|||||+|.+.++|.+||+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~-----~~~~~~~~~~~g~afV~f~~~~~A~~A~~~   73 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGSVRAR-----IVTDRETGSSKGFGFVDFNSEEDAKAAKEA   73 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTCSEEE-----EEECSSSCSEEEEEEEECSSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCCeEEE-----EEecCCCCCcCcEEEEEECCHHHHHHHHHH
Confidence            4579999999999999999999999886544     33333  33489999999999999999985

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.21  E-value=2.7e-11  Score=98.29  Aligned_cols=59  Identities=25%  Similarity=0.454  Sum_probs=53.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHh
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ++|||+|||.++++++|+++|++||.|.  .+.+..++. ..+|||||+|.+.++|.+||+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~--~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~   60 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIA--NIKIMIDKNNKNVNYAFVEYHQSHDANIALQT   60 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEE--EEEEECCCC-CCEEEEEEEESSHHHHHHHHHH
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeE--EEEEEECCCCCCCCEEEEEeCCHHHHHHHHHH
Confidence            5899999999999999999999999999  888877653 3489999999999999999954

>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=99.20  E-value=1.5e-11  Score=99.17  Aligned_cols=62  Identities=21%  Similarity=0.329  Sum_probs=51.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEc------eEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSE------GVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~------~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+.+|++||.|...      .+.+. ..+..+|||||+|.+.++|.+||+.
T Consensus        44 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~-~~g~~~g~afV~f~~~~~A~~Ai~~  111 (143)
T 3egn_A           44 PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM-KEGRMKGQAFIGLPNEKAAAKALKE  111 (143)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE-EETTTEEEEEEECSSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec-cCCCcccEEEEEeCCHHHHHHHHHH
Confidence            56899999999999999999999999998721      13333 2345699999999999999999985

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.20  E-value=3.6e-11  Score=101.17  Aligned_cols=63  Identities=27%  Similarity=0.331  Sum_probs=56.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .|.|..++ +..+|||||+|.+.++|.+||+..
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~--~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~l  149 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLK--KAAVDYDRSGRSLGTADVHFERRADALKAMKQY  149 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCS--EEEECCCTTSSCSCCEEEEESCHHHHHHHHHHS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHh
Confidence            4579999999999999999999999999999  88887766 233899999999999999999853

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=9.2e-11  Score=88.34  Aligned_cols=56  Identities=21%  Similarity=0.354  Sum_probs=50.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+||  ++++++|+++|++||.|.  .+.+.    ..+|||||+|.+.++|.+||+.
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~--~v~i~----~~~g~afV~f~~~~~a~~Ai~~   68 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNII--DLSMD----PPRNCAFVTYEKMESADQAVAE   68 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEE--EEEEE----TTTTEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEE--EEEec----CCCCEEEEEECCHHHHHHHHHH
Confidence            35789999996  999999999999999999  77774    3578999999999999999976

>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=99.19  E-value=2.5e-11  Score=89.93  Aligned_cols=57  Identities=21%  Similarity=0.329  Sum_probs=51.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|++| .|.  .+.+.    ..+|||||+|.+.++|.+||+..
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~--~~~i~----~~~g~afV~f~~~~~a~~Ai~~l   60 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLK--YCYVD----RNKRTAFVTLLNGEQAQNAIQMF   60 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCC--CEEEE----GGGTEEEECCSCHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeE--EEEEe----CCCcEEEEEECCHHHHHHHHHHh
Confidence            46899999999999999999999999 898  77774    35899999999999999999843

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.18  E-value=9.9e-11  Score=94.88  Aligned_cols=61  Identities=21%  Similarity=0.376  Sum_probs=55.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus        86 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~--~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~  148 (166)
T 3md3_A           86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYL--SGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS  148 (166)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHTTSTTEE--EEEEEECTTTCCEEEEEEEEESCHHHHHHHHHH
T ss_pred             CCceEEECCCCCCCCHHHHHHHHhccCCee--EEEEEecCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence            468999999999999999999999999999  78887665444  89999999999999999985

>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=99.18  E-value=4.5e-11  Score=114.01  Aligned_cols=63  Identities=24%  Similarity=0.475  Sum_probs=56.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++|+++|+.+|++||.|.  .|.|+.++.++  +|||||+|.+.++|.+||++.
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~--~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~l  164 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIK--RIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA  164 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCee--EEEeeccCCCCCccceEEEeeccHHHHHHHHHHc
Confidence            3568999999999999999999999999999  88888775544  899999999999999999773

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.18  E-value=5.4e-11  Score=95.47  Aligned_cols=59  Identities=19%  Similarity=0.299  Sum_probs=52.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccE-EEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICY-AFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgf-gFV~F~~~~~a~~Ai~a~  270 (275)
                      .-.+|||+||++.+|+++|+++|++||.|.  .|.+..+   .+|| |||+|.+.++|.+||++.
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~--~V~i~~~---~~gfqAFVef~~~~~A~~Ai~~L   86 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVL--KIITFTK---NNQFQALLQYADPVSAQHAKLSL   86 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEE--EEEEEEE---TTEEEEEEEESCHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEE--EEEEEcC---CCCcEEEEEECCHHHHHHHHHHc
Confidence            467899999999999999999999999999  7777653   3577 999999999999999864

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.18  E-value=1.5e-10  Score=92.09  Aligned_cols=58  Identities=19%  Similarity=0.220  Sum_probs=50.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccE-EEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICY-AFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgf-gFV~F~~~~~a~~Ai~a~  270 (275)
                      ....|||+||++.+++++|+.+|++||.|.  .|.|...    .|| |||+|.+.++|.+||++.
T Consensus        24 ~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~--~v~i~~~----~Gf~aFVef~~~~~A~~A~~~L   82 (124)
T 2e5i_A           24 KVLLLSIQNPLYPITVDVLYTVCNPVGKVQ--RIVIFKR----NGIQAMVEFESVLCAQKAKAAL   82 (124)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTTSCEE--EEEEEES----SSEEEEEEESSHHHHHHHHHHH
T ss_pred             cEEEEEEcCcCCCCCHHHHHHHHHhcCCEE--EEEEEeC----CCCEEEEEECCHHHHHHHHHHh
Confidence            356789999999999999999999999999  7777542    376 999999999999999864

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.16  E-value=3.2e-11  Score=96.42  Aligned_cols=58  Identities=17%  Similarity=0.297  Sum_probs=51.2

Q ss_pred             cEEEEcCC----CCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCC----H-HH---HHHHHH
Q 023954          209 KSVYVRNL----PPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFED----M-TG---VRNAVE  268 (275)
Q Consensus       209 ~~ifV~nL----p~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~----~-~~---a~~Ai~  268 (275)
                      ..|||+||    ++.+++.+|+.+|+.||.|.  .+.+..|+.+|  +|||||+|.+    . ++   |.+||+
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~--~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~   74 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEIS--HFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVR   74 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCS--EEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHH
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeE--EEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHH
Confidence            68999999    99999999999999999999  89999998887  8999999996    3 22   778877

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.16  E-value=1.1e-10  Score=99.11  Aligned_cols=62  Identities=23%  Similarity=0.526  Sum_probs=56.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~--~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~  186 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIK--SATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS  186 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCee--EEEEEecCCCCCcCceEEEEecCHHHHHHHHHH
Confidence            3568999999999999999999999999999  88887775444  89999999999999999985

>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=99.16  E-value=5.6e-11  Score=97.35  Aligned_cols=60  Identities=22%  Similarity=0.450  Sum_probs=55.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus        94 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~--~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~  155 (172)
T 2g4b_A           94 AHKLFIGGLPNYLNDDQVKELLTSFGPLK--AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG  155 (172)
T ss_dssp             TTCEEEECCCTTCCHHHHHHHHHTTSCEE--EEEEEECTTTCSEEEEEEEEESSTTHHHHHHHH
T ss_pred             CCEEEEEcCCCcCCHHHHHHHHHhcCCce--EEEEEecCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence            68999999999999999999999999999  88887775444  89999999999999999986

>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=99.15  E-value=1.3e-10  Score=95.14  Aligned_cols=62  Identities=21%  Similarity=0.367  Sum_probs=54.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..++. ..+|||||+|.+.++|.+||++.
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~--~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l  156 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIE--ECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM  156 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTSCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEE--EEEEEECCCCCEEEEEEEEECCHHHHHHHHHHh
Confidence            468999999999999999999999999999  787766543 33899999999999999999764

>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=99.15  E-value=1.9e-10  Score=93.23  Aligned_cols=61  Identities=20%  Similarity=0.404  Sum_probs=54.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~--~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~  149 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRII--TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG  149 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEe--EEEEEecCCCCCccceEEEEeCCHHHHHHHHHH
Confidence            467899999999999999999999999999  78887765444  89999999999999999985

>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=99.15  E-value=6.1e-11  Score=105.89  Aligned_cols=68  Identities=24%  Similarity=0.361  Sum_probs=57.7

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ....++|||+|||+++++++|+++|+.||.|.  .|.+..++..++|||||+|.+.++|.+||+.....|
T Consensus        38 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~  105 (292)
T 2ghp_A           38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPII--HVDVADSLKKNFRFARIEFARYDGALAAITKTHKVV  105 (292)
T ss_dssp             ----CEEEEEEECTTCCHHHHHHHHGGGSCEE--EEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE--EEEEEECCCCCcEEEEEEECCHHHHHHHHHhCCcEe
Confidence            34689999999999999999999999999999  888888766668999999999999999997555443

>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=99.14  E-value=8.3e-11  Score=101.04  Aligned_cols=59  Identities=19%  Similarity=0.189  Sum_probs=53.3

Q ss_pred             CCcEEEEcCCC-CCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLP-PSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp-~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+++|||+||+ +.+++++|+++|++||.|.  .|++..+   .+|||||+|.+.++|++||+..
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~--~v~i~~~---~~g~afV~f~~~~~A~~Ai~~l   62 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVE--KVKFMKS---KPGAAMVEMADGYAVDRAITHL   62 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEE--EEEECTT---STTCEEEEESSHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeE--EEEEecC---CCCEEEEEECCHHHHHHHHHHh
Confidence            46899999999 8999999999999999999  8888764   3799999999999999999853

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.14  E-value=2.2e-10  Score=95.95  Aligned_cols=62  Identities=21%  Similarity=0.452  Sum_probs=56.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~--~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~  175 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLK--AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG  175 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEE--EEEEEECTTTCSEEEEEEEEESSSSHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcc--EEEEeecCCCCCcceEEEEEECCHHHHHHHHHH
Confidence            4579999999999999999999999999999  88887775444  89999999999999999986

>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=99.13  E-value=2.1e-10  Score=93.44  Aligned_cols=62  Identities=24%  Similarity=0.430  Sum_probs=55.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+..
T Consensus        88 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~--~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l  151 (168)
T 1b7f_A           88 KDTNLYVTNLPRTITDDQLDTIFGKYGSIV--QKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL  151 (168)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCEEEeCCCCCCCHHHHHHhhhcCCcEE--EEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            468999999999999999999999999999  88887765444  899999999999999999843

>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=99.12  E-value=7.7e-11  Score=101.22  Aligned_cols=62  Identities=16%  Similarity=0.177  Sum_probs=55.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCce--eEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGEL--SSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I--~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|++||.|  .  .+++..+++..+|||||+|.+.++|.+||...
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~--~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~l  185 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPT--SVKVFSGKSERSSSGLLEWDSKSDALETLGFL  185 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCS--EEEECSCCSSSSEEEEEECSSHHHHHHHHHHH
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceE--EEEEEcCCCCCceEEEEEeCCHHHHHHHHHHh
Confidence            46889999999999999999999999999  6  77887766444799999999999999999864

>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=99.11  E-value=7.2e-10  Score=98.38  Aligned_cols=61  Identities=21%  Similarity=0.319  Sum_probs=54.4

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ....++|||+|||.++++++|+++|++||.|.  .+.+..++   +|||||+|.+.++|.+||+..
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~--~v~~~~~~---~g~afV~f~~~~~A~~A~~~l  264 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFK--EVRLVPGR---HDIAFVEFDNEVQAGAARDAL  264 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeE--EEEEecCC---CcEEEEEeCCHHHHHHHHHHc
Confidence            34578999999999999999999999999999  88887543   589999999999999999864

>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=99.10  E-value=2.4e-10  Score=99.08  Aligned_cols=59  Identities=24%  Similarity=0.253  Sum_probs=54.1

Q ss_pred             CCCcEEEEcCCCC-CCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPP-SVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~-~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+ ++++++|+++|++||.|.  .|.+..++   +|||||+|.+.++|.+||+.
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~--~v~i~~~~---~g~afV~F~~~~~A~~Ai~~   91 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQ--RVKILFNK---KENALVQMADGNQAQLAMSH   91 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEE--EEEECCTT---SCCEEEEESCHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeE--EEEEEECC---CCEEEEEECCHHHHHHHHHH
Confidence            3579999999999 999999999999999999  88887764   78999999999999999974

>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=99.09  E-value=2.5e-10  Score=101.41  Aligned_cols=62  Identities=21%  Similarity=0.411  Sum_probs=54.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHH----HHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIA----EEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~----~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+    ++|++||.|.  .|.+.. .+..||||||+|.+.++|.+||+..
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~--~v~~~~-~~~~~g~afV~f~~~~~a~~A~~~l   72 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQIL--DILVSR-SLKMRGQAFVIFKEVSSATNALRSM   72 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeE--EEEEcC-CCCcceEEEEEECCHHHHHHHHHHh
Confidence            457999999999999999977    8999999999  777765 4446899999999999999999653

>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=99.05  E-value=6.1e-11  Score=97.66  Aligned_cols=66  Identities=18%  Similarity=0.307  Sum_probs=53.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEe-cCCCCCccEEEEEeCCHHHHHHHHHhcCcc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIR-SRKDVGICYAFVEFEDMTGVRNAVEVCILM  273 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~-~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~  273 (275)
                      ...++|||+|||+++++++|+++|.+||.+.  .+.++ ...+..+|||||+|.+.++|.+||+.....
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~--~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~   77 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKN--DLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLK   77 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHH--TCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcc--eEEEEECCCCccccEEEEEECCHHHHHHHHhcCCCE
Confidence            4679999999999999999999999999887  42222 223345899999999999999999754443

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.05  E-value=2e-10  Score=96.62  Aligned_cols=57  Identities=25%  Similarity=0.266  Sum_probs=52.5

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          208 IKSVYVRNLPP-SVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       208 ~~~ifV~nLp~-~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .++|||+|||+ ++++++|+++|++||.|.  .+.+..++   +|||||+|.+.++|.+||+.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~--~v~i~~~~---~g~afV~f~~~~~a~~A~~~   60 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQ--RVKILFNK---KENALVQMADGNQAQLAMSH   60 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCS--EEECSTTC---SSCCEEECTTTHHHHHHHHH
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEE--EEEEEeCC---CCEEEEEECCHHHHHHHHHH
Confidence            58999999999 999999999999999999  88887654   78999999999999999984

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.03  E-value=7.5e-11  Score=98.77  Aligned_cols=61  Identities=21%  Similarity=0.352  Sum_probs=49.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccC-----------ceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCcc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFG-----------ELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILM  273 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG-----------~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~  273 (275)
                      ..++|||+|||+++++++|+++|++||           .|.  .+.+.    ..+|||||+|.+.++|.+||+.+...
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~--~~~~~----~~~g~afV~F~~~~~A~~Al~l~g~~   74 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVL--AVQIN----QDKNFAFLEFRSVDETTQAMAFDGII   74 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEE--EEEEE----TTTTEEEEEESCSHHHHHHGGGTTEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceE--EeEec----CCCCEEEEEeCCHHHHHHHHHhcCCE
Confidence            468999999999999999999999995           344  33332    24789999999999999999544443

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.02  E-value=7e-10  Score=83.95  Aligned_cols=51  Identities=22%  Similarity=0.401  Sum_probs=44.1

Q ss_pred             cEEEEcCCCCCCCHHH----HHHHHhcc-CceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          209 KSVYVRNLPPSVSESE----IAEEFKKF-GELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~----L~~~F~~f-G~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      +.|||+|||+++++++    |+++|++| |+|.  .|       ++ |||||.|.+.++|.+||+.
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl--~V-------tg-G~AfV~F~~~esA~~A~~~   65 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVL--SI-------TG-CSAILRFINQDSAERAQKR   65 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEE--EC-------CT-TCEEEEESSHHHHHHHHHH
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeE--EE-------ec-CEEEEEECCHHHHHHHHHH
Confidence            3499999999999987    55899999 5998  55       23 8999999999999999975

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.02  E-value=3.9e-10  Score=99.40  Aligned_cols=59  Identities=22%  Similarity=0.332  Sum_probs=53.2

Q ss_pred             CCCcEEEEcCCCCCC---------CHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSV---------SESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~---------te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+||+..+         ++++|+.+|++||.|.  .|.|..    .||||||+|.+.++|+.||++.
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~--~v~v~~----~kG~AFV~F~~~~~Ae~A~~am  199 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDID--RIRYVE----SKNCGFVKFKYQANAEFAKEAM  199 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEE--EEEEEG----GGTEEEEEESSHHHHHHHHHHH
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEE--EEEEEC----CCCEEEEEeCCHHHHHHHHHHh
Confidence            357999999999998         7999999999999999  888875    4789999999999999999764

>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=99.01  E-value=6.4e-10  Score=90.95  Aligned_cols=62  Identities=23%  Similarity=0.441  Sum_probs=50.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcc----C-------ceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKF----G-------ELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~f----G-------~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      +.++|||+|||+++++++|+++|++|    |       .|.  .+.+..    .+|||||+|.+.++|.+||..+...|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~--~~~~~~----~~g~afV~f~~~~~A~~A~~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVL--AVQINQ----DKNFAFLEFRSVDETTQAMAFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEE--EEEEET----TTTEEEEEESSHHHHHHHGGGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCcee--eeEecC----CCCEEEEEeCCHHHHHHHHHhCCcEe
Confidence            56899999999999999999999999    5       555  444433    37899999999999999995444443

>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=99.01  E-value=5.6e-10  Score=91.85  Aligned_cols=58  Identities=22%  Similarity=0.353  Sum_probs=51.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+   ...+..+|||||+|.+.++|.+||+.
T Consensus        98 ~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~--~~---~~~~~~~g~afV~f~~~~~A~~A~~~  155 (175)
T 1fje_B           98 AARTLLAKNLSFNITEDELKEVFEDALEIR--LV---SQDGKSKGIAYIEFKSEADAEKNLEE  155 (175)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHCTTCSEEE--EE---CSSSSCCSEEEEECSSHHHHHHHHHH
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhcCeEE--Ee---cCCCCCceEEEEEECCHHHHHHHHHH
Confidence            468999999999999999999999999998  44   44455689999999999999999986

>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=98.99  E-value=9.9e-10  Score=97.11  Aligned_cols=61  Identities=30%  Similarity=0.476  Sum_probs=54.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++|||+|||..+++++|+++|++||.|.  .+.+..+. +..+|||||+|.+.++|.+||+..
T Consensus        96 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~--~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l  157 (261)
T 3sde_A           96 GAALTVKNLSPVVSNELLEQAFSQFGPVE--KAVVVVDDRGRATGKGFVEFAAKPPARKALERC  157 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEEETTSCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeE--EEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHh
Confidence            57899999999999999999999999999  77776653 334899999999999999999874

>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=98.99  E-value=9.6e-10  Score=97.18  Aligned_cols=58  Identities=26%  Similarity=0.429  Sum_probs=52.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++|+++|+++|++||.|.  .|.+..    .+|||||+|.+.++|.+||+.
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--~v~i~~----~kg~afV~f~~~~~A~~A~~~   77 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPS--EVFINR----DRGFGFIRLESRTLAEIAKAE   77 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCS--EEEEET----TTTEEEEECSSHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEE--EEEEeC----CCcEEEEEECCHHHHHHHHHH
Confidence            3578999999999999999999999999999  787754    368999999999999999984

>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=98.97  E-value=1.7e-09  Score=96.06  Aligned_cols=60  Identities=25%  Similarity=0.404  Sum_probs=54.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+.
T Consensus        95 ~~~l~v~nlp~~~t~~~l~~~f~~~G~i~--~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~  156 (284)
T 3smz_A           95 DALLCVANLPPSLTQQQFEELVRPFGSLE--RCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD  156 (284)
T ss_dssp             SCEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHhcCCee--EEEEEeeCCCCccceEEEEEECCHHHHHHHHHH
Confidence            47999999999999999999999999999  88877665444  89999999999999999954

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=98.97  E-value=7.6e-10  Score=102.41  Aligned_cols=59  Identities=19%  Similarity=0.288  Sum_probs=51.8

Q ss_pred             CCCcEEEEcC--CCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRN--LPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~n--Lp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ....+|||+|  |++.+|+++|+++|++||.|.  .|.+..    +||||||+|.+.++|++||++.
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~--~v~~~~----~kgfaFV~f~~~~~A~~Ai~~l   76 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVD--ALLMPP----NKPYSFARYRTTEESKRAYVTL   76 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEE--EEECCT----TCSEEEEEESSHHHHHHHHHHT
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeE--EEEEeC----CCCEEEEEECCHHHHHHHHHHh
Confidence            4578999999  578999999999999999998  665532    6899999999999999999875

>3nv0_A Nuclear RNA export factor 2; NTF2-like domain, beta sheet heterodimer interface, nucleopo binding pocket, water mediated interface; 1.84A {Caenorhabditis elegans}

Probab=98.95  E-value=4.6e-10  Score=96.68  Aligned_cols=62  Identities=13%  Similarity=0.111  Sum_probs=54.2

Q ss_pred             CCCccceEEee--eeecccCCCcEEEEEEeEEEec--------CccccccceeEEEeeecCCCCeEeecCcc
Q 023954            2 SLNYSGIEIKT--AHSLESWNGGVLVMVSGSVQVK--------DFSARRKFVQTFFLAPQEKVPNHLMGGEI   63 (275)
Q Consensus         2 sl~f~~~~i~t--~D~q~s~~~gi~v~v~G~~~~~--------~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~   63 (275)
                      +||.++|.+.+  +|||+..+++|+|+|+|.++..        ++...|.|+|+|+|.|.++|.+||.||..
T Consensus       109 ~LP~T~H~~~s~~vD~~p~~~~~l~i~V~G~f~e~~~~~~~~~~~~~~r~FsRtFiL~P~~~g~~~I~ND~L  180 (205)
T 3nv0_A          109 RLPATIHLMDTFVVDVFLVSATLLGFTLHGTFRDGPSAIKPENTEEHDNYFTRTFMVAPRGEGKVAIVSDQL  180 (205)
T ss_dssp             HSCCEEECGGGCEEEEEEECSSCEEEEEEEEEEETHHHHSCCSCSTTCEEEEEEEEEEECSTTCEEEEEEEE
T ss_pred             hCCCeEEecCceEEEEEEeCCCeEEEEEEEEEEEcccccccccCCCCCceeEEEEEEEECCCCcEEEEecEE
Confidence            58877899986  8999998888999999999975        13578999999999999878889999985

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=98.94  E-value=3.1e-09  Score=81.90  Aligned_cols=62  Identities=29%  Similarity=0.305  Sum_probs=51.6

Q ss_pred             CCcEEEEcCCCC-----CCCHHHHHHHHhccCceeEceEEEecCCC---CCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPP-----SVSESEIAEEFKKFGELSSEGVVIRSRKD---VGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~-----~~te~~L~~~F~~fG~I~~~~v~v~~~~~---~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..+.|+|+||..     +-++++|+++|++||.|.  .+.|..++.   .++|||||+|.+.++|.+|+++.
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~--~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~l   76 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVG--KCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDL   76 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEE--EEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEE--EEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHH
Confidence            468999999952     237899999999999999  888877643   35899999999999999999863

>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=98.93  E-value=1.8e-09  Score=95.97  Aligned_cols=57  Identities=19%  Similarity=0.321  Sum_probs=50.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++|| |.  .+.+    +..+|||||+|.+.++|.+||+.
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~--~~~~----~~~~g~afV~f~~~~~A~~A~~~   76 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LK--YCFV----DKYKGTAFVTLLNGEQAEAAINA   76 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EE--EEEE----ETTTTEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CE--EEEE----ecCCCEEEEEeCCHHHHHHHHHH
Confidence            3568999999999999999999999999 88  6666    23578999999999999999975

>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=98.93  E-value=1.4e-09  Score=97.07  Aligned_cols=66  Identities=24%  Similarity=0.464  Sum_probs=56.1

Q ss_pred             CCCcEEEEcCCCCC-CCHHHHHHHHhccCceeEceEEEecCC---CCCccEEEEEeCCHHHHHHHHHhcCcc
Q 023954          206 EEIKSVYVRNLPPS-VSESEIAEEFKKFGELSSEGVVIRSRK---DVGICYAFVEFEDMTGVRNAVEVCILM  273 (275)
Q Consensus       206 ~~~~~ifV~nLp~~-~te~~L~~~F~~fG~I~~~~v~v~~~~---~~grgfgFV~F~~~~~a~~Ai~a~pi~  273 (275)
                      ...++|||+|||.. +++++|+++|++||.|.  .+.+..+.   +..+|||||+|.+.++|.+||..+...
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~--~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~~l~g~~  277 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIE--KINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSL  277 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEE--EEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEE
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCee--EEEEEecCCcCCCCceEEEEEeCCHHHHHHHHHhcCCE
Confidence            35789999999999 99999999999999999  88887765   344899999999999999999333433

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.92  E-value=9e-09  Score=78.71  Aligned_cols=58  Identities=21%  Similarity=0.200  Sum_probs=48.1

Q ss_pred             CcEEEEcCCC-------CCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLP-------PSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp-------~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++|-|+-..       .++++++|+++|++||.|.  .|.|..   ..||||||+|.+.++|.+||+..
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~--~v~i~~---~~rGfaFVeF~~~~~A~~Ai~~~   74 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVL--NLVLSS---KKPGTAVVEFATVKAAELAVQNE   74 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEE--EEEEES---SSSSEEEEEESCHHHHHHHHHTC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEE--EEEEcc---CCCCEEEEEECCHHHHHHHHHhc
Confidence            4566666443       4589999999999999999  787762   35899999999999999999873

>1jkg_B TAP; NTF2-like domain, transport protein; 1.90A {Homo sapiens} SCOP: d.17.4.2 PDB: 1jn5_B 1go5_A

Probab=98.89  E-value=1.3e-09  Score=96.64  Aligned_cols=65  Identities=15%  Similarity=0.171  Sum_probs=55.5

Q ss_pred             CCCCccceEEe--eeeecccCCCcEEEEEEeEEEecC---ccccccceeEEEeeecCCCCeEeecCcccc
Q 023954            1 MSLNYSGIEIK--TAHSLESWNGGVLVMVSGSVQVKD---FSARRKFVQTFFLAPQEKVPNHLMGGEIQA   65 (275)
Q Consensus         1 ~sl~f~~~~i~--t~D~q~s~~~gi~v~v~G~~~~~~---~~~~~~F~Q~F~L~~~~~g~~~v~~~~~~~   65 (275)
                      .+||.++|.+.  ++|+|+..+++|+|+|+|.++.++   .+..|.|+|||+|.|.++|.+||.||.+..
T Consensus        98 ~~LP~t~H~~~s~~vD~~~~~~~~i~i~V~G~f~e~~~~~~~~~r~F~rtFvL~p~~~~~~~I~ND~l~l  167 (250)
T 1jkg_B           98 NELPKTQHDVNSFVVDISAQTSTLLCFSVNGVFKEVDGKSRDSLRAFTRTFIAVPASNSGLCIVNDELFV  167 (250)
T ss_dssp             TTSCCEEECGGGCEEEEEEECSSCEEEEEEEEEEECSSTTTTCEEEEEEEEEEEECTTSSEEEEEEEEEE
T ss_pred             HhCCCeeEeccceEEeeeecCCCEEEEEEEEEEEECCCCCCCCceeeEEEEEEEECCCCcEEEEeeEEEE
Confidence            36887788888  899999888899999999999865   357899999999999876778999999743

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=98.88  E-value=4e-09  Score=88.63  Aligned_cols=59  Identities=20%  Similarity=0.295  Sum_probs=52.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccC-ceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFG-ELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG-~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||.++++++|+++|++|| .|.  .+.+..+   ++|||||+|.+.++|.+||+..
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~--~v~i~~~---~~g~afV~f~~~~~A~~A~~~l  178 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVK--GFKFFQK---DRKMALIQMGSVEEAVQALIDL  178 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCC--EEEESST---TSSCEEEECSSHHHHHHHHHHH
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCce--EEEEEeC---CCcEEEEEeCCHHHHHHHHHHh
Confidence            468999999999999999999999999 998  7877543   3789999999999999999843

>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=98.87  E-value=1.2e-08  Score=88.25  Aligned_cols=58  Identities=21%  Similarity=0.309  Sum_probs=52.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccC-ceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFG-ELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG-~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||.++++++|+++|++|| .|.  .+.+..+   ++|||||+|.+.++|.+||+.
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~--~v~i~~~---~~g~afV~f~~~~~A~~Ai~~  208 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVK--GFKFFQK---DRKMALIQMGSVEEAVQALID  208 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEE--EEEECSS---STTCEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCee--EEEEEEC---CCcEEEEEECCHHHHHHHHHH
Confidence            469999999999999999999999999 999  7877542   378999999999999999984

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.84  E-value=1.2e-08  Score=78.90  Aligned_cols=61  Identities=16%  Similarity=0.266  Sum_probs=49.6

Q ss_pred             CCCcEEEEcCCCCCCC-----------HHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVS-----------ESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~t-----------e~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...+.|+|+||.....           +++|+++|++||.|.  .+.|. ++ ..+|||||+|.+.++|.+||+..
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~--~v~i~-~~-~~~G~afV~f~~~~~A~~Ai~~l   84 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIR--KLLLF-DR-HPDGVASVSFRDPEEADYCIQTL   84 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCS--EEEEE-TT-CTTCEEEEECSCHHHHHHHHHHS
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEe--EEEEe-cC-CCCEEEEEEECCHHHHHHHHHHc
Confidence            3578999999944332           579999999999999  77664 33 26899999999999999999764

>1of5_A MRNA export factor MEX67; nuclear protein, repeat, leucine- rich repeat, nuclear transport; 2.8A {Saccharomyces cerevisiae} SCOP: d.17.4.2

Probab=98.68  E-value=7.6e-09  Score=89.92  Aligned_cols=66  Identities=12%  Similarity=0.269  Sum_probs=53.0

Q ss_pred             CCCccceEE------eeeeecccCC-CcEEEEEEeEEEecCcc-------------------------------ccccce
Q 023954            2 SLNYSGIEI------KTAHSLESWN-GGVLVMVSGSVQVKDFS-------------------------------ARRKFV   43 (275)
Q Consensus         2 sl~f~~~~i------~t~D~q~s~~-~gi~v~v~G~~~~~~~~-------------------------------~~~~F~   43 (275)
                      +||.++|.|      .++|||+... +||||+|+|.++..+..                               ..|.|+
T Consensus       100 ~LPkT~H~l~~~~~s~~vD~~~~~~~~~i~itV~G~f~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rsF~  179 (221)
T 1of5_A          100 TLPKTKHHLQEQPNEYSMETISYPQINGFVITLHGFFEETGKPELESNKKTGKNNYQKNRRYNHGYNSTSNNKLSKKSFD  179 (221)
T ss_dssp             HSCCEEECTTTSGGGCEEEEEEEGGGTEEEEEEEEEEEEC-----------------------------CCSCCEEEEEE
T ss_pred             hCCCeeEecccCCCceEEEeEEcCCCCeEEEEEEEEEEECCCcccccccccccccccccccccccccccccccCCccceE
Confidence            578778999      6999999865 68999999999976632                               579999


Q ss_pred             eEEEeeecCCCCeEeecCccccccc
Q 023954           44 QTFFLAPQEKVPNHLMGGEIQAREY   68 (275)
Q Consensus        44 Q~F~L~~~~~g~~~v~~~~~~~~~~   68 (275)
                      |||+|.|. +|.++|.||.+..+.+
T Consensus       180 RTFvL~P~-~~~~~I~nD~l~ir~~  203 (221)
T 1of5_A          180 RTWVIVPM-NNSVIIASDLLTVRAY  203 (221)
T ss_dssp             EEEEEEEE-TTEEEEEEEEEEEEEC
T ss_pred             EEEEEEec-CCeEEEEeeEEEeecC
Confidence            99999999 5667999999754433

>1q40_B MEX67, mRNA export factor MEX67; NTF2-fold, nuclear export, translation; 1.95A {Candida albicans} SCOP: d.17.4.2

Probab=98.66  E-value=1.1e-08  Score=88.71  Aligned_cols=67  Identities=16%  Similarity=0.241  Sum_probs=51.4

Q ss_pred             CCCccceEE------eeeeecccC-CCcEEEEEEeEEEecCc------------------------------ccccccee
Q 023954            2 SLNYSGIEI------KTAHSLESW-NGGVLVMVSGSVQVKDF------------------------------SARRKFVQ   44 (275)
Q Consensus         2 sl~f~~~~i------~t~D~q~s~-~~gi~v~v~G~~~~~~~------------------------------~~~~~F~Q   44 (275)
                      +||.++|.|      -++|||+-. .+||||+|+|.++..+.                              ...|.|+|
T Consensus       106 ~LPkT~H~l~~~~~s~~vD~~~~p~~~~ilitV~G~f~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rsF~R  185 (219)
T 1q40_B          106 QLPKTRHDIIATPELFSMEVYKFPTLNGIMITLHGSFDEVAQPEVDGSASSAPSGPRGGSRYHSGPKHKRIPLSKKSFDR  185 (219)
T ss_dssp             TSCEEECCTTTCGGGCEEEEEECSSTTCEEEEEEEEEEEEECCSSCCCC----------CCSSSSSCCCCCCCCCEEEEE
T ss_pred             HCCCeeEecccCCCceEEEeEecCCCCeEEEEEEEEEEECCCccccccccccccccccccccccccccccccCCccceEE
Confidence            688678999      699999432 47899999999987552                              26899999


Q ss_pred             EEEeeecCCCCeEeecCccccccc
Q 023954           45 TFFLAPQEKVPNHLMGGEIQAREY   68 (275)
Q Consensus        45 ~F~L~~~~~g~~~v~~~~~~~~~~   68 (275)
                      ||+|.|.++|.++|.||.+..+.+
T Consensus       186 tFvL~P~~~~~~~I~nD~l~ir~~  209 (219)
T 1q40_B          186 TFVVIPGPNGSMIVASDTLLIRPY  209 (219)
T ss_dssp             EEEEECC---CCEEEEEEEEEEEC
T ss_pred             EEEEEECCCCcEEEEeeEEEEecC
Confidence            999999966777999999754443

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=98.63  E-value=1.1e-08  Score=78.46  Aligned_cols=56  Identities=21%  Similarity=0.331  Sum_probs=45.1

Q ss_pred             EcCCCCCCCHHHHHHHH------------hccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhc
Q 023954          213 VRNLPPSVSESEIAEEF------------KKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       213 V~nLp~~~te~~L~~~F------------~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +.||++++++++|++.|            ++||.|.  .+.|..++. .++|||||+|.+.++|.+|+++.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~--~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~l   88 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVE--EMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDL   88 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEE--EEEECCSSSSSSEEEEEEEESCHHHHHHHHHHH
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceE--EEEEEeCCCCCccEEEEEEECCHHHHHHHHHHH
Confidence            45677777887777666            9999999  888876653 34999999999999999999853

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=98.61  E-value=7.1e-08  Score=74.12  Aligned_cols=62  Identities=21%  Similarity=0.360  Sum_probs=50.0

Q ss_pred             CCcEEEEcCC--CCCCC--------HHHHHHHHhccCceeEceEEEecCCC----CCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNL--PPSVS--------ESEIAEEFKKFGELSSEGVVIRSRKD----VGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nL--p~~~t--------e~~L~~~F~~fG~I~~~~v~v~~~~~----~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..+.|.++|+  +....        +++|+++|++||.|.  .+.|..++.    .++|||||+|.+.++|.+||++.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~--~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~l   79 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVK--SIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL   79 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEE--EEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEE--EEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHh
Confidence            4578899998  33332        368999999999999  888877653    35899999999999999999764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.58  E-value=1.5e-07  Score=74.38  Aligned_cols=60  Identities=8%  Similarity=0.020  Sum_probs=52.8

Q ss_pred             cCCCcEEEEcCCCCC-CCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCC-HHHHHHHHHhc
Q 023954          205 EEEIKSVYVRNLPPS-VSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED-MTGVRNAVEVC  270 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~-~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~-~~~a~~Ai~a~  270 (275)
                      -..++-|||+||+.+ ++.++|+++|++||.|.  .|.+..+.    ..|||.|.+ ..+|..|+++.
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~--~Vd~~~g~----~tgfVrf~~~~~~A~~av~~l   76 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIK--WIDFVRGA----KEGIILFKEKAKEALGKAKDA   76 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEE--EEECCTTC----SEEEEEESSCHHHHHHHHHHT
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEE--EEEEecCC----CEEEEEECCChHHHHHHHHHh
Confidence            357899999999999 99999999999999999  88876643    379999999 88899998874

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.53  E-value=1.2e-07  Score=74.46  Aligned_cols=62  Identities=31%  Similarity=0.406  Sum_probs=50.0

Q ss_pred             CCcEEEEcCCCC-----CCCHHHHHHHHhccCceeEceEEEecCCC------CCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPP-----SVSESEIAEEFKKFGELSSEGVVIRSRKD------VGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~-----~~te~~L~~~F~~fG~I~~~~v~v~~~~~------~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..+.|+++|+-.     +-.+++|+++|++||.|.  .|.|..++.      .++||+||+|.+.++|.+||++.
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~--~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~L   91 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVN--RVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL   91 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEE--EEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEe--EEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHH
Confidence            468899999832     123588999999999999  888776542      23799999999999999999864

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.27  E-value=9.2e-07  Score=69.01  Aligned_cols=59  Identities=14%  Similarity=0.206  Sum_probs=46.2

Q ss_pred             CcEEEEcCCCCCC----------CHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSV----------SESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~----------te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+.|.++|+=..-          .+++|+++|++||.|.  .|.|..+  +++|||||+|.+.++|.+||++.
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~--~v~i~~~--~~~G~~fV~f~~~e~A~~Ai~~l   75 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVI--HIYVDKN--SAQGNVYVKCPSIAAAIAAVNAL   75 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCS--EEEECTT--CTTCCEEEECSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEE--EEEEecC--CCcEEEEEEECCHHHHHHHHHHh
Confidence            4678888872211          2257899999999999  7877554  35899999999999999999863

>1q42_A MTR2, mRNA transport regulator MTR2; NTF2-fold, nuclear export, translation; 1.75A {Candida albicans} SCOP: d.17.4.2 PDB: 1q40_A

Probab=97.92  E-value=9.1e-06  Score=68.18  Aligned_cols=51  Identities=16%  Similarity=0.133  Sum_probs=38.2

Q ss_pred             CCccceEEeeeeecccCC-CcEEEEEEeEEEecCccccccceeEEEeeecCCC
Q 023954            3 LNYSGIEIKTAHSLESWN-GGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKV   54 (275)
Q Consensus         3 l~f~~~~i~t~D~q~s~~-~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g   54 (275)
                      ||=+.|.|+++|||+.++ +.+||.|.|.|+.++ +.+++|.|+|.|..+.++
T Consensus        98 lP~SqHqL~SlDahpIpGq~T~lI~asGkVrFDe-sgr~~fgQsf~Lta~~~~  149 (201)
T 1q42_A           98 TPLSSHQLTSYDGHLIPGTGTFVVHFSAKVRFDQ-SGRNRLGESADLFQENNS  149 (201)
T ss_dssp             SCCEEEEEEEEEEEEETTTTEEEEEEEEEEEEBC-SSCCTTSCCC--------
T ss_pred             CCCcceeeeeeecceeCCCcEEEEEEeEEEEECC-CCcCcCCCcEEEecccCC
Confidence            454589999999999974 469999999999988 889999999999776433

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.62  E-value=0.00012  Score=54.67  Aligned_cols=60  Identities=18%  Similarity=0.202  Sum_probs=45.6

Q ss_pred             CCcEEEEcCCC----CCCCH----HHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLP----PSVSE----SEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp----~~~te----~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...+|+|..++    .+.-.    .+|.+.|.+||.|.  .+++..++      +||+|.+.++|.+||+-....|
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi--~vr~~~d~------~fVtF~d~~sAlaAi~mnG~~v   73 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVI--LIRFVEDK------MWVTFLEGSSALNVLSLNGKEL   73 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEE--EEEECSSS------EEEEESSHHHHHHGGGGTTCEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeE--EEEEecCC------EEEEECChHHHHHHHhcCCeEe
Confidence            35678887665    23333    56899999999999  78887653      8999999999999998555433

>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=97.55  E-value=0.00014  Score=62.05  Aligned_cols=48  Identities=33%  Similarity=0.457  Sum_probs=39.9

Q ss_pred             CHHHHHHHHhccCceeEceEEEecCCC------CCccEEEEEeCCHHHHHHHHHhc
Q 023954          221 SESEIAEEFKKFGELSSEGVVIRSRKD------VGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       221 te~~L~~~F~~fG~I~~~~v~v~~~~~------~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+++|++.|++||.|.  .+.|..+..      .++||+||+|.+.++|.+||++.
T Consensus       142 ~~~dl~~e~~~~G~v~--~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l  195 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVN--RVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL  195 (222)
T ss_dssp             HHHHHHHHHTTTSCEE--EEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCCeE--EEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHh
Confidence            4578999999999999  787764322      34899999999999999999864

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.30  E-value=0.00017  Score=54.12  Aligned_cols=60  Identities=20%  Similarity=0.266  Sum_probs=46.8

Q ss_pred             CCcEEEEcCCCCC------CCH---HHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPS------VSE---SEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~------~te---~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...+|+|..++..      ..+   .+|.+.|.+||.+.  .+++..++      +||+|.+.++|.+||+-....|
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi--lvr~v~d~------~fVtF~d~~sAl~AI~ldG~~v   82 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIV--LVRINQGQ------MLVTFADSHSALSVLDVDGMKV   82 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCS--EEEEETTE------EEEECSCSHHHHHHHHGGGSEE
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEE--EEEEecCc------EEEEEcChHHHHHHHhcCCeee
Confidence            4678999887642      232   46889999999998  78887764      9999999999999998554443

>1of5_B MTR2, YKL186C, mRNA transport regulator MTR2; nuclear protein, repeat, leucine- rich repeat, nuclear transport; 2.8A {Saccharomyces cerevisiae} SCOP: d.17.4.2

Probab=97.18  E-value=0.00029  Score=58.41  Aligned_cols=44  Identities=18%  Similarity=0.130  Sum_probs=25.1

Q ss_pred             ceEEeeeeecccC-CCcEEEEEEeEEEecCccccccceeEEEeeec
Q 023954            7 GIEIKTAHSLESW-NGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQ   51 (275)
Q Consensus         7 ~~~i~t~D~q~s~-~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~   51 (275)
                      +|+|.+.|||-.. .|.|||+|+|.|..+. ..+-+|.|+|.|.|.
T Consensus        77 ~hel~S~D~HVIngsgsivv~VsgkVRFdE-sgrd~fgEtfvLvpn  121 (184)
T 1of5_B           77 QHALTGVDYHAIPGSGTLICNVNCKVRFDE-SGRDKMGQDATVPIQ  121 (184)
T ss_dssp             EEEEEEEEEEEETTTTEEEEEEEEEEECC-----------------
T ss_pred             eEEEEeEEEEEECCCCeEEEEEEEEEEECC-CCCCCCCCeEEECCC
Confidence            8999999999875 4579999999999976 666799999999986

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.41  E-value=0.021  Score=43.36  Aligned_cols=60  Identities=18%  Similarity=0.216  Sum_probs=47.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhc-----cCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKK-----FGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~-----fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      -+++|.|.|||..+.++.|+-+|++     -|.|.  .+....      +-|+|+|.+...+++.|+...+.|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~--~v~~~~------~~AvItF~d~~va~rVL~k~~H~L   71 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVL--SWQRLG------CGGVLTFREPADAERVLAQADHEL   71 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEE--EEEEET------TEEEEEESSHHHHHHHHTCSCCBS
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceee--EEEEcC------CcEEEEEcChHHHHHHhcCCccee
Confidence            4789999999999999999999987     25555  444432      469999999999999999854443

>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=96.35  E-value=0.015  Score=43.73  Aligned_cols=52  Identities=23%  Similarity=0.336  Sum_probs=44.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHH
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~  268 (275)
                      .+-++| +.|......||..+|+.||.|.   |.+..+.     -|||.|.+.+.|..|+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~---I~WidDT-----sAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQ---ISWIDDT-----SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCC---CEEEETT-----EEEEECSCHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEE---EEEEcCC-----eEEEEecCHHHHHHHHH
Confidence            456666 9999999999999999999774   6666664     69999999999999887

>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=95.79  E-value=0.0099  Score=44.83  Aligned_cols=52  Identities=23%  Similarity=0.360  Sum_probs=43.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      +-++| +.|......+|..+|+.||.|   .|.+..+.     -|||.|.+.+.|..||..
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv---~I~WidDT-----sAlvvf~~~~~a~~al~~   58 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI---QISWIDDT-----SAFVSLSQPEQVKIAVNT   58 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE---EEEEEETT-----EEEEEEEEECHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE---EEEEEcCC-----eEEEEecCHHHHHHHHHh
Confidence            45666 999999999999999999966   46666664     699999999999998874

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=95.77  E-value=0.033  Score=42.85  Aligned_cols=55  Identities=16%  Similarity=0.103  Sum_probs=48.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhcc-----CceeEceEEEecCCCCCccEEEEEeCCHHHHHHHH
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKF-----GELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV  267 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~f-----G~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai  267 (275)
                      ..++|-+-|||-.++++.++.+...+     |.|.  .|.++.+-    |-|+|+|.|...|-+|.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~--KI~L~pDH----~GAivef~d~~~AgKas   79 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIR--KILLVSDF----NGAIIIFRDSKFAAKML   79 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCS--EEEEETTT----TEEEEECSCHHHHHHHH
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCcccee--EEEEecCC----CceEEEEccchhhHHHH
Confidence            46888899999999999999999999     9999  88888763    46999999999888875

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.45  E-value=0.011  Score=56.31  Aligned_cols=59  Identities=19%  Similarity=0.274  Sum_probs=43.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCc
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCIL  272 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi  272 (275)
                      .++|||. .+..+++.+|.+.|++||.|.  .+.+-.++   +.|+.|+|.+.+++..++....+
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~--~~~~~~~~---g~~~~vef~~~~~~~~~~~~~~~  111 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPIN--NHFFYESF---GLYAVVEFCQKESIGSLQNGTHT  111 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCC--CEEEECSS---SEEEEEECC---CCHHHHSSCCC
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcc--eEEEEccC---CeEEEEEeCCHHHHHHHHhccCC
Confidence            5899997 799999999999999999999  66554433   37999999999999988876643

>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=95.44  E-value=0.051  Score=42.32  Aligned_cols=61  Identities=16%  Similarity=0.208  Sum_probs=47.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..+-|-|-+.|... ...+-+.|++||.|.  ....  .  .+..+-.|.|.+..+|++||..+..+|
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv--~~~~--~--~~~NWihI~Y~s~~~A~rAL~kNG~ii   83 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNIL--KHVM--S--NTGNWMHIRYQSKLQARKALSKDGRIF   83 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEE--EEEE--C--SSSSEEEEEESSHHHHHHHHTTTTCEE
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEE--Eecc--C--CCCCeEEEEeCCHHHHHHHHHhCCeEe
Confidence            45778888888875 456677899999999  4433  2  235689999999999999999886655

>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=94.89  E-value=0.096  Score=38.78  Aligned_cols=58  Identities=17%  Similarity=0.312  Sum_probs=43.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC----ccEEEEEeCCHHHHHHHHH
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG----ICYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g----rgfgFV~F~~~~~a~~Ai~  268 (275)
                      ++|-||+||+++|++++.+.++....+.  .......+.+.    .+-|||.|.+.+++..-.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d--~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~   63 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHD--YFEFFSNDTSLYPHMYARAYINFKNQEDIILFRD   63 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEE--EEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHH
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccce--EEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHH
Confidence            5788999999999999999999888765  55554333221    5789999999877665443

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=92.71  E-value=0.073  Score=42.09  Aligned_cols=65  Identities=11%  Similarity=0.276  Sum_probs=44.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEec------------C--CC-CCccEEEEEeCCHHHHHHHHHhcCcc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRS------------R--KD-VGICYAFVEFEDMTGVRNAVEVCILM  273 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~------------~--~~-~grgfgFV~F~~~~~a~~Ai~a~pi~  273 (275)
                      ..|-|-+.|..... .+-+.|++||.|..+ +....            .  .. ++.++-.|.|++..+|.+||..++.+
T Consensus         8 ~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~-~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMAN-QVIAYFQEFGTILED-FEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             CEEEEECCCGGGHH-HHHHHHGGGSCBCSC-CGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             eEEEEEecCHHHHH-HHHHHHHhhceEeee-ccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            45566677666554 456679999999841 21110            0  01 24678899999999999999999766


Q ss_pred             CC
Q 023954          274 WH  275 (275)
Q Consensus       274 ig  275 (275)
                      |+
T Consensus        86 i~   87 (132)
T 3p3d_A           86 FN   87 (132)
T ss_dssp             ET
T ss_pred             eC
Confidence            53

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=85.99  E-value=0.66  Score=34.65  Aligned_cols=59  Identities=14%  Similarity=0.235  Sum_probs=37.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCC----CccEEEEEeCCHHHHHHHHH
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV----GICYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~----grgfgFV~F~~~~~a~~Ai~  268 (275)
                      .-+|-||.||+.+|++++.+.++.+=.+.  .......+.+    ..+-|||.|.+.+++..-.+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d--~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~   71 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHD--YFEFFAADLSLYPHLYSRAYINFRNPDDILLFRD   71 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEE--ECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHH
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccc--eEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHH
Confidence            56789999999999998766555432222  2111111111    14779999999988765443

>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=80.07  E-value=5.8  Score=37.97  Aligned_cols=54  Identities=22%  Similarity=0.320  Sum_probs=42.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..-++|+ ++..+...+|.++|+.||.+.   |.+..+.     .+||.|.+.+.+..++++-
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v~---V~widdt-----~a~V~~~~~~~a~~~l~~~  493 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNIQ---ISWIDDT-----SAFVSLSQPEQVQIAVNTS  493 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCCE---EEECSSS-----EEEEECSCHHHHHHHHHHH
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCEE---EEEEcCC-----eEEEEECCHHHHHHHHHHH
Confidence            4556665 888889999999999999764   5555443     6999999999998887653

---

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	275
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-11
d1gy7a_	121	d.17.4.2 (A:) Nuclear transport factor-2 (NTF2) {B	5e-11
d1zo2a1	117	d.17.4.2 (A:10-126) Nuclear transport factor-2 (NT	1e-10
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	4e-10
d1gy6a_	125	d.17.4.2 (A:) Nuclear transport factor-2 (NTF2) {R	5e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	8e-10
d1jkga_	139	d.17.4.2 (A:) NTF2-related export protein 1 (p15)	1e-09
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-09
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-09
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-09
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	8e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	9e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-08
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-08
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-08
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-08
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	9e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-06
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-06
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-06
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	7e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	8e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-05
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-05
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	3e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-05
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	4e-05
d2qiya1	139	d.17.4.2 (A:3-141) UBP3-associated protein BRE5 {B	5e-05
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	5e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	8e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	8e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-04
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-04
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-04
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-04
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	5e-04
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	7e-04
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	8e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.001
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	0.002
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	0.003

>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 = 57.3 bits (138), Expect = 1e-11
 Identities = 15/65 (23%), Positives = 31/65 (47%), Gaps = 2/65 (3%)

Query: 206 EEIK--SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGV 263
           E IK  ++YV NLP ++++ ++   F K+G +  + ++           AFV +      
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 264 RNAVE 268
           + A+ 
Sbjct: 62  QEAIS 66

>d1gy7a_ d.17.4.2 (A:) Nuclear transport factor-2 (NTF2) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 121

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: Nuclear transport factor-2 (NTF2)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 56.8 bits (137), Expect = 5e-11
 Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 3/56 (5%)

Query: 1   MSLNYSGI--EIKTA-HSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK 53
           +SL +  +   I T      S  G VLVM++G + + +    ++F Q F L P   
Sbjct: 52  VSLPFQKVQHRITTLDAQPASPYGDVLVMITGDLLIDEEQNPQRFSQVFHLIPDGN 107

>d1zo2a1 d.17.4.2 (A:10-126) Nuclear transport factor-2 (NTF2) {Cryptosporidium parvum [TaxId: 5807]} Length = 117

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: Nuclear transport factor-2 (NTF2)
species: Cryptosporidium parvum [TaxId: 5807]

 Score = 55.6 bits (134), Expect = 1e-10
 Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 3/54 (5%)

Query: 1   MSLNYSGI--EIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQE 52
            SLN+  +  EI       S N G +V V+G V++ D     KF Q F L P  
Sbjct: 51  NSLNFQRVQFEITRVDCQPSPNNGSIVFVTGDVRIDD-GQPLKFSQVFNLMPSG 103

>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 = 54.2 bits (130), Expect = 2e-10
 Identities = 17/59 (28%), Positives = 29/59 (49%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           S+YV +L P V+E+ + E+F   G + S  V         + YA+V F+       A++
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 60

>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 = 53.0 bits (127), Expect = 4e-10
 Identities = 15/58 (25%), Positives = 30/58 (51%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++V  L P   E +I E F  FGE+ S  + + ++ +    + F+ F++   V+  +E
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59

>d1gy6a_ d.17.4.2 (A:) Nuclear transport factor-2 (NTF2) {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 125

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: Nuclear transport factor-2 (NTF2)
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 54.1 bits (130), Expect = 5e-10
 Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 3/55 (5%)

Query: 1   MSLNYSGI--EIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK 53
            SL +  I   I       + +  ++ MV G ++  +      F Q F L     
Sbjct: 55  SSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDP-IMGFHQMFLLKNIND 108

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.3 bits (125), Expect = 8e-10
 Identities = 10/66 (15%), Positives = 30/66 (45%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
           ++ E+++ +++  L    ++  +   F+++G L+   V+          + FV +  +  
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 263 VRNAVE 268
           V  A+ 
Sbjct: 61  VDAAMN 66

>d1jkga_ d.17.4.2 (A:) NTF2-related export protein 1 (p15) {Human (Homo sapiens) [TaxId: 9606]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: NTF2-related export protein 1 (p15)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.4 bits (128), Expect = 1e-09
 Identities = 16/63 (25%), Positives = 23/63 (36%), Gaps = 7/63 (11%)

Query: 1   MSLNYSGIEIKTAHS------LESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKV 54
             L  S  +I                  VLV++ GSV+ +  + +R F Q F L  Q   
Sbjct: 62  EMLPSSEFQISVVDCQPVHDEATPSQTTVLVVICGSVKFEG-NKQRDFNQNFILTAQASP 120

Query: 55  PNH 57
            N 
Sbjct: 121 SNT 123

>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 = 51.9 bits (124), Expect = 2e-09
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 202 VEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVI-RSRKDVGICYAFVEFEDM 260
           V  ++    + VRN+P   ++ EI E F  FGEL +  +    +       + FV+F   
Sbjct: 2   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 61

Query: 261 TGVRNAVE 268
              + A  
Sbjct: 62  QDAKKAFN 69

>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 = 51.2 bits (122), Expect = 2e-09
 Identities = 11/58 (18%), Positives = 29/58 (50%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +YV  LP ++++ E+ + F ++G + +  +++     V     F+ F+       A++
Sbjct: 9   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

>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 = 51.1 bits (122), Expect = 3e-09
 Identities = 16/60 (26%), Positives = 27/60 (45%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
            ++YV NL    +E +I E F K G++    + +   K     + FVE+       NA+ 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

>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 = 50.4 bits (120), Expect = 3e-09
 Identities = 13/58 (22%), Positives = 24/58 (41%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +++  L    ++  + E F +FGE+    V+          + FV F D  GV   + 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

>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 = 53.1 bits (126), Expect = 4e-09
 Identities = 10/73 (13%), Positives = 30/73 (41%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
           ++ E+++ +++  L    ++  +   F+++G L+   V+          + FV +  +  
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 263 VRNAVEVCILMWH 275
           V  A+        
Sbjct: 61  VDAAMNARPHKVD 73

>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 = 49.6 bits (118), Expect = 6e-09
 Identities = 10/58 (17%), Positives = 26/58 (44%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +++  L    ++ ++ + F KFGE+    + +         + FV F++   V   ++
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD 59

>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 = 50.1 bits (119), Expect = 8e-09
 Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 1/80 (1%)

Query: 189 EKSWADTGEEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDV 248
           EK+      E     ++E+ + +++  L    +E  +   ++++G+L+   V+       
Sbjct: 2   EKTLETVPLE-RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKR 60

Query: 249 GICYAFVEFEDMTGVRNAVE 268
              + FV F  M  V  A+ 
Sbjct: 61  SRGFGFVTFSSMAEVDAAMA 80

>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 = 49.7 bits (118), Expect = 9e-09
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 202 VEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMT 261
           +ED+ + +++YV NL   V+E  I + F + G   S    + +       Y FVEF +  
Sbjct: 2   MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKS--CKMITEHTSNDPYCFVEFYEHR 59

Query: 262 GVRNAVE 268
               A+ 
Sbjct: 60  DAAAALA 66

>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 = 49.2 bits (117), Expect = 1e-08
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           + V NL   VS+++I E F +FG    +  V   R    +  A V FE       A++
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGT-LKKAAVHYDRSGRSLGTADVHFERKADALKAMK 59

>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 = 48.9 bits (116), Expect = 1e-08
 Identities = 16/67 (23%), Positives = 27/67 (40%)

Query: 202 VEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMT 261
           + +  +  +VYV  L   VSE  + E F + G + +  +           Y FVEF    
Sbjct: 3   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 62

Query: 262 GVRNAVE 268
               A++
Sbjct: 63  DADYAIK 69

>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 = 48.2 bits (114), Expect = 2e-08
 Identities = 15/66 (22%), Positives = 30/66 (45%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
            + +    + V  L    +E ++ E F K+G ++   +V   +      +AFV FE++  
Sbjct: 4   ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 63

Query: 263 VRNAVE 268
            + A E
Sbjct: 64  AKEAKE 69

>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 = 48.1 bits (114), Expect = 2e-08
 Identities = 12/59 (20%), Positives = 29/59 (49%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++ V  LP  +++ E+   F+  G +++  ++   +      YAFV+F      + A++
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

>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 = 48.2 bits (114), Expect = 3e-08
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIR-SRKDVGICYAFVEFEDMTGVRNAVEV 269
           +++ NL P + E  + + F  FG +     ++R         YAF+ F        A+E 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 270 C 270
            
Sbjct: 61  M 61

>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 = 48.0 bits (114), Expect = 3e-08
 Identities = 13/63 (20%), Positives = 24/63 (38%)

Query: 206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRN 265
           ++   + V  LP   +E ++ E F  FGE+    V    +      + FV F +      
Sbjct: 6   QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 65

Query: 266 AVE 268
            + 
Sbjct: 66  VMS 68

>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 = 46.9 bits (111), Expect = 1e-07
 Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRN 265
           E  + +Y+RNLP  ++  E+ + F K+G +    V            A+V +ED+   +N
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKN 61

Query: 266 AVE 268
           A +
Sbjct: 62  ACD 64

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 12/60 (20%), Positives = 28/60 (46%), Gaps = 3/60 (5%)

Query: 212 YVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR---KDVGICYAFVEFEDMTGVRNAVE 268
           +++NL  S +E  +   F K G + S  +  +       + + + FVE++     + A++
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

>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 = 45.5 bits (107), Expect = 2e-07
 Identities = 11/58 (18%), Positives = 25/58 (43%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++V  L  + +  ++   F++FG++    ++     +    + FV FE    V    E
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

>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 = 44.7 bits (105), Expect = 4e-07
 Identities = 14/59 (23%), Positives = 25/59 (42%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++ V  LP ++++ E    F   GE+ S  +V        + Y FV + D      A+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

>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 = 44.3 bits (104), Expect = 7e-07
 Identities = 13/64 (20%), Positives = 26/64 (40%)

Query: 205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVR 264
            ++  ++ V NL     E+++ E F+ FG +S   +           +AF+ F       
Sbjct: 5   ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 64

Query: 265 NAVE 268
            A+ 
Sbjct: 65  RAIA 68

>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 = 43.9 bits (103), Expect = 9e-07
 Identities = 14/60 (23%), Positives = 27/60 (45%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           + +YV  L   V +  +   F  FG+++   + +    +    +AFVEFE       A++
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

>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 = 43.9 bits (103), Expect = 1e-06
 Identities = 11/66 (16%), Positives = 28/66 (42%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
            +E + ++V+   L   +   ++ + F   G++    ++           A+VEF ++  
Sbjct: 13  PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 72

Query: 263 VRNAVE 268
           V  A+ 
Sbjct: 73  VPLAIG 78

>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 = 43.1 bits (101), Expect = 2e-06
 Identities = 14/58 (24%), Positives = 28/58 (48%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +++  LP  +++ ++ E    FG L +  +V  S   +   YAF E+ D+     A+ 
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

>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 = 42.8 bits (100), Expect = 2e-06
 Identities = 12/61 (19%), Positives = 27/61 (44%)

Query: 208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
           +K ++V  +     E  + + F+++G++    ++          +AFV F+D   V   V
Sbjct: 2   VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 61

Query: 268 E 268
            
Sbjct: 62  I 62

>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 = 43.0 bits (101), Expect = 2e-06
 Identities = 11/59 (18%), Positives = 24/59 (40%), Gaps = 6/59 (10%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +VY   +   +++  + + F  FG+      ++  R      Y+FV F       +A+ 
Sbjct: 20  TVYCGGIASGLTDQLMRQTFSPFGQ------IMEIRVFPEKGYSFVRFSTHESAAHAIV 72

>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 = 42.3 bits (99), Expect = 3e-06
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 6/58 (10%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++V NLPP ++E E+ + F+K+G+                 + F+  E  T    A  
Sbjct: 11  LFVGNLPPDITEEEMRKLFEKYGK------AGEVFIHKDKGFGFIRLETRTLAEIAKV 62

>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 = 42.2 bits (99), Expect = 4e-06
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 10/71 (14%)

Query: 200 SAVEDEEEIKS-VYVRNLPP-SVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEF 257
           S   D   + S V++ NL    V +S++   F K+G+      ++      G  +AFV++
Sbjct: 6   SGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGK------IVGCSVHKG--FAFVQY 57

Query: 258 EDMTGVRNAVE 268
            +    R AV 
Sbjct: 58  VNERNARAAVA 68

>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 = 42.1 bits (98), Expect = 5e-06
 Identities = 17/66 (25%), Positives = 29/66 (43%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
            D  E K+V++RNL     E  + E  ++FG+L    VV+    +     AF +F     
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 263 VRNAVE 268
            +  + 
Sbjct: 63  AQKCLA 68

>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 = 41.6 bits (97), Expect = 7e-06
 Identities = 12/70 (17%), Positives = 28/70 (40%)

Query: 199 ISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFE 258
           +   + +     ++V  LP   +++ + + F+ FG++    V+   +      Y FV   
Sbjct: 1   MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA 60

Query: 259 DMTGVRNAVE 268
           D      A +
Sbjct: 61  DRAAAERACK 70

>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 = 41.2 bits (96), Expect = 8e-06
 Identities = 16/59 (27%), Positives = 27/59 (45%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
            ++V ++     E EI E+F  +GE+ +  + +  R      YA VE+E       A E
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +++++NL  S+    + + F  FG + S    +   ++    Y FV FE       A+E
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILS--CKVVCDENGSKGYGFVHFETQEAAERAIE 66

>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 = 40.4 bits (94), Expect = 2e-05
 Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
           E +   K ++V N+P    + ++ + F +FG++      I   +     + FV FE+   
Sbjct: 6   ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDV--EIIFNERGSKGFGFVTFENSAD 63

Query: 263 VRNAVE 268
              A E
Sbjct: 64  ADRARE 69

>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 = 39.7 bits (92), Expect = 2e-05
 Identities = 13/66 (19%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
           +++ + +SVY++  P   +  +I E  +  G++ +   + R+         FV F+ +  
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNI-QMRRTLHKAFKGSIFVVFDSIES 59

Query: 263 VRNAVE 268
            +  VE
Sbjct: 60  AKKFVE 65

>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 = 40.1 bits (93), Expect = 2e-05
 Identities = 17/58 (29%), Positives = 25/58 (43%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++VRNL  + SE ++ + F  +G LS     I S       +AFV F        A  
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

>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 = 40.1 bits (93), Expect = 3e-05
 Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC--YAFVEFEDMTGVRNAVE 268
           +++  +P      EI EE  K  E   + +V  S  D      +AFVE+E       A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

>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 = 39.7 bits (92), Expect = 3e-05
 Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 9/66 (13%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGIC-------YAFVEFEDMT 261
           + +YV N+P  ++E  + + F     L    +       V          +AF+EF  + 
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGG--LTQAPGNPVLAVQINQDKNFAFLEFRSVD 59

Query: 262 GVRNAV 267
               A+
Sbjct: 60  ETTQAM 65

>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 = 39.4 bits (91), Expect = 3e-05
 Identities = 12/62 (19%), Positives = 24/62 (38%), Gaps = 4/62 (6%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
            ++++ N+PPSVSE ++   F   G +    V            A ++   +     A+ 
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALI 66

Query: 269 VC 270
             
Sbjct: 67  DL 68

>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 = 39.3 bits (91), Expect = 3e-05
 Identities = 11/69 (15%), Positives = 24/69 (34%), Gaps = 7/69 (10%)

Query: 206 EEIKSVYVRNLPPS-VSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVR 264
           E  + V++ +         ++ +  + FG +S+            I  AF+E       +
Sbjct: 6   ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISN------HLILNKINEAFIEMATTEDAQ 59

Query: 265 NAVEVCILM 273
            AV+     
Sbjct: 60  AAVDYYTTT 68

>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 = 39.0 bits (90), Expect = 4e-05
 Identities = 12/58 (20%), Positives = 30/58 (51%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +Y+R L P  ++ ++ +  + +G++ S   ++    +    Y FV+F+  +  + AV 
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 58

>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 = 39.2 bits (91), Expect = 4e-05
 Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 6/66 (9%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
           +    +K +YVRNL  S SE  I +EF      ++       R      YAFV F +   
Sbjct: 3   DTMSSVKILYVRNLMLSTSEEMIEKEF------NNIKPGAVERVKKIRDYAFVHFSNRED 56

Query: 263 VRNAVE 268
              A++
Sbjct: 57  AVEAMK 62

>d2qiya1 d.17.4.2 (A:3-141) UBP3-associated protein BRE5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: UBP3-associated protein BRE5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.0 bits (93), Expect = 5e-05
 Identities = 11/59 (18%), Positives = 19/59 (32%), Gaps = 7/59 (11%)

Query: 1   MSLNYSGIEIKT------AHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEK 53
              +     +K              +  +L+M +G +     +   KF QTF L P   
Sbjct: 68  SRNDAKVRSLKLKLDTIDFQYTGHLHKSILIMATGEMFWTG-TPVYKFCQTFILLPSSN 125

>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 = 39.6 bits (92), Expect = 5e-05
 Identities = 11/61 (18%), Positives = 25/61 (40%), Gaps = 4/61 (6%)

Query: 208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
           +  + V NL   V+   + + F KFG +       ++ +      A +++ D    ++A 
Sbjct: 7   VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ----FQALLQYADPVSAQHAK 62

Query: 268 E 268
            
Sbjct: 63  L 63

>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 = 39.3 bits (91), Expect = 5e-05
 Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 5/72 (6%)

Query: 197 EEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVE 256
           E+    +     +++  +NL  +++E E+ E F+   E     +V +  K  G   A++E
Sbjct: 5   EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALE---IRLVSQDGKSKG--IAYIE 59

Query: 257 FEDMTGVRNAVE 268
           F+        +E
Sbjct: 60  FKSEADAEKNLE 71

>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 = 40.3 bits (93), Expect = 5e-05
 Identities = 13/69 (18%), Positives = 34/69 (49%)

Query: 200 SAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFED 259
               + + ++++ V  +P +V E ++ + F+++G + S  +V          Y FV+F+ 
Sbjct: 34  QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93

Query: 260 MTGVRNAVE 268
            +  + A+ 
Sbjct: 94  GSSAQQAIA 102

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.2 bits (88), Expect = 8e-05
 Identities = 10/58 (17%), Positives = 25/58 (43%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +++ N PPS ++  I +  +    ++    +   R +    +A+++       R  VE
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

>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 = 38.1 bits (88), Expect = 8e-05
 Identities = 15/58 (25%), Positives = 25/58 (43%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           + V+N+P +VS  EI + F  +  +     +  + K +    A V FE       AV 
Sbjct: 12  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 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 = 38.0 bits (88), Expect = 1e-04
 Identities = 8/60 (13%), Positives = 21/60 (35%), Gaps = 7/60 (11%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC 270
           V V   P + +   I  +F ++G       +++        +  + ++     R A+   
Sbjct: 7   VTVFGFPQASAS-YILLQFAQYGN------ILKHVMSNTGNWMHIRYQSKLQARKALSKD 59

>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 = 38.6 bits (89), Expect = 1e-04
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 8/74 (10%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVV----IRSRKDV----GICYAF 254
           +++ +  ++YV+ L  SV+  ++A+ FK+ G +          I    D         A 
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 255 VEFEDMTGVRNAVE 268
           V +ED    + AVE
Sbjct: 63  VSYEDPPTAKAAVE 76

>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 = 38.5 bits (89), Expect = 1e-04
 Identities = 13/66 (19%), Positives = 35/66 (53%)

Query: 203 EDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTG 262
           ++  E  ++++ +LP    + ++ + F  FG + S  V I  + ++  C+ FV +++   
Sbjct: 13  KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVS 72

Query: 263 VRNAVE 268
            + A++
Sbjct: 73  AQAAIQ 78

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 1e-04
 Identities = 13/72 (18%), Positives = 21/72 (29%), Gaps = 6/72 (8%)

Query: 197 EEISAVEDEEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVE 256
           E I  V    +   V    L   VS +++    +K G       V          Y+F  
Sbjct: 9   EGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGL------VDALLMPPNKPYSFAR 62

Query: 257 FEDMTGVRNAVE 268
           +      + A  
Sbjct: 63  YRTTEESKRAYV 74

>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 = 37.4 bits (86), Expect = 1e-04
 Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 6/58 (10%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +Y+ NL P+V+  ++ + F       +  V+++S       YAFV++ D      A+E
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS------GYAFVDYPDQNWAIRAIE 55

>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 = 37.4 bits (86), Expect = 2e-04
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 3/58 (5%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           +YV NLPP +   +I + F K+G +     +    +  G  +AFVEFED     +AV 
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIR---DIDLKNRRGGPPFAFVEFEDPRDAEDAVY 71

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 2e-04
 Identities = 15/64 (23%), Positives = 31/64 (48%)

Query: 205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVR 264
           +  ++SV+V N+P   +E ++ + F + G + S  +V          Y F E++D     
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 265 NAVE 268
           +A+ 
Sbjct: 65  SAMR 68

>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 = 37.3 bits (86), Expect = 2e-04
 Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 1/62 (1%)

Query: 207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNA 266
            +  V ++       E    E  +K+GE+  E  V  +  D  +   +V+F        A
Sbjct: 26  AVSDVEMQEHYDEFFEEVFTEMEEKYGEV-EEMNVCDNLGDHLVGNVYVKFRREEDAEKA 84

Query: 267 VE 268
           V 
Sbjct: 85  VI 86

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 3e-04
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
             V+V      ++E E+ E F ++G+     V+          +AFV F D    ++   
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGD-----VMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

>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 = 36.4 bits (83), Expect = 3e-04
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV 269
           +V V+NLP S +++++ + FK  G +    V +         +A +EF    G   A+  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPI--IHVDVADSLKKNFRFARIEFARYDGALAAITK 59

Query: 270 C 270
            
Sbjct: 60  T 60

>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 = 36.2 bits (83), Expect = 5e-04
 Identities = 13/61 (21%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKK-FGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAV 267
            ++Y+ NL   + + E+ +     F        ++ SR       AFV F++++   NA+
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 268 E 268
            
Sbjct: 64  R 64

>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 = 35.9 bits (82), Expect = 7e-04
 Identities = 14/58 (24%), Positives = 26/58 (44%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
            ++ NLP  V+E  I E F+     +       S  +    + + EFED+  + +A+ 
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (81), Expect = 8e-04
 Identities = 14/58 (24%), Positives = 28/58 (48%)

Query: 211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           ++V  L    +E  + + F K+G++S   VV          + FV FE++   ++A+ 
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

>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 = 35.2 bits (80), Expect = 0.001
 Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 6/60 (10%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
             V+VR L  SV E+++ E  +KFG +    ++           A VEFE++   +  V 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVT 69

>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 = 34.8 bits (79), Expect = 0.002
 Identities = 8/67 (11%), Positives = 16/67 (23%), Gaps = 3/67 (4%)

Query: 210 SVYVRNLPPSV-SESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
            +        V SESE   +F+      +       +         + F +     +A  
Sbjct: 7   GLIACVANDDVFSESETRAKFESLF--RTYDKDTTFQYFKSFKRVRINFSNPLSAADARL 64

Query: 269 VCILMWH 275
                  
Sbjct: 65  RLHKTEF 71

>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 = 34.4 bits (78), Expect = 0.003
 Identities = 15/60 (25%), Positives = 26/60 (43%)

Query: 209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE 268
           K +Y++NL P V+E ++   F +F E     +  R         AF+ F +      A+ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	275
d1zo2a1	117	Nuclear transport factor-2 (NTF2) {Cryptosporidium	99.65
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.63
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.62
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.62
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
d1gy6a_	125	Nuclear transport factor-2 (NTF2) {Rat (Rattus nor	99.6
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.6
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.6
d1gy7a_	121	Nuclear transport factor-2 (NTF2) {Baker's yeast (	99.59
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.58
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.57
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.56
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.56
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.56
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.56
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.55
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.55
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.54
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.54
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.54
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.54
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.54
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.53
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.53
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.53
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.53
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.52
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.52
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.52
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.52
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.52
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.51
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.51
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.51
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.51
d1jkga_	139	NTF2-related export protein 1 (p15) {Human (Homo s	99.51
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.5
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.5
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.49
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.49
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.46
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.46
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.46
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.46
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.45
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.44
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.44
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.44
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.42
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.41
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.4
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.4
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.4
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.39
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.38
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.38
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.37
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.37
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.37
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.37
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.37
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.36
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.36
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.35
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.34
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.34
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.33
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.33
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.33
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.33
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.32
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.32
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.32
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.29
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.29
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.28
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.27
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.26
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.23
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.22
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.22
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.22
d2qiya1	139	UBP3-associated protein BRE5 {Baker's yeast (Sacch	99.21
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.19
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.18
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.13
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.07
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.0
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.95
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	98.79
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.51
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.26
d1of5b_	165	mRNA transport regulator MTR2 {Baker's yeast (Sacc	96.64
d1q40b_	205	NTF2-like domain of mRNA export factor MEX67 {Yeas	95.28
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	95.22
d1q42a_	174	mRNA transport regulator MTR2 {Yeast (Candida albi	94.32
d1jkgb_	186	NTF2-like domain of Tip associating protein, TAP {	93.69
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	91.1
d1of5a_	221	NTF2-like domain of mRNA export factor MEX67 {Bake	89.07
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	83.34

>d1zo2a1 d.17.4.2 (A:10-126) Nuclear transport factor-2 (NTF2) {Cryptosporidium parvum [TaxId: 5807]}

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: Nuclear transport factor-2 (NTF2)
species: Cryptosporidium parvum [TaxId: 5807]

Probab=99.65  E-value=4.9e-17  Score=126.61  Aligned_cols=62  Identities=31%  Similarity=0.434  Sum_probs=56.6

Q ss_pred             CCCcc--ceEEeeeeecccCCCcEEEEEEeEEEecCccccccceeEEEeeecCCCCeEeecCccc
Q 023954            2 SLNYS--GIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQ   64 (275)
Q Consensus         2 sl~f~--~~~i~t~D~q~s~~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~~   64 (275)
                      +|+|+  +|+|.++|||++.+|||||+|+|.|+.++ +++|+|+|+|+|+++++|.|||.||.|+
T Consensus        52 ~l~~~~~~~~i~~~D~Qp~~~~~ili~V~G~~~~~~-~~~~~F~q~F~L~~~~~~~~~I~nD~FR  115 (117)
T d1zo2a1          52 SLNFQRVQFEITRVDCQPSPNNGSIVFVTGDVRIDD-GQPLKFSQVFNLMPSGNGGFMIFNDLFR  115 (117)
T ss_dssp             HHCCSCEEEEEEEEEEEECTBSSEEEEEEEEEEETT-CCCEEEEEEEEEEECSSSCEEEEEEEEE
T ss_pred             hCCCccceEEEeeEEEEEcCCCCEEEEEEEEEEeCC-CCcceeEEEEEEeEcCCCCEEEEeEEee
Confidence            47887  89999999999999999999999999998 7889999999999988777799999863

>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=99.63  E-value=1.7e-16  Score=113.95  Aligned_cols=64  Identities=22%  Similarity=0.403  Sum_probs=57.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccCC
Q 023954          210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMWH  275 (275)
Q Consensus       210 ~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~ig  275 (275)
                      +|||+|||+++|+++|+++|++||.|.  .+.|..++.++  ||||||+|.+.++|++||+....+|+
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~--~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~   66 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVE--SIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVG   66 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEE--EEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBT
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcc--cccccccccccccccEEEEEECCHHHHHHHHhhCCCEEC
Confidence            699999999999999999999999999  88888776554  89999999999999999988776664

>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=99.62  E-value=2.1e-16  Score=114.00  Aligned_cols=65  Identities=18%  Similarity=0.308  Sum_probs=59.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccCC
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMWH  275 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~ig  275 (275)
                      ++|||+|||+++++++|+++|++||.|.  .+.|..++.++  ||||||+|.+.++|++||+.++.+|+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~--~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~   67 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVK--ECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELD   67 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCC--CEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCS
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcc--eeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEEC
Confidence            5899999999999999999999999999  88888877655  89999999999999999998877664

>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=99.62  E-value=5.6e-16  Score=111.03  Aligned_cols=63  Identities=17%  Similarity=0.354  Sum_probs=57.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       210 ~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      +|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|++||+.....|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~--~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l   65 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVV--DCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKL   65 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEE--EEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCB
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhcccc--ccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEE
Confidence            599999999999999999999999999  88888877655  8999999999999999999876665

>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=99.62  E-value=8.2e-16  Score=112.59  Aligned_cols=66  Identities=14%  Similarity=0.352  Sum_probs=59.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|++||+....+|
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~--~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i   72 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLT--DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKV   72 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhcccc--ceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEE
Confidence            458999999999999999999999999999  88887776655  8999999999999999999876554

>d1gy6a_ d.17.4.2 (A:) Nuclear transport factor-2 (NTF2) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: Nuclear transport factor-2 (NTF2)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.60  E-value=2.4e-16  Score=124.12  Aligned_cols=61  Identities=16%  Similarity=0.218  Sum_probs=55.1

Q ss_pred             CCCcc--ceEEeeeeecccCCCcEEEEEEeEEEecCccccccceeEEEeeecCCCCeEeecCccc
Q 023954            2 SLNYS--GIEIKTAHSLESWNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQ   64 (275)
Q Consensus         2 sl~f~--~~~i~t~D~q~s~~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~~   64 (275)
                      +|+++  +++|.++|||++.++||||+|+|.|+.++ +++|+|+|+|+|++++++ |||.||.|+
T Consensus        56 ~lp~~~~~~~i~~~D~Q~~~~~~ili~V~G~~~~~~-~~~~~F~qtF~L~~~~~~-y~I~NDiFR  118 (125)
T d1gy6a_          56 SLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADE-DPIMGFHQMFLLKNINDA-WVCTNDMFR  118 (125)
T ss_dssp             HCSCSCEEEEEEEEEEEECTTSCEEEEEEEEEEETT-SCCEEEEEEEEEEEETTE-EEEEEEEEE
T ss_pred             cCCCcccEEEEeEEEEEEcCCCCEEEEEEEEEEECC-CCCcceEEEEEEeccCCE-EEEEeeEEE
Confidence            57887  69999999999999999999999999988 788999999999998755 599999864

>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=99.60  E-value=1e-15  Score=113.59  Aligned_cols=63  Identities=22%  Similarity=0.365  Sum_probs=57.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCI  271 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~p  271 (275)
                      ..++|||+|||+++|+++|+++|++||.|.  .+.|..++.+|  ||||||+|.+.++|.+||+...
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~--~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~   71 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVL--MVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH   71 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEE--EEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCE
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccc--eeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCC
Confidence            568899999999999999999999999999  88888876655  8999999999999999998654

>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=99.60  E-value=5.8e-16  Score=117.84  Aligned_cols=66  Identities=17%  Similarity=0.345  Sum_probs=59.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||+++++++|+++|.+||.|.  .+.|..++.++  +|||||+|.+.++|++||+.+..+|
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~--~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l   86 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLT--DCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSI   86 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCS--EEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCccc--ceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeE
Confidence            458999999999999999999999999999  88888776554  8999999999999999998876665

>d1gy7a_ d.17.4.2 (A:) Nuclear transport factor-2 (NTF2) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: Nuclear transport factor-2 (NTF2)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.59  E-value=3.7e-16  Score=122.27  Aligned_cols=62  Identities=24%  Similarity=0.394  Sum_probs=54.5

Q ss_pred             CCCcc--ceEEeeeeeccc-CCCcEEEEEEeEEEecCccccccceeEEEeeecCCCCeEeecCccc
Q 023954            2 SLNYS--GIEIKTAHSLES-WNGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKVPNHLMGGEIQ   64 (275)
Q Consensus         2 sl~f~--~~~i~t~D~q~s-~~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g~~~v~~~~~~   64 (275)
                      +|+|+  +|+|+++||||+ .+|+|||+|+|.++.++++.+|+|+|+|+|++++++ |||.||.|+
T Consensus        53 ~lp~~~~~~~i~~~D~Qp~~~~~~ili~V~G~~~~~~~~~~~~F~qtF~L~~~~~~-y~I~nD~FR  117 (121)
T d1gy7a_          53 SLPFQKVQHRITTLDAQPASPYGDVLVMITGDLLIDEEQNPQRFSQVFHLIPDGNS-YYVFNDIFR  117 (121)
T ss_dssp             HSCCSCEEEEEEEEEEEESSTTSCEEEEEEEEEEETTCSSCEEEEEEEEEEEETTE-EEEEEEEEE
T ss_pred             hCCCcccEEEEeeEeeEEccCCCeEEEEEEEEEEECCCCCcceeEEEEEEEeeCCE-EEEEEEEEE
Confidence            68887  799999999996 577899999999999876678999999999999866 599999864

>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=99.58  E-value=2.7e-15  Score=113.85  Aligned_cols=67  Identities=19%  Similarity=0.407  Sum_probs=59.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|++||+....+|
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~--~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l   76 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIE--EAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPII   76 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEE--EEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEE
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhccccc--ceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcC
Confidence            3568899999999999999999999999999  88888776554  8999999999999999999775443

>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=99.57  E-value=3.8e-15  Score=107.26  Aligned_cols=66  Identities=21%  Similarity=0.420  Sum_probs=58.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccCC
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMWH  275 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~ig  275 (275)
                      .++|||+|||+++|+++|+++|++||.|.  .+.+..++.++  +|||||+|.+.+++.+||+.+..+|+
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~--~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~   69 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIE--VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVN   69 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEET
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhcccc--ccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEEC
Confidence            47999999999999999999999999999  77777766555  89999999999999999987766553

>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=99.56  E-value=5.1e-15  Score=109.48  Aligned_cols=64  Identities=23%  Similarity=0.366  Sum_probs=58.6

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +...++|||+|||.++++++|+++|++||.|.  .+.+..++.+++|||||+|.+.++|.+||+..
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~--~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l   68 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCK--SCKMITEHTSNDPYCFVEFYEHRDAAAALAAM   68 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEE--EEEEECCCCSSCCEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCce--eeeeecccCccceeeEEEECCHHHHHHHHHHc
Confidence            34568999999999999999999999999999  88888888878999999999999999999863

>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=99.56  E-value=3.6e-15  Score=106.83  Aligned_cols=65  Identities=23%  Similarity=0.331  Sum_probs=59.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccCC
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMWH  275 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~ig  275 (275)
                      .+|||+|||+++++++|+++|++||.|.  .+.+..++..++|||||+|.+.++|++||.....+||
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~--~v~~~~~~~~~~~~afV~F~~~~~a~~Al~~~~~~i~   65 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPII--HVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVG   65 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEE--EEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEET
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceE--EEEEEeeccccceEEEEEEcchHHhHHHHHhcCcEEC
Confidence            4799999999999999999999999999  8999888777789999999999999999988776664

>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=99.56  E-value=1.9e-14  Score=114.49  Aligned_cols=66  Identities=20%  Similarity=0.417  Sum_probs=58.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh-cCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV-CILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a-~pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .|.|..++.++  ||||||+|.+.++|.+||+. +..+|
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~  109 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIE--SVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI  109 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEE--EEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhcccc--ccccccccccccccceeeEEECCHHHHHHHHHHhCCCEE
Confidence            457899999999999999999999999999  88888776655  89999999999999999987 45554

>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=99.56  E-value=6.5e-15  Score=107.80  Aligned_cols=62  Identities=19%  Similarity=0.389  Sum_probs=55.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ++++|||+|||+++|+++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+..
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~--~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~l   68 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRII--TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL   68 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcc--ccccccccccccCCCeeEEEEcCHHHHHHHHHHh
Confidence            467899999999999999999999999999  88887766544  899999999999999999753

>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=99.55  E-value=8.1e-15  Score=107.16  Aligned_cols=63  Identities=24%  Similarity=0.409  Sum_probs=56.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+++..++.++  ||||||+|.+.++|.+||+..
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~--~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l   68 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIV--QKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL   68 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEe--eeeeecccccccCceeEEEEECCHHHHHHHHHHH
Confidence            3567899999999999999999999999999  88888766555  899999999999999999863

>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=99.55  E-value=1.2e-14  Score=108.18  Aligned_cols=62  Identities=24%  Similarity=0.372  Sum_probs=57.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+.+..++...+|||||+|.+.++|.+||+.
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~--~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~   70 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKIL--DVEIIFNERGSKGFGFVTFENSADADRAREK   70 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEE--EEEEECCTTTTCCEEEEEESCHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceee--eccccccccCCcceeEEEECCHHHHHHHHHH
Confidence            4578899999999999999999999999999  8888888777799999999999999999976

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=1e-14  Score=108.51  Aligned_cols=66  Identities=26%  Similarity=0.362  Sum_probs=57.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc-CccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC-ILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~-pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|++||++. ...|
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~--~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~   76 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVV--NTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKL   76 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEE--EEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCcc--ccceeecccccccccceEEEECCHHHHHHHHHHcCCCEE
Confidence            457999999999999999999999999999  88888776655  899999999999999999864 4433

>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=99.54  E-value=7.2e-15  Score=106.51  Aligned_cols=60  Identities=25%  Similarity=0.449  Sum_probs=54.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|++||+.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~--~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~   63 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPIN--TCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV   63 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEE--EEECCEETTTTEECSEEEEEESSHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcc--eeeeeeecccCCccccceEEECCHHHHHHHHHH
Confidence            46899999999999999999999999999  88887766555  89999999999999999975

>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=99.54  E-value=7.1e-15  Score=107.64  Aligned_cols=64  Identities=20%  Similarity=0.401  Sum_probs=56.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc-CccC
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC-ILMW  274 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~-pi~i  274 (275)
                      ++|||+|||+++|+++|+++|++||.|.  .++|..++.+|  ||||||+|.+.++|.+||+.. ...|
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~--~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l   68 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLK--AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL   68 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEE--EEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccc--eEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEE
Confidence            5799999999999999999999999999  88988876655  899999999999999999964 4443

>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=99.54  E-value=1.1e-14  Score=105.83  Aligned_cols=61  Identities=26%  Similarity=0.348  Sum_probs=55.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++|+++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|.+||++
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~   70 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIA--DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER   70 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEE--EEEEEECSSSSSEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCc--cccccccccccccccceEEEECCHHHHHHHHHH
Confidence            467899999999999999999999999999  88887766544  89999999999999999975

>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=99.54  E-value=1.3e-14  Score=107.91  Aligned_cols=62  Identities=26%  Similarity=0.381  Sum_probs=56.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...++|||+|||+++|+++|+++|++||.|.  .|.+..++.++  +|||||+|.+.++|.+||+.
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~--~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~   68 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIK--KIIMGLDKMKKTACGFCFVEYYSRADAENAMRY   68 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcc--eeccccccccccccceEEEEECCHHHHHHHHHH
Confidence            3578999999999999999999999999999  88888776655  89999999999999999985

>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=99.53  E-value=4.7e-15  Score=112.25  Aligned_cols=66  Identities=20%  Similarity=0.329  Sum_probs=58.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      +.++|||+|||+++++++|+++|+.||.|.  .+.|..++.+|  ||||||+|.+.++|.+||+.+...|
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~--~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~   84 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVR--DVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRL   84 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEE--EEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEE--EEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEE
Confidence            457899999999999999999999999999  88888876554  9999999999999999998665544

>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=99.53  E-value=1.7e-14  Score=106.15  Aligned_cols=62  Identities=27%  Similarity=0.424  Sum_probs=56.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .+++.|||+|||+++++++|+++|++||.|.  .+++..++.++  +|||||+|.+.++|++||+.
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~--~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~   68 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIK--NIHLNLDRRTGFSKGYALVEYETHKQALAAKEA   68 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTSSEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcc--cccccccccccccccceeEEECCHHHHHHHHHH
Confidence            3578999999999999999999999999999  88888776555  89999999999999999986

>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=99.53  E-value=6.1e-15  Score=108.82  Aligned_cols=61  Identities=21%  Similarity=0.480  Sum_probs=56.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..+|||+|||+++++++|+++|++||.|.  .+.|..++++++|||||+|.+.++|++||+..
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~--~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l   68 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNIL--SCKVVCDENGSKGYGFVHFETQEAAERAIEKM   68 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEE--EEEECCBTTBCCSCEEEEESCHHHHHHHTTSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCce--EEEEEeecCCCcceeEEEECCHHHHHHHHHHc
Confidence            46799999999999999999999999999  88998888777999999999999999999764

>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=99.53  E-value=7.3e-15  Score=104.50  Aligned_cols=64  Identities=19%  Similarity=0.368  Sum_probs=56.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccCC
Q 023954          210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMWH  275 (275)
Q Consensus       210 ~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~ig  275 (275)
                      +|||+|||+++|+++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|++||+.+..+|+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~--~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~   66 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVD--DAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEIN   66 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCS--EECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBT
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcc--eeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEEC
Confidence            599999999999999999999999999  77776666544  89999999999999999997776653

>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=99.52  E-value=1.6e-14  Score=104.41  Aligned_cols=59  Identities=25%  Similarity=0.465  Sum_probs=54.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       210 ~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +|||+|||+++|+++|+++|++||.|.  .++|..++.++  +|||||+|.+.++|.+||+..
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~--~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l   62 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPIL--SIRVCRDMITRRSLGYAYVNFQQPADAERALDTM   62 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTS
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEe--EEEEEecccccCCCCceEEEECCHHHHHHHHHHc
Confidence            799999999999999999999999999  88988877655  899999999999999999863

>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=99.52  E-value=1.5e-14  Score=106.66  Aligned_cols=66  Identities=21%  Similarity=0.400  Sum_probs=56.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh-cCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV-CILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a-~pi~i  274 (275)
                      +.++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|++||+. ....|
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~--~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~   72 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQIS--EVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSV   72 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCC--EEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhcccccc--ceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEE
Confidence            568899999999999999999999999999  77766654444  89999999999999999975 34443

>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=99.52  E-value=1.5e-14  Score=105.90  Aligned_cols=66  Identities=20%  Similarity=0.318  Sum_probs=57.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||.++|+++|+++|++||.|.  .+.|+.++. ..||||||+|.+.++|.+||+...+.|
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~--~v~l~~~~~~~~kG~afV~f~~~e~a~~al~~~~~~~   71 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVL--NIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKY   71 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEE--EEEEEECTTCCEEEEEEEEESCHHHHHHHHTCCCCEE
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccc--cceeeeeccCCcceEEEEEEcCHHHHHHHHHHCCCEE
Confidence            468999999999999999999999999999  888876542 338999999999999999998776554

>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=99.52  E-value=6.7e-15  Score=108.58  Aligned_cols=66  Identities=23%  Similarity=0.353  Sum_probs=57.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc-CccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC-ILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~-pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|++||++. ...|
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~--~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i   72 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL   72 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCC--CEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEE
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEE--ecccccccccccccceeEEEECCHHHHHHHHHHcCCCEE
Confidence            357999999999999999999999999999  88887766544  899999999999999999863 4443

>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=99.52  E-value=1.5e-14  Score=106.92  Aligned_cols=62  Identities=24%  Similarity=0.466  Sum_probs=56.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+.+..++.++  ||||||+|.+.++|.+||+..
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~--~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l   70 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSIS--RIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV   70 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEE--EEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccc--cccccccccccccccceeEEECCHHHHHHHHHHh
Confidence            568999999999999999999999999999  88888776554  899999999999999999874

>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=99.51  E-value=2.1e-14  Score=108.58  Aligned_cols=62  Identities=18%  Similarity=0.483  Sum_probs=55.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+++|||+|||+++++++|+++|++||.|.  .+.+..++.++  ||||||+|.+.++|.+||++.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~l   80 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVV--SAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM   80 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCS--EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhcccc--ccceeeecccCCCccceEEEeCCHHHHHHHHHHh
Confidence            467899999999999999999999999999  77777766554  899999999999999999753

>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=99.51  E-value=1.9e-14  Score=108.05  Aligned_cols=66  Identities=23%  Similarity=0.248  Sum_probs=57.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc-CccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC-ILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~-pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|++||+.. ...|
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~--~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~   75 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLS--ELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVF   75 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEE--EEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEES
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCce--eeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEE
Confidence            467899999999999999999999999999  88887776555  899999999999999999864 3443

>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=99.51  E-value=2.3e-14  Score=103.65  Aligned_cols=59  Identities=24%  Similarity=0.460  Sum_probs=53.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ++|||+|||+++++++|+++|++||.|.  .+.+..+...+  +|||||+|.+.++|++||+.
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~--~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~   63 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIE--SCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT   63 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcc--cccceeeccCCCceeeEEEEECCHHHHHHHHHH
Confidence            5799999999999999999999999999  88887665544  89999999999999999975

>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=99.51  E-value=1.6e-14  Score=109.34  Aligned_cols=66  Identities=21%  Similarity=0.418  Sum_probs=58.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc-CccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC-ILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~-pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.|..++.++  +|||||+|.+.++|.+||+.. ...|
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~--~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~   75 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVV--SFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREF   75 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCS--EEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSC
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhcccccc--ccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEE
Confidence            457899999999999999999999999999  88887776655  899999999999999999873 4444

>d1jkga_ d.17.4.2 (A:) NTF2-related export protein 1 (p15) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: NTF2-related export protein 1 (p15)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=9.3e-15  Score=116.91  Aligned_cols=62  Identities=24%  Similarity=0.334  Sum_probs=54.3

Q ss_pred             CCCccceEEeeeeecccCC------CcEEEEEEeEEEecCccccccceeEEEeeecCCC---CeEeecCccc
Q 023954            2 SLNYSGIEIKTAHSLESWN------GGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKV---PNHLMGGEIQ   64 (275)
Q Consensus         2 sl~f~~~~i~t~D~q~s~~------~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g---~~~v~~~~~~   64 (275)
                      +|++.+|+|.++|||++++      +||||+|+|.|+.++ +++|+|+|+|+|+|++.+   .|||.||.|+
T Consensus        63 ~lp~~~~~i~~~D~q~~~~~~~~~~~~ilI~V~G~v~~~~-~~~r~F~QtF~L~~~~~~~~~~y~I~nD~fR  133 (139)
T d1jkga_          63 MLPSSEFQISVVDCQPVHDEATPSQTTVLVVICGSVKFEG-NKQRDFNQNFILTAQASPSNTVWKIASDCFR  133 (139)
T ss_dssp             HSCCEEEEEEEEEEEECCTTTSTTCCEEEEEEEEEEEETT-SCCEEEEEEEEEEEECCSSSCEEEEEEEEEE
T ss_pred             hCCCceeEEEEEEEEEcCcccccCCCeEEEEEEEEEEcCC-CCcceeEEEEEEEecCCCCCCcEEEEeeEEE
Confidence            5788899999999999753      589999999999998 788999999999998644   3899999874

>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=99.50  E-value=2.4e-14  Score=104.44  Aligned_cols=62  Identities=21%  Similarity=0.387  Sum_probs=53.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC-----ccEEEEEeCCHHHHHHHHHh-cCccC
Q 023954          211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG-----ICYAFVEFEDMTGVRNAVEV-CILMW  274 (275)
Q Consensus       211 ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g-----rgfgFV~F~~~~~a~~Ai~a-~pi~i  274 (275)
                      |||+|||+++|+++|+++|++||.|.  .+.|..++.++     ||||||+|.+.++|.+||+. ...+|
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~--~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~   68 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIK--SCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTV   68 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEE--EEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCcc--ccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            79999999999999999999999999  77776654432     79999999999999999976 34443

>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=99.50  E-value=2.9e-14  Score=106.43  Aligned_cols=63  Identities=25%  Similarity=0.389  Sum_probs=55.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCI  271 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~p  271 (275)
                      ++++|||+|||+++|+++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|.+||+...
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~--~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~   71 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLK--YVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAAS   71 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEE--EEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccce--eeeeccccccccccceEEEEEcCHHHHHHHHHHcc
Confidence            578999999999999999999999999998  77776665444  8999999999999999998753

>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=99.49  E-value=3.9e-14  Score=101.90  Aligned_cols=58  Identities=28%  Similarity=0.379  Sum_probs=52.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC-CCccEEEEEeCCHHHHHHHHHh
Q 023954          210 SVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD-VGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       210 ~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~-~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      +|||+|||+++++++|+++|++||.|.  .+.+..++. ..+|||||+|.+.++|.+||+.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~--~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~   60 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLK--KAAVHYDRSGRSLGTADVHFERKADALKAMKQ   60 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEE--EEEESCSSCCCSCCEEEEEESCHHHHHHHHHH
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCe--EEEEEEeeccccceeEEEEECCHHHHHHHHHH
Confidence            799999999999999999999999999  888876643 3489999999999999999986

>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=99.49  E-value=4.6e-14  Score=105.12  Aligned_cols=61  Identities=28%  Similarity=0.476  Sum_probs=54.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC---CCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK---DVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~---~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.|..+.   +..||||||+|.+.++|.+||+.
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~--~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~   70 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELK--TVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA   70 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEE--EEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCce--EEEEEeccccCCCcccEEEEEECCHHHHHHHHHH
Confidence            468899999999999999999999999999  88876543   33489999999999999999985

>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=99.46  E-value=6.4e-14  Score=105.85  Aligned_cols=69  Identities=17%  Similarity=0.077  Sum_probs=56.5

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccCC
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMWH  275 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~ig  275 (275)
                      ...++.|||+|||+++|+++|+++|..||.+.  ...++...+..+|||||+|.+.++|++||+.+..+|+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~--v~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~   80 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNPMR--VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQ   80 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCSE--EEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSS
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCcce--eeeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEEC
Confidence            34678999999999999999999999998654  3334444444599999999999999999987776664

>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=99.46  E-value=3.3e-14  Score=104.18  Aligned_cols=66  Identities=24%  Similarity=0.477  Sum_probs=54.6

Q ss_pred             CCcEEEEcCCCCCCCH-HHHHHHHhccCceeEceEEEecC-CC--CCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSE-SEIAEEFKKFGELSSEGVVIRSR-KD--VGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te-~~L~~~F~~fG~I~~~~v~v~~~-~~--~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ++++|||+|||+++++ ++|+++|++||.|.  .+.|..+ +.  ..+|||||+|.+.++|.+||+.+..+|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~--~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~   72 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIE--KINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLL   72 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEE--EEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhcc--ceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEE
Confidence            5789999999999864 56999999999999  7877543 22  348999999999999999998666554

>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=99.46  E-value=1.3e-13  Score=103.99  Aligned_cols=62  Identities=21%  Similarity=0.372  Sum_probs=53.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .+.++|||+|||+++++++|+++|++||.|.  .+.+..+. +.++|||||+|.+.++|++||+.
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~--~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~   78 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVI--STRILRDSSGTSRGVGFARMESTEKCEAVIGH   78 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEE--EEEEEECSSSCEEEEEEEEESCHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccccc--ceeeecccccccccceeEEeCCHHHHHHHHHH
Confidence            3468999999999999999999999999998  66665543 33499999999999999999975

>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=99.46  E-value=5.8e-14  Score=99.18  Aligned_cols=57  Identities=21%  Similarity=0.497  Sum_probs=51.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh
Q 023954          211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       211 ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a  269 (275)
                      |||+|||+++|+++|+++|++||.|.  .+.+..++.++  +|||||+|.+.++|++||+.
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~--~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~   59 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIV--STKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA   59 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEE--EEEEECCSSSCSCCSEEEEEESCHHHHHHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhcccc--ccccccccccccccceeEEEECCHHHHHHHHHH
Confidence            79999999999999999999999999  77776665444  89999999999999999975

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.45  E-value=6e-14  Score=101.36  Aligned_cols=59  Identities=15%  Similarity=0.313  Sum_probs=49.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCC--CCccEEEEEeCCHHHHHHHHHh
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKD--VGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~--~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ++|||+|||+++|+++|+++|++||.|.  .+.+..++.  ..+|||||+|.+.++|++||+.
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~--~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~   62 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVA--LSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK   62 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCC--CEEECC-------CCEEEEECSSHHHHHHHHHH
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEE--eeeeecccccccccceeEEEECCHHHHHHHHHH
Confidence            6899999999999999999999999998  555544433  3489999999999999999975

>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=99.44  E-value=6.8e-14  Score=101.51  Aligned_cols=59  Identities=27%  Similarity=0.529  Sum_probs=51.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhc
Q 023954          211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       211 ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      |||+|||+++++++|+++|++||.|.. .+.+..++.++  +|||||+|.+.++|.+||+..
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~-~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~   61 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQ-TPKIMRDPDTGNSKGYAFINFASFDASDAAIEAM   61 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSS-CCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTT
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceee-eEEEEeeccccccCceEEEEECCHHHHHHHHHhC
Confidence            799999999999999999999999962 44676666554  899999999999999999854

>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=99.44  E-value=1.7e-13  Score=105.14  Aligned_cols=61  Identities=25%  Similarity=0.447  Sum_probs=54.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+++|||+|||.++++++|+++|++||.|.  .|++..+. ..+|||||+|.+.++|..||+..
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~--~i~~~~~~-~~kG~afV~f~~~~~A~~Ai~~l   66 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIR--QIRVGNTP-ETRGTAYVVYEDIFDAKNACDHL   66 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEE--EEEEECST-TTTTEEEEEESSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeE--eecccccC-CcCCeEEEEECCHHHHHHHHHHh
Confidence            368999999999999999999999999999  88887543 35899999999999999999754

>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=99.44  E-value=2.7e-13  Score=102.63  Aligned_cols=68  Identities=21%  Similarity=0.176  Sum_probs=55.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHhcCccCC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEVCILMWH  275 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a~pi~ig  275 (275)
                      ....|||+|||+++|+++|+++|..||.+.. .+.++.++ +..+|||||+|.+.++|++||+.+...|+
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~-~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~   82 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPN-GMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIG   82 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEE-EEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceE-EEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEc
Confidence            4567999999999999999999999999983 34444332 23389999999999999999987665553

>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=99.42  E-value=2.2e-13  Score=102.09  Aligned_cols=70  Identities=27%  Similarity=0.319  Sum_probs=55.9

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeE------ceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHh-cCccC
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSS------EGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEV-CILMW  274 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~------~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a-~pi~i  274 (275)
                      ....++|||+|||+++++++|+++|++||.|..      ..+.+..++.++  +|||||+|.+.++|.+||+. ...+|
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            346789999999999999999999999999841      134455555444  89999999999999999986 34443

>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=99.41  E-value=2.7e-13  Score=101.09  Aligned_cols=61  Identities=23%  Similarity=0.302  Sum_probs=52.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCc-eeEceEEEecCC---CCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGE-LSSEGVVIRSRK---DVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~-I~~~~v~v~~~~---~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++|||+|||.++++++|+++|++||. |.  .+.+..+.   +.+||||||+|.+.++|.+||+..
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~--~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l   65 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVL--DVIVYASAADKMKNRGFAFVEYESHRAAAMARRKL   65 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEE--EEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTT
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcce--EEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHH
Confidence            379999999999999999999999996 77  77776543   344899999999999999999764

>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=99.40  E-value=2.5e-13  Score=103.47  Aligned_cols=57  Identities=32%  Similarity=0.479  Sum_probs=51.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .|.|..    .+|||||+|.+.++|.+||+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~--~v~l~~----~kg~afV~f~~~~~A~~A~~~   65 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLG--RVLLPE----GGITAIVEFLEPLEARKAFRH   65 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEE--EEECCS----SSSCEEEEESCHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCcc--EEEeec----cCceEEEEEcCHHHHHHHHHH
Confidence            457999999999999999999999999999  776643    478999999999999999986

>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=99.40  E-value=3.2e-13  Score=101.99  Aligned_cols=65  Identities=23%  Similarity=0.356  Sum_probs=53.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC---CCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK---DVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~---~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++|| +.  .+.+..++   +..+|||||+|.+.++|++|++.+..+|
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~--~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~   81 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-IS--AVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESL   81 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EE--EEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cc--cceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEE
Confidence            458999999999999999999999999 55  45554432   2348999999999999999988766554

>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=99.40  E-value=6.9e-14  Score=102.86  Aligned_cols=58  Identities=24%  Similarity=0.358  Sum_probs=51.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++|+++|+++|++||.|.  .+.+..+   .+|||||+|.+.++|++||..
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~--~v~~~~~---~~gfafV~f~~~~~a~~a~~~   61 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVM--DVFIPKP---FRAFAFVTFADDQIAQSLCGE   61 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCC--EEECCSS---CCSCCEEECSCHHHHHHTTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCce--EEEEeec---cCceEEEEECCHHHHHHHHhC
Confidence            468999999999999999999999999999  6655432   478999999999999999873

>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=99.39  E-value=5.4e-13  Score=96.83  Aligned_cols=60  Identities=23%  Similarity=0.288  Sum_probs=53.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||.++++++|+.+|++||.|.  .+++..+   .+|||||+|.+.++|.+|++..
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~--~v~~~~~---~~g~afV~f~~~~~A~~A~~~l   65 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFK--EVRLVPN---RHDIAFVEFTTELQSNAAKEAL   65 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEE--EEEECTT---TCSCEEEEESSHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEE--Eeeeecc---cceeEEEecCCHHHHHHHHHHh
Confidence            3468999999999999999999999999999  7877653   3689999999999999999864

>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=99.38  E-value=5e-14  Score=104.40  Aligned_cols=66  Identities=17%  Similarity=0.268  Sum_probs=55.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecC-CCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR-KDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~-~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.|+.+ .+..||||||+|.+.+++++||+.+...|
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~--~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~   78 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKN--DLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKV   78 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHH--TCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEE
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEE--EeeeeecCCCCccEEeEEeeCCHHHHHHHHhcCCcEE
Confidence            467999999999999999999999999998  6655433 34558999999999999999998665544

>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=99.38  E-value=3e-13  Score=103.00  Aligned_cols=60  Identities=18%  Similarity=0.275  Sum_probs=53.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...+|||+||++++|+++|+++|++||.|.  .+.+..++  .+|||||+|.+.++|.+||+..
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~--~~~i~~~~--~~g~aFV~f~~~e~A~~Ai~~l   65 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVL--KIITFTKN--NQFQALLQYADPVSAQHAKLSL   65 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEE--EEEEEEET--TEEEEEEEESCHHHHHHHHHHH
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEE--EEEEEeeC--CCCeEEEEECCHHHHHHHHHHH
Confidence            468899999999999999999999999999  77776554  4799999999999999999764

>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=99.37  E-value=1.2e-12  Score=97.24  Aligned_cols=60  Identities=35%  Similarity=0.607  Sum_probs=53.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..+ ..++|||||+|.+.++|++||+.
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~--~~~~~~~-~~~~g~afV~f~~~e~a~~Ai~~   72 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIR--DIDLKNR-RGGPPFAFVEFEDPRDAEDAVYG   72 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEECCS-SSSSCCEEEEESCHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceE--EEEeccc-ccccceEEEEECCHHHHHHHHHH
Confidence            457899999999999999999999999999  7776543 34689999999999999999986

>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=99.37  E-value=5.2e-13  Score=102.46  Aligned_cols=69  Identities=17%  Similarity=0.191  Sum_probs=57.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccCC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMWH  275 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~ig  275 (275)
                      ..+.|||+|||+++|+++|+++|+.||.+....+.+....+..+|||||+|.+.++|++||+.+..+||
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~   85 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMG   85 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCST
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCC
Confidence            567899999999999999999999999997312223334445599999999999999999998877765

>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=99.37  E-value=8e-13  Score=98.72  Aligned_cols=57  Identities=18%  Similarity=0.398  Sum_probs=52.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+.+..+    ||||||+|.+.++|.+||+.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~--~v~i~~~----kg~afV~f~~~~~A~~Ai~~   73 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIM--EIRVFPE----KGYSFVRFSTHESAAHAIVS   73 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEE--EEEEETT----TTEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCce--EEEEEec----ceEEEEEECCHHHHHHHHHH
Confidence            457899999999999999999999999999  8888764    68999999999999999976

>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=99.37  E-value=3.2e-13  Score=101.87  Aligned_cols=68  Identities=13%  Similarity=0.189  Sum_probs=56.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecC-CCCCccEEEEEeCCHHHHHHHHHhcCccCC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR-KDVGICYAFVEFEDMTGVRNAVEVCILMWH  275 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~-~~~grgfgFV~F~~~~~a~~Ai~a~pi~ig  275 (275)
                      ...+|||+|||+++|+++|+++|..||.+.. .+.+..+ .+..+|||||+|.+.++|++||+.+..+|+
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~-~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~   75 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDEN-AVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLN   75 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCST-TEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEET
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEE-EEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeEC
Confidence            4567999999999999999999999999872 3555443 334599999999999999999987766553

>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=99.37  E-value=1.7e-12  Score=98.14  Aligned_cols=65  Identities=28%  Similarity=0.342  Sum_probs=55.6

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh---cCccCC
Q 023954          205 EEEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV---CILMWH  275 (275)
Q Consensus       205 ~~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a---~pi~ig  275 (275)
                      ....+.|||+|||.++++++|+.+|++||.|.  .+.+..    .||||||+|++.++|.+||+.   .+++|+
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~--~~~~~~----~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~   79 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTIC--YVMMMP----FKRQALVEFENIDSAKECVTFAADVPVYIA   79 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEE--EEEEET----TTTEEEEEESSHHHHHHHHHHHHHSCCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccce--EEEEEe----cceeEEEEeCCHHHHHHHHHHHcCCCcEEe
Confidence            34678999999999999999999999999999  777754    367999999999999999975   355553

>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=99.36  E-value=8.7e-13  Score=96.49  Aligned_cols=57  Identities=28%  Similarity=0.489  Sum_probs=51.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+.+..+    +|||||+|++.++|.+||+.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~--~i~~~~~----k~~afV~f~~~~~A~~A~~~   63 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAG--EVFIHKD----KGFGFIRLETRTLAEIAKVE   63 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCS--EEEEETT----TTEEEEECSSSHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCce--Eeeeecc----cceEEEEECCHHHHHHHHHH
Confidence            356899999999999999999999999999  7877654    67999999999999999986

>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=99.36  E-value=3e-13  Score=99.64  Aligned_cols=62  Identities=24%  Similarity=0.417  Sum_probs=53.7

Q ss_pred             CCcEEEEcCCCCCCCHHHH---HHHHhccCceeEceEEEecCCCCC-----ccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEI---AEEFKKFGELSSEGVVIRSRKDVG-----ICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L---~~~F~~fG~I~~~~v~v~~~~~~g-----rgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      +.+.|||+|||+++++++|   +++|++||.|.  .+.+..++.++     +|||||+|.+.++|.+||+..
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~--~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~l   76 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIH--KVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCV   76 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEE--EEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHH
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCce--EEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHh
Confidence            3567999999999999999   67899999999  88887765433     599999999999999999753

>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=99.35  E-value=5.4e-13  Score=97.73  Aligned_cols=54  Identities=24%  Similarity=0.294  Sum_probs=49.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .+|||+|||+++++++|+++|++||.|.  .+.+..     +|||||+|.+.++|++||+.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~--~~~i~~-----~g~afV~f~~~~~a~~Ai~~   54 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVC--YADVYR-----DGTGVVEFVRKEDMTYAVRK   54 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEE--EEEECT-----TSEEEEEESSHHHHHHHHHH
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccc--cccccc-----cceeeEEeCCHHHHHHHHHH
Confidence            3699999999999999999999999999  777754     37999999999999999975

>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=99.34  E-value=1.3e-12  Score=95.14  Aligned_cols=67  Identities=24%  Similarity=0.203  Sum_probs=54.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEec-CCCCCccEEEEEeCCHHHHHHHHHh-cCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRS-RKDVGICYAFVEFEDMTGVRNAVEV-CILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~-~~~~grgfgFV~F~~~~~a~~Ai~a-~pi~i  274 (275)
                      ..+.|||+|||+++++++|+++|+.||.+.. .+.+.. ..+..+|||||+|.+.++|++||+. +..+|
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~-~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l   76 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPG-SVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI   76 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTT-TCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhccccee-EEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEE
Confidence            3578999999999999999999999999973 344443 3334489999999999999999986 44443

>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=99.34  E-value=1.3e-12  Score=99.06  Aligned_cols=58  Identities=24%  Similarity=0.253  Sum_probs=51.7

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPP-SVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~-~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+.|||+||++ .+++++|+++|++||.|.  .+.|..++   +|||||+|++.++|.+||+..
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~--~v~i~~~~---kg~afV~f~~~~~A~~ai~~l   60 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQ--RVKILFNK---KENALVQMADGNQAQLAMSHL   60 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEE--EEEECCTT---SCCEEEEESCHHHHHHHHHHH
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccc--eEEEEecc---cceEEEEECCHHHHHHHHHHh
Confidence            47899999965 599999999999999999  88887653   789999999999999999863

>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=99.33  E-value=2e-12  Score=94.74  Aligned_cols=58  Identities=21%  Similarity=0.324  Sum_probs=52.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ...+.|||+|||.++++++|+++|++||.|.  .+.+..+    +|||||+|.+.++|.+||+.
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~--~v~~~~~----~~~afV~f~~~e~A~~a~~~   63 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVT--NILMLKG----KNQAFLELATEEAAITMVNY   63 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEE--EEEEETT----TTEEEEEESSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcccccc--ccccccc----ceEEEEEeCCHHHHHHHHHH
Confidence            4678999999999999999999999999999  7777653    57999999999999999874

>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=99.33  E-value=2e-12  Score=94.27  Aligned_cols=62  Identities=29%  Similarity=0.320  Sum_probs=52.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh-cCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV-CILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a-~pi~i  274 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..    .||||||+|.+.++|.+||+. +..+|
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~--~~~~~~----~rg~afV~f~~~~~A~~Ai~~l~~~~i   69 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGA--VERVKK----IRDYAFVHFSNREDAVEAMKALNGKVL   69 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTC--EEEEEE----CSSEEEEEESSHHHHHHHHHHHSSEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceee--eEEEcc----ccEEEEEEeCCHHHHHHHHHHcCCCEE
Confidence            457899999999999999999999999998  666643    468999999999999999986 34433

>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=99.33  E-value=2.4e-12  Score=94.15  Aligned_cols=60  Identities=20%  Similarity=0.216  Sum_probs=51.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+.+...+  ++|||||+|++.++|.+||...
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~--~~~~~~~~--~~~~afV~f~~~~~A~~A~~~l   68 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVV--KGFKFFQK--DRKMALIQMGSVEEAVQALIDL   68 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCE--EEEEECSS--STTCEEEEESSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEE--EEEEeeec--ccceeEEEECCHHHHHHHHHhc
Confidence            467899999999999999999999999998  55554433  5789999999999999999763

>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=99.33  E-value=1e-12  Score=98.49  Aligned_cols=57  Identities=26%  Similarity=0.439  Sum_probs=49.9

Q ss_pred             CCCcEEEEcCCC-CCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLP-PSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp-~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+||+ ..+++.+|+++|++||.|.  .+.|      .||||||+|++.++|++||+..
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~--~~~i------~rg~aFV~f~~~~~A~~Ai~~l   70 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIV--GCSV------HKGFAFVQYVNERNARAAVAGE   70 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEE--EEEE------ETEEEEEEESSHHHHHHHHHTT
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEE--EEEE------eCCeEEEEECCHHHHHHHHHHc
Confidence            345789999997 5788899999999999999  7776      3689999999999999999864

>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=99.32  E-value=5.1e-13  Score=100.33  Aligned_cols=66  Identities=26%  Similarity=0.354  Sum_probs=55.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecC--CCCCccEEEEEeCCHHHHHHHHHhc-CccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSR--KDVGICYAFVEFEDMTGVRNAVEVC-ILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~--~~~grgfgFV~F~~~~~a~~Ai~a~-pi~i  274 (275)
                      ..++|||+|||.++++++|+++|++||.|.  .+.+..+  .+..+|||||+|.+.++|.+||+.. ..+|
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~--~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~   85 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKK--GPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKL   85 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSS--SSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccee--eEEeecccccccccccceEEeccHHHHHHHHHHhCCCEE
Confidence            468999999999999999999999999998  5555443  3445899999999999999999864 4444

>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=99.32  E-value=5.1e-13  Score=96.41  Aligned_cols=56  Identities=23%  Similarity=0.340  Sum_probs=48.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .+|||+|||.++++++|+++|++||.|.  .+.+..    .||||||+|.+.++|.+||+..
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~--~~~~~~----~rg~aFV~f~~~~~A~~Ai~~l   57 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPL--AGQVLL----KSGYAFVDYPDQNWAIRAIETL   57 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCC--SSCEEE----ETTEEEECCSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEE--EeEEec----ccceEEEEECCHHHHHHHHHHh
Confidence            4799999999999999999999999998  444433    3689999999999999999863

>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=99.32  E-value=2e-12  Score=96.99  Aligned_cols=63  Identities=22%  Similarity=0.317  Sum_probs=54.2

Q ss_pred             CCCcEEEEcCCCCC-CCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHH---hcCccC
Q 023954          206 EEIKSVYVRNLPPS-VSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVE---VCILMW  274 (275)
Q Consensus       206 ~~~~~ifV~nLp~~-~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~---a~pi~i  274 (275)
                      ..++.|||+|||.+ +|+++|.++|++||.|.  .+.+..+    +|||||+|.+.++|.+||+   .+++.|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~--~v~~~~~----k~~afV~f~~~~~A~~Ai~~~~~~~~~~   82 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIK--NYILMRM----KSQAFIEMETREDAMAMVDHCLKKALWF   82 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCS--EEEEETT----TTEEEEECSSHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhcccccee--EEEEeec----CCcEEEEecchHHHHHHHHHHhcCCceE
Confidence            35789999999985 89999999999999999  7877653    5799999999999999986   446655

>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=99.29  E-value=7.5e-12  Score=93.70  Aligned_cols=56  Identities=20%  Similarity=0.262  Sum_probs=51.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..     +|||||+|.+.++|++||+.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~--~~~i~~-----~g~afV~f~~~~~a~~Ai~~   69 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVC--YADVQK-----DGMGMVEYLRKEDMEYALRK   69 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEE--EEEEET-----TTEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccc--cccccc-----cceEEEEECCHHHHHHHHHH
Confidence            457899999999999999999999999999  777764     47999999999999999976

>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=99.29  E-value=2.1e-12  Score=96.16  Aligned_cols=60  Identities=20%  Similarity=0.292  Sum_probs=51.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...++|||+|||+++++++|+++|++||.|.  .+..   .+..+|||||+|.+.++|++||+..
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~--~~~~---~~~~~~~afV~f~~~~~A~~A~~~l   73 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIR--LVSQ---DGKSKGIAYIEFKSEADAEKNLEEK   73 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEEC--CEEE---TTEEEEEEEEEESSHHHHHHHHHHT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccce--eeee---cCccccEEEEEeCCHHHHHHHHHHc
Confidence            3568999999999999999999999999987  4432   3345899999999999999999864

>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=99.28  E-value=4.8e-12  Score=90.85  Aligned_cols=60  Identities=20%  Similarity=0.278  Sum_probs=51.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc-CccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC-ILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~-pi~i  274 (275)
                      .+++|||+||+  +|+++|+++|++||.|.  .+.+..+    +|||||+|.+.++|.+||++. ..+|
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~--~v~~~~~----~~~afV~f~~~~~A~~Ai~~lng~~~   64 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNII--DLSMDPP----RNCAFVTYEKMESADQAVAELNGTQV   64 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCS--CEEEETT----TTEEEEECSSHHHHHHHHHHHTTCBC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccc--eeeeccC----CCEEEEEEcccHHHHHHHHHhCCCEE
Confidence            57899999985  89999999999999999  7877643    679999999999999999763 4443

>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=99.27  E-value=3.7e-12  Score=104.46  Aligned_cols=66  Identities=14%  Similarity=0.352  Sum_probs=58.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      ..++|||+|||+++|+++|+++|++||.|.  .+.+..+..++  +|||||+|.+.++|.+|+......+
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~--~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~   72 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLT--DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKV   72 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEE--EEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcc
Confidence            458999999999999999999999999999  77877765555  8999999999999999999876543

>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=99.26  E-value=5.5e-12  Score=94.08  Aligned_cols=58  Identities=22%  Similarity=0.481  Sum_probs=52.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..++|||+|||+++++++|+++|++||.|.  .+.+..    ++|||||+|.+.++|.+||+..
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~--~~~~~~----~~~~afV~f~~~~~A~~A~~~l   73 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIR--TIDHVK----GDSFAYIQYESLDAAQAACAKM   73 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEE--EEEECS----SSCCEEEEESSHHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccc--eEeeec----cccEEEeccCCHHHHHHHHHHh
Confidence            468999999999999999999999999999  777754    3679999999999999999863

>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=99.23  E-value=6.2e-12  Score=92.22  Aligned_cols=56  Identities=21%  Similarity=0.335  Sum_probs=47.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++|||+|||+++++++|+++|++|| ++  .+.+..    .+|||||+|.+.++|++||+..
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~--~~~~~~----~kg~afV~f~~~~~A~~Ai~~l   60 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LK--YCYVDR----NKRTAFVTLLNGEQAQNAIQMF   60 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CC--CEEEEG----GGTEEEECCSCHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ce--eeeeec----cCCceEEEECCHHHHHHHHHHh
Confidence            57899999999999999999999999 33  334432    4789999999999999999763

>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=99.22  E-value=1.8e-11  Score=100.22  Aligned_cols=63  Identities=22%  Similarity=0.460  Sum_probs=56.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC--ccEEEEEeCCHHHHHHHHHhcC
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG--ICYAFVEFEDMTGVRNAVEVCI  271 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g--rgfgFV~F~~~~~a~~Ai~a~p  271 (275)
                      ..++|||+|||+.+++++|+++|+.||.|.  .+.+..++.++  +|||||+|.+.++|.+||+...
T Consensus        96 ~~~~i~V~~lp~~~te~~L~~~f~~~G~v~--~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~  160 (183)
T d1u1qa_          96 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIE--VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY  160 (183)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHGGGSCEE--EEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSC
T ss_pred             ccceeEEccCCCcCCHHHHhhhhccCCcee--eeeeecccccCccceeEEEEECCHHHHHHHHHhCC
Confidence            467899999999999999999999999999  88888766554  8999999999999999997654

>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=99.22  E-value=1.5e-11  Score=87.50  Aligned_cols=53  Identities=19%  Similarity=0.309  Sum_probs=45.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          211 VYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       211 ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      |||+|||+++++++|+++|++|| +.  .+.+..    .+|||||+|.+.++|.+||+.-
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~--~~~~~~----~~g~afv~f~~~~~A~~Ai~~l   53 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LK--YCFVDK----YKGTAFVTLLNGEQAEAAINTF   53 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EE--EEEEET----TTTEEEEEESSHHHHHHHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-cc--ceeecc----cceeEEEEECCHHHHHHHHHHh
Confidence            79999999999999999999999 44  444432    4789999999999999999753

>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=99.22  E-value=4.4e-12  Score=93.45  Aligned_cols=60  Identities=22%  Similarity=0.430  Sum_probs=50.3

Q ss_pred             CcEEEEcCCCCCCCHHHHH----HHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIA----EEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~----~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      .++|||+|||+++++++|+    .+|++||.|.  .|.+... +..+|||||+|.+.++|.+||++.
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~--~i~~~~~-~~~~g~afV~F~~~~~A~~A~~~~   66 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQIL--DILVSRS-LKMRGQAFVIFKEVSSATNALRSM   66 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEE--EEECCHH-HHHTTCEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhccccccc--ceEEeee-ccCCCceEEEECCHHHHHHHHHHh
Confidence            5899999999999999886    4689999999  6666432 224899999999999999999864

>d2qiya1 d.17.4.2 (A:3-141) UBP3-associated protein BRE5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: UBP3-associated protein BRE5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.21  E-value=6e-12  Score=99.68  Aligned_cols=56  Identities=21%  Similarity=0.298  Sum_probs=49.0

Q ss_pred             ceEEeeeeecccC--CCcEEEEEEeEEEecCccccccceeEEEeeecCCC-CeEeecCcc
Q 023954            7 GIEIKTAHSLESW--NGGVLVMVSGSVQVKDFSARRKFVQTFFLAPQEKV-PNHLMGGEI   63 (275)
Q Consensus         7 ~~~i~t~D~q~s~--~~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~~~~g-~~~v~~~~~   63 (275)
                      ++.|.++|+|+++  +++|+|+|+|.++.++ ++.|+|+|+|+|+|+++| .|||.||.+
T Consensus        78 ~~~i~~~d~~~~~~~~~~i~v~V~G~~~~~~-~~~r~F~qtFvL~p~~~~~~~~I~nDif  136 (139)
T d2qiya1          78 KLKLDTIDFQYTGHLHKSILIMATGEMFWTG-TPVYKFCQTFILLPSSNGSTFDITNDII  136 (139)
T ss_dssp             EEEEEEEEEEEESGGGCEEEEEEEEEEEETT-CCCEEEEEEEEEEECC---CEEEEEEEE
T ss_pred             EEeeeeeeeeecccCCCEEEEEEeeEEecCC-CCccceEEEEEEEecCCCCEEEEEeeEE
Confidence            7899999999864  7889999999999998 888999999999998875 579999985

>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=99.19  E-value=7.4e-13  Score=97.41  Aligned_cols=63  Identities=21%  Similarity=0.392  Sum_probs=50.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEec-------CCCCCccEEEEEeCCHHHHHHHHHhcCcc
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRS-------RKDVGICYAFVEFEDMTGVRNAVEVCILM  273 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~-------~~~~grgfgFV~F~~~~~a~~Ai~a~pi~  273 (275)
                      ++|||+|||+++|+++|+++|++||.+.  .+.+..       ..+.++|||||+|.+.++|++||+-+...
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~--~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~   71 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLG--GLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGII   71 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTT--TSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEE--EEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcE
Confidence            7899999999999999999999999887  443321       22345899999999999999998755443

>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=99.18  E-value=1.4e-11  Score=90.56  Aligned_cols=59  Identities=20%  Similarity=0.302  Sum_probs=51.8

Q ss_pred             CCCcEEEEcCCCCC-CCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNLPPS-VSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nLp~~-~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...+.|||+|||.. +|+++|.++|+.||.|.  .+.+..+    ++||||.|++.++|.+|++..
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~--~i~i~~~----k~~afV~f~~~~~A~~A~~~l   65 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVIS--NHLILNK----INEAFIEMATTEDAQAAVDYY   65 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEE--EEEECSS----SSCEEEEESSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeE--EEEeecc----ceEEEEEEcchhhHHHHHHHH
Confidence            45788999999986 88999999999999999  7877653    569999999999999999853

>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=99.13  E-value=3.7e-11  Score=90.35  Aligned_cols=58  Identities=19%  Similarity=0.308  Sum_probs=50.5

Q ss_pred             CCcEEEEcC--CCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRN--LPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~n--Lp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..+++||+|  |+.++|+++|+++|++||.|.  .+.+..    ++|||||+|.+.++|.+|+++.
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~--~i~~~~----~k~~aFV~f~~~e~A~~A~~~l   76 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVD--ALLMPP----NKPYSFARYRTTEESKRAYVTL   76 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEE--EEECCT----TCSCEEEEESSHHHHHHHHHHT
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCccc--EEeecc----CccEEEEEECCHHHHHHHHHHh
Confidence            457888855  999999999999999999999  776654    3679999999999999999864

>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=99.07  E-value=1.6e-10  Score=88.43  Aligned_cols=57  Identities=11%  Similarity=0.146  Sum_probs=48.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCH-HHHHHHHHhc
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDM-TGVRNAVEVC  270 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~-~~a~~Ai~a~  270 (275)
                      ...+|||||+..+|+++|+.+|++||.|.  .|.|..    ++|||||.|.+. ++|..|+.+.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~--~v~i~~----~kg~gfV~F~~~~~~A~~a~~~~   68 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIK--WIDFVR----GAKEGIILFKEKAKEALGKAKDA   68 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEE--EEECCT----TCSEEEEEESSCHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChh--eEEEec----CCceEEEEecCcHHHHHHHHHHh
Confidence            45569999999999999999999999999  888864    478999999984 6777777765

>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=99.00  E-value=2.6e-10  Score=82.32  Aligned_cols=60  Identities=13%  Similarity=0.207  Sum_probs=49.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          208 IKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       208 ~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      .+.|||+|+|++++++.|+ +|++||.|.  .+.+..    .+|||||+|.+.++|++||+.+...|
T Consensus         4 ~~wV~V~G~p~~~~~~il~-~F~~~G~I~--~~~~~~----~~~~~fV~f~~~~~A~~Al~~nG~~~   63 (81)
T d1wwha1           4 DTWVTVFGFPQASASYILL-QFAQYGNIL--KHVMSN----TGNWMHIRYQSKLQARKALSKDGRIF   63 (81)
T ss_dssp             GGEEEEECCCGGGHHHHHH-HHHTTSCEE--EEEECS----SSSEEEEEESSHHHHHHHHTTTTCEE
T ss_pred             ccEEEEECCChHHHHHHHH-HHHhhhhhh--eEEecC----CCCEEEEEEcccHHHHHHHhcCCCeE
Confidence            4679999999999876664 799999999  666532    36899999999999999998766555

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.95  E-value=2.4e-10  Score=86.22  Aligned_cols=58  Identities=10%  Similarity=0.056  Sum_probs=49.8

Q ss_pred             CCcEEEEcCCCCCC-CH----HHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNLPPSV-SE----SEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nLp~~~-te----~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...+|||+||+.++ ++    ++|+.+|++||.|.  .+++..    ++|||||+|.+.++|.+||++.
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~--~~~~~k----~~~~afV~f~~~~~A~~Ai~~l   66 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDT--TFQYFK----SFKRVRINFSNPLSAADARLRL   66 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSC--EEEEET----TTTEEEEECSSTTHHHHHHHTS
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccce--EEEEec----CCCEEEEEECCHHHHHHHHHHh
Confidence            46889999999886 33    56999999999999  777764    4789999999999999999876

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.79  E-value=3.9e-10  Score=85.09  Aligned_cols=59  Identities=19%  Similarity=0.186  Sum_probs=51.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCC-CCCccEEEEEeCCHHHHHHHHHh
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRK-DVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~-~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      ..+||+++..++++++|+++|++||.|.  .|.|..+. +..||||||+|.+.++|.+||+.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~--~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~   87 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVE--EMNVCDNLGDHLVGNVYVKFRREEDAEKAVID   87 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEE--EEEECCSSSSSSEEEEEEEESCHHHHHHHHHH
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEE--EEEeecCCCCCEeeEEEEEEechhHHHHHHHH
Confidence            5688999999999999999999999999  88876543 33499999999999999999986

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.51  E-value=9.3e-08  Score=70.90  Aligned_cols=61  Identities=20%  Similarity=0.330  Sum_probs=49.2

Q ss_pred             CCCcEEEEcCC--CCCC---------CHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhc
Q 023954          206 EEIKSVYVRNL--PPSV---------SESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       206 ~~~~~ifV~nL--p~~~---------te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ...+.|+|+||  +.++         ..++|+..|++||.|.  .+.+..++  .+||+||.|.+.++|.+|+++.
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~--~v~~~~~~--~~G~~fV~f~~~e~A~~A~~~l   77 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIR--KLLLFDRH--PDGVASVSFRDPEEADYCIQTL   77 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCS--EEEEETTC--TTCEEEEECSCHHHHHHHHHHS
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEE--EEeccCCC--CccEEEEEECCHHHHHHHHHHh
Confidence            35789999999  4432         1257899999999999  77776543  5789999999999999999874

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.26  E-value=3.8e-07  Score=68.02  Aligned_cols=62  Identities=21%  Similarity=0.354  Sum_probs=48.4

Q ss_pred             CCcEEEEcCC--CCCC--------CHHHHHHHHhccCceeEceEEEecCCCC----CccEEEEEeCCHHHHHHHHHhc
Q 023954          207 EIKSVYVRNL--PPSV--------SESEIAEEFKKFGELSSEGVVIRSRKDV----GICYAFVEFEDMTGVRNAVEVC  270 (275)
Q Consensus       207 ~~~~ifV~nL--p~~~--------te~~L~~~F~~fG~I~~~~v~v~~~~~~----grgfgFV~F~~~~~a~~Ai~a~  270 (275)
                      ..+.|.|+||  +..+        ..++|++.|++||.|.  .+.|..+...    ++||+||+|.+.++|.+|++..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~--~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l   78 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVK--SIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL   78 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEE--EEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceE--EEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHH
Confidence            3577999999  4443        2357899999999999  8887654332    2699999999999999999754

>d1of5b_ d.17.4.2 (B:) mRNA transport regulator MTR2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: mRNA transport regulator MTR2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.64  E-value=0.0009  Score=52.88  Aligned_cols=42  Identities=14%  Similarity=0.092  Sum_probs=25.6

Q ss_pred             cceEEeeeeecccCCC-cEEEEEEeEEEecCccccccceeEEEe
Q 023954            6 SGIEIKTAHSLESWNG-GVLVMVSGSVQVKDFSARRKFVQTFFL   48 (275)
Q Consensus         6 ~~~~i~t~D~q~s~~~-gi~v~v~G~~~~~~~~~~~~F~Q~F~L   48 (275)
                      .+|+|.++|||+..+. ++||.|+|.|+.|+ ..+-|--|++-|
T Consensus        63 T~H~l~s~DcqpIpG~gT~vi~~sgkVrfDe-sgr~k~G~~~~~  105 (165)
T d1of5b_          63 TQHALTGVDYHAIPGSGTLICNVNCKVRFDE-SGRDKMGQDATV  105 (165)
T ss_dssp             CEEEEEEEEEEEETTTTEEEEEEEEEEECC--------------
T ss_pred             eeEEEEEEeeeEcCCCcEEEEEEeeEEEECC-CCCCCCCCcccc
Confidence            3899999999998754 58888999999987 888888999988

>d1q40b_ d.17.4.2 (B:) NTF2-like domain of mRNA export factor MEX67 {Yeast (Candida albicans) [TaxId: 5476]}

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: NTF2-like domain of mRNA export factor MEX67
species: Yeast (Candida albicans) [TaxId: 5476]

Probab=95.28  E-value=0.0081  Score=49.21  Aligned_cols=52  Identities=13%  Similarity=0.231  Sum_probs=36.5

Q ss_pred             eeeeccc-CCCcEEEEEEeEEEecC------------------------------ccccccceeEEEeeecCCCCeEeec
Q 023954           12 TAHSLES-WNGGVLVMVSGSVQVKD------------------------------FSARRKFVQTFFLAPQEKVPNHLMG   60 (275)
Q Consensus        12 t~D~q~s-~~~gi~v~v~G~~~~~~------------------------------~~~~~~F~Q~F~L~~~~~g~~~v~~   60 (275)
                      .+||..- ..+|++|.|.|.+.--+                              ....|.|+-||.|+|.++|...|.|
T Consensus       110 ~vD~~~~~~~~~l~itVhG~F~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~RsF~RTFil~P~~~g~~~I~n  189 (205)
T d1q40b_         110 SMEVYKFPTLNGIMITLHGSFDEVAQPEVDGSASSAPSGPRGGSRYHSGPKHKRIPLSKKSFDRTFVVIPGPNGSMIVAS  189 (205)
T ss_dssp             EEEEEECSSTTCEEEEEEEEEEEEECCSSCCCC----------CCSSSSSCCCCCCCCCEEEEEEEEEECC---CCEEEE
T ss_pred             EEEeEecCCCCEEEEEEEeEEEeccCccccccccccccccccccccccccccccccccccceeEEEEEEecCCCcEEEEc
Confidence            6788643 23689999999987311                              0125789999999999888778899


Q ss_pred             Ccc
Q 023954           61 GEI   63 (275)
Q Consensus        61 ~~~   63 (275)
                      |..
T Consensus       190 D~L  192 (205)
T d1q40b_         190 DTL  192 (205)
T ss_dssp             EEE
T ss_pred             CeE
Confidence            985

>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=95.22  E-value=0.032  Score=39.62  Aligned_cols=58  Identities=17%  Similarity=0.312  Sum_probs=45.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCC----ccEEEEEeCCHHHHHHHHH
Q 023954          209 KSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVG----ICYAFVEFEDMTGVRNAVE  268 (275)
Q Consensus       209 ~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~g----rgfgFV~F~~~~~a~~Ai~  268 (275)
                      ++|-||+||++.|++++.+.++..|++.  .......+.+.    -+-|||.|.+.+++..-.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d--~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~   63 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHD--YFEFFSNDTSLYPHMYARAYINFKNQEDIILFRD   63 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEE--EEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHH
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceE--EEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHH
Confidence            5788999999999999999999888887  66555433322    4889999999988765443

>d1q42a_ d.17.4.2 (A:) mRNA transport regulator MTR2 {Yeast (Candida albicans) [TaxId: 5476]}

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: mRNA transport regulator MTR2
species: Yeast (Candida albicans) [TaxId: 5476]

Probab=94.32  E-value=0.027  Score=44.13  Aligned_cols=47  Identities=17%  Similarity=0.127  Sum_probs=37.3

Q ss_pred             CCccceEEeeeeecccCC-CcEEEEEEeEEEecCccccccceeEEEeee
Q 023954            3 LNYSGIEIKTAHSLESWN-GGVLVMVSGSVQVKDFSARRKFVQTFFLAP   50 (275)
Q Consensus         3 l~f~~~~i~t~D~q~s~~-~gi~v~v~G~~~~~~~~~~~~F~Q~F~L~~   50 (275)
                      ++-++|.++++||+...+ |++||-|+|.|..|+ ..+-|.-|.+.|..
T Consensus        76 vp~TqH~Lts~D~H~IPGtgt~i~nv~~KVRFDE-sGrdk~Gq~a~l~~  123 (174)
T d1q42a_          76 TPLSSHQLTSYDGHLIPGTGTFVVHFSAKVRFDQ-SGRNRLGESADLFQ  123 (174)
T ss_dssp             SCCEEEEEEEEEEEEETTTTEEEEEEEEEEEEBC-SSCCTTSCCC----
T ss_pred             ccceeeeeeeeeeeeeCCCceEEEEeeeEEEecC-cCCCcCCCcceeec
Confidence            344489999999999874 569999999999987 88999999998844

>d1jkgb_ d.17.4.2 (B:) NTF2-like domain of Tip associating protein, TAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: NTF2-like domain of Tip associating protein, TAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.69  E-value=0.055  Score=43.37  Aligned_cols=44  Identities=20%  Similarity=0.276  Sum_probs=35.1

Q ss_pred             CCcEEEEEEeEEEecCc---cccccceeEEEeeecCCCCeEeecCcc
Q 023954           20 NGGVLVMVSGSVQVKDF---SARRKFVQTFFLAPQEKVPNHLMGGEI   63 (275)
Q Consensus        20 ~~gi~v~v~G~~~~~~~---~~~~~F~Q~F~L~~~~~g~~~v~~~~~   63 (275)
                      ..+++|.|.|.+.-.+.   ...|.|+-||.|.|.++|.+.|.||..
T Consensus       119 ~~~l~itV~G~F~E~~~~~~~~~rsF~RTFil~P~~~~~~~I~nD~L  165 (186)
T d1jkgb_         119 STLLCFSVNGVFKEVDGKSRDSLRAFTRTFIAVPASNSGLCIVNDEL  165 (186)
T ss_dssp             SSCEEEEEEEEEEECSSTTTTCEEEEEEEEEEEECTTSSEEEEEEEE
T ss_pred             CCEEEEEEeeEEEecCCCCCcceeEEEEEEEEeecCCCceEEEecEE
Confidence            45799999999985321   235889999999998877778899985

>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=91.10  E-value=0.5  Score=33.60  Aligned_cols=55  Identities=22%  Similarity=0.316  Sum_probs=44.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHh
Q 023954          207 EIKSVYVRNLPPSVSESEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEV  269 (275)
Q Consensus       207 ~~~~ifV~nLp~~~te~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a  269 (275)
                      .-..+|.-..|......+|.++|+.||.|.   |....+.     -|||...+.+.++.+++.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~---VswIddT-----Sa~V~L~~~e~~~~v~~~   68 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ---ISWIDDT-----SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCC---CEEEETT-----EEEEECSCHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceE---EEEecCc-----eEEEEecCHHHHHHHHHH
Confidence            445677778999999999999999999996   3444443     599999999998888753

>d1of5a_ d.17.4.2 (A:) NTF2-like domain of mRNA export factor MEX67 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Cystatin-like
superfamily: NTF2-like
family: NTF2-like
domain: NTF2-like domain of mRNA export factor MEX67
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.07  E-value=0.14  Score=41.90  Aligned_cols=51  Identities=10%  Similarity=0.231  Sum_probs=36.5

Q ss_pred             eeeeccc-CCCcEEEEEEeEEEecCc-------------------------------cccccceeEEEeeecCCCCeEee
Q 023954           12 TAHSLES-WNGGVLVMVSGSVQVKDF-------------------------------SARRKFVQTFFLAPQEKVPNHLM   59 (275)
Q Consensus        12 t~D~q~s-~~~gi~v~v~G~~~~~~~-------------------------------~~~~~F~Q~F~L~~~~~g~~~v~   59 (275)
                      .+||-.- -.+|++|.|.|.+.--+.                               -..|.|.-||.|+|.+ |...|.
T Consensus       116 ~vd~~~~~~~~~l~itvhG~F~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~RsFdRTFil~P~~-~g~~I~  194 (221)
T d1of5a_         116 SMETISYPQINGFVITLHGFFEETGKPELESNKKTGKNNYQKNRRYNHGYNSTSNNKLSKKSFDRTWVIVPMN-NSVIIA  194 (221)
T ss_dssp             EEEEEEEGGGTEEEEEEEEEEEEC-----------------------------CCSCCEEEEEEEEEEEEEET-TEEEEE
T ss_pred             EEEEEEcCCCCEEEEEEeEEEEeccCcccccccccccccccccccccccccccccccccccceeEEEEEecCC-CcEEEE
Confidence            5777543 235799999999985210                               1247899999999975 556899


Q ss_pred             cCcc
Q 023954           60 GGEI   63 (275)
Q Consensus        60 ~~~~   63 (275)
                      ||..
T Consensus       195 nD~L  198 (221)
T d1of5a_         195 SDLL  198 (221)
T ss_dssp             EEEE
T ss_pred             eCeE
Confidence            9985

>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=83.34  E-value=0.71  Score=32.32  Aligned_cols=44  Identities=18%  Similarity=0.266  Sum_probs=34.5

Q ss_pred             HHHHHHHhccCceeEceEEEecCCCCCccEEEEEeCCHHHHHHHHHhcCccC
Q 023954          223 SEIAEEFKKFGELSSEGVVIRSRKDVGICYAFVEFEDMTGVRNAVEVCILMW  274 (275)
Q Consensus       223 ~~L~~~F~~fG~I~~~~v~v~~~~~~grgfgFV~F~~~~~a~~Ai~a~pi~i  274 (275)
                      .+|-+.|..||++.  -+++..+      --.|+|.+..+|.+|++-..+.|
T Consensus        39 ~~Llq~l~~~GeVi--LvRFv~d------~mwVTF~dG~SAL~al~l~g~~v   82 (95)
T d1ufwa_          39 TELMQTLGSYGTIV--LVRINQG------QMLVTFADSHSALSVLDVDGMKV   82 (95)
T ss_dssp             HHHHHHHHHHSCCS--EEEEETT------EEEEECSCSHHHHHHHHGGGSEE
T ss_pred             HHHHHHHhhCCeEE--EEEEeCC------eEEEEECCcHHHHHHhccCCeEE
Confidence            35677789999988  6666554      57899999999999998765543