Citrus Sinensis ID: 046223

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------41
Protein Sequence
MGETGISRFQGNLDPRAQEFRPTTLFRPPQVYYPYGAASPPTLPPYPSNDVQVVPFGGVGYAQYPTHPQLGVPLPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTIYQTRNSDCPPPPLSADPPSYSPRSFASQAPHFRKKSPSNSFKGNPNNVNVTCSIEPSVASLSLANAIEDININPARRTRNCY
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccccEEEEEEccccEEEEEEccHHHHHHHHHHHHHHHcccccEEEEEEcccccccccccccccccccccccccccccEEEEEEccccccccccccccccccccEEEEEEccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEccccccEEEEEEccHHHHHHHHHHHcccEEcccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHcHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHHcccEEEEHHHccccEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHccccHHcccccccccccccccccccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEEccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEccccccccEEEEEEcHHHHHHHHHHHccccccccEEEEEEccccccHHHHHHHccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mgetgisrfqgnldpraqefrpttlfrppqvyypygaaspptlppypsndvqvvpfggvgyaqypthpqlgvplpppstgptrtlvlsyvpgdvsetIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQqsyglknpyssglmlmnndnnnnnlatgcydnQVVAESLMIMNsyapvlppparglvagrpvwaqfivptcnavpdgnnqgTIVVFNLDSGVSSSTLKEIFQAFgpvkelretplkkHQRFIEFYDVRDAAKALKEMNGQEIYGKHVViefsrpgghskkffyanssscasslnystiyqtrnsdcpppplsadppsysprsfasqaphfrkkspsnsfkgnpnnvnvtcsiepsvaSLSLANaiedininparrtrncy
Flexible Loop (DISEMBL)
mgetgisrfqgnldpraqefrpttlfRPPQVYYPYGAASPPTLPPYPSNDVQVVPFGGVGYAQYPTHPQLGVPLPPPSTGPTRTLVLSYVpgdvsetivrrdlevfgevrgvqmERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAfgpvkelretplkkhqrfiEFYDVRDAAKALKEmngqeiygKHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTIYQTRNSDCPPPPLSADPPSYSPRSFASQAPHfrkkspsnsfkgnpNNVNVTCSIEPSVASLSLanaiedininparrtrncy
Low Complexity Region (SEG)
MGETGISRFQGNLDPRAQEFRPTTLFRPPQVYYPYGAASPPTLPPYPSNDVQVVPFGGVGYAQYPTHPQLGVPLPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMnndnnnnnLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFyanssscasslnysTIYQTRNsdcpppplsadppsyspRSFASQAPHFRKKSPSNSFKGNPNNVNVTCSIEPSVASLSLANAIEDININPARRTRNCY
Disordered region (IsUnstruct)
***********************TLFRPPQVYYPYGAA*******YPSNDVQVVPFGGVGYAQYPTHPQLGV*********TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEI************************************GCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTIY*************************************************TCSI***VASLSLANAIED*************
Disordered Region (DISOPRED)
******S*****************LFRP*QVYY***********************************************PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY**************************AESLM*********************VWAQFIV**********NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE**************************************************************************************************************
Disordered Region (DISEMBL)
MGETGISRFQGNLDPRAQEFRPTTLFRPPQVYYPYGAASPPTLPPYPSNDVQVVPFGGVGYAQYPTHPQLGVPLPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTIYQTRNSDCPPPP**************************NSFKGNPNNVNVTCSIEPSVASLSLANAIEDININPARRTRNCY
Disordered Region (DISPRO)
*********QGNLDPRAQEFRPTTLFRPPQVYYPYGAASPPTLPPYPSNDVQVVPFGGVGYAQYPTHPQLGVPLPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTIYQTRNSDCPPPPLSADPPSYSPRSFASQAPHFRKKSPSNSFKGNPNNVNVTCSI*************EDININPARR***C*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGETGISRFQGNLDPRAQEFRPTTLFRPPQVYYPYGAASPPTLPPYPSNDVQVVPFGGVGYAQYPTHPQLGVPLPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDxxxxxxxxxxxxxxxxxxxxxSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTIYQTRNSDCPPPPLSADPPSYSPRSFASQAPHFRKKSPSNSFKGNPNNVNVTCSIEPSVASLSLANAIEDININPARRTRNCY
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	408	2.2.26 [Sep-21-2011]
O65001	656	Protein terminal ear1 OS=	N/A	no	0.656	0.408	0.355	2e-35
A2WY46	680	Protein terminal ear1 hom	N/A	no	0.497	0.298	0.373	1e-33
Q0JGS5	683	Protein terminal ear1 hom	yes	no	0.497	0.297	0.373	1e-33
Q6ZI17	848	Protein MEI2-like 2 OS=Or	no	no	0.281	0.135	0.456	1e-21
Q6EQX3	811	Protein MEI2-like 5 OS=Or	no	no	0.240	0.120	0.5	1e-21
Q9SJG8	843	Protein MEI2-like 2 OS=Ar	no	no	0.323	0.156	0.401	2e-21
Q9SVV9	759	Protein MEI2-like 3 OS=Ar	no	no	0.598	0.321	0.302	3e-21
Q8VWF5	800	Protein MEI2-like 5 OS=Ar	no	no	0.237	0.121	0.515	6e-21
Q64M78	1001	Protein MEI2-like 4 OS=Or	no	no	0.259	0.105	0.390	1e-13
Q9LYN7	907	Protein MEI2-like 4 OS=Ar	no	no	0.25	0.112	0.349	7e-11

>sp|O65001|TE1_MAIZE Protein terminal ear1 OS=Zea mays GN=TE1 PE=2 SV=1

 Score =  150 bits (379), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 112/315 (35%), Positives = 160/315 (50%), Gaps = 47/315 (14%)

Query: 5   GISRFQGNL-DPRAQEFRPTTLF------RPPQVYYPYGAASPPTLPPYPSNDVQVVPFG 57
           G     GNL D  AQEF PT          P Q+Y P+   + P  PP     +Q VP  
Sbjct: 3   GFPEATGNLLDAAAQEFHPTVCAPYPLQPLPQQLYCPHPYPAMPVPPPPQIAMLQPVPPM 62

Query: 58  GVGYAQYPTHPQLGVPLP---PPSTGPT-RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQ 113
            +  A     PQ G  LP   P   GP+ R +VL  VP    E  V + +  FG +R V 
Sbjct: 63  AMAMA-----PQPGYTLPTTTPVVNGPSSRVVVLGLVPPHAQEADVAQAMAPFGAIRSVD 117

Query: 114 MERLM-EGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMNNDNNNNN 172
              +  EG+ TVHF+D+R AE+A   +REQHM+ Q +   L   Y++  +          
Sbjct: 118 ACAVASEGVATVHFFDIRAAELALTCVREQHMRQQSR---LGQLYAAAAVAPAWAPAPTP 174

Query: 173 LATGCYDNQVVAESLMIMNSYAPVLPPP---ARGLVAGRPVWAQFIVPTCNAVPDGNNQG 229
            A   +D                  P P    RGLV G  VWA F         DG+N+G
Sbjct: 175 QA---WD-----------------WPHPNDDGRGLVLGHAVWAHF----ATGADDGDNRG 210

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           ++VV +   GVS + L+++FQAFG +K++RE+  +   +F++F+D RDAA+AL E+NGQE
Sbjct: 211 SLVVLSPLPGVSVADLRQVFQAFGDLKDVRESAQRPSHKFVDFFDTRDAARALAELNGQE 270

Query: 290 IYGKHVVIEFSRPGG 304
           ++G+ +V+EF+RP G
Sbjct: 271 LFGRRLVVEFTRPSG 285

Probable RNA-binding protein. Involved in the regulation of leaf initiation rate and shoot development. Seems to act more predominantly in the early stages of the leaf development, rather than in the later phase.
Zea mays (taxid: 4577)

>sp|A2WY46|EAR1_ORYSI Protein terminal ear1 homolog OS=Oryza sativa subsp. indica GN=PLA2 PE=2 SV=1

 Score =  144 bits (364), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 93/249 (37%), Positives = 135/249 (54%), Gaps = 46/249 (18%)

Query: 68  PQLGVPLPPPST---GP-TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLM-EGIV 122
           PQ G  +P  +T   GP +R +VLS VP    E  + R +  FG VR V    +  EG+ 
Sbjct: 79  PQPGYCVPAAATVVDGPASRAVVLSLVPPHAPEDEIARAMAPFGAVRAVDASAVASEGVA 138

Query: 123 TVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQV 182
           TV+F+DLR AE A   +REQH++ Q                             C   Q+
Sbjct: 139 TVYFFDLRSAEHAVTGVREQHIRQQ-----------------------------CRLGQL 169

Query: 183 VAESLMIMNSYAPVLPPPA--------RGLVAGRPVWAQFIVPTCNAVPD-GNNQGTIVV 233
            A +     S +P  PPPA        RGLV G+ VWA F     + VPD G ++G++VV
Sbjct: 170 YAAAAAAAAS-SPTWPPPAWDWPHDDNRGLVLGQAVWAHFA--AASTVPDDGASRGSLVV 226

Query: 234 FNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK 293
            N    +S   L+EIFQA+G VK++RE+ L+   +F+EF+D RDA +AL E+NG+E++G+
Sbjct: 227 LNSLPAMSVFELREIFQAYGDVKDVRESALRPSNKFVEFFDTRDADRALHELNGKELFGR 286

Query: 294 HVVIEFSRP 302
            +V+E++RP
Sbjct: 287 RLVVEYTRP 295

Probable RNA-binding protein. Involved in the regular timing (plastochron) of lateral organs formation. May regulate the rate of leaf initiation and the duration of vegetative phase. Seems to be redundant to the function of PLASTOCHRON1, but to act in an independent pathway.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q0JGS5|EAR1_ORYSJ Protein terminal ear1 homolog OS=Oryza sativa subsp. japonica GN=PLA2 PE=2 SV=1

 Score =  144 bits (363), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 93/249 (37%), Positives = 135/249 (54%), Gaps = 46/249 (18%)

Query: 68  PQLGVPLPPPST---GP-TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLM-EGIV 122
           PQ G  +P  +T   GP +R +VLS VP    E  + R +  FG VR V    +  EG+ 
Sbjct: 79  PQPGYCVPAAATVVDGPASRAVVLSLVPPHAPEDEIARAMAPFGAVRAVDASAVASEGVA 138

Query: 123 TVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQV 182
           TV+F+DLR AE A   +REQH++ Q                             C   Q+
Sbjct: 139 TVYFFDLRSAEHAVTGVREQHIRQQ-----------------------------CRLGQL 169

Query: 183 VAESLMIMNSYAPVLPPPA--------RGLVAGRPVWAQFIVPTCNAVPD-GNNQGTIVV 233
            A +     S +P  PPPA        RGLV G+ VWA F     + VPD G ++G++VV
Sbjct: 170 YAAAAAAAAS-SPTWPPPAWDWPHDDNRGLVLGQAVWAHFA--AASTVPDDGASRGSLVV 226

Query: 234 FNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK 293
            N    +S   L+EIFQA+G VK++RE+ L+   +F+EF+D RDA +AL E+NG+E++G+
Sbjct: 227 LNSLPAMSVFELREIFQAYGDVKDVRESALRPSNKFVEFFDTRDADRALHELNGKELFGR 286

Query: 294 HVVIEFSRP 302
            +V+E++RP
Sbjct: 287 RLVVEYTRP 295

Probable RNA-binding protein. Involved in the regular timing (plastochron) of lateral organs formation. May regulate the rate of leaf initiation and the duration of vegetative phase. Seems to be redundant to the function of PLASTOCHRON1, but to act in an independent pathway.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q6ZI17|OML2_ORYSJ Protein MEI2-like 2 OS=Oryza sativa subsp. japonica GN=ML2 PE=2 SV=1

 Score =  104 bits (260), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 57/125 (45%), Positives = 75/125 (60%), Gaps = 10/125 (8%)

Query: 188 MIMNSYAPVLPPPARGLVAG--------RPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSG 239
            +M SY  +    ARG + G        R +   F +P  N      NQGT+V+FNLD  
Sbjct: 235 FVMISYFDIRA--ARGAMRGLQNKPLRRRKLDIHFSIPKENPSDKDLNQGTLVIFNLDPS 292

Query: 240 VSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF 299
           VS+  +++IF  +G VKE+RETP KKH +FIEFYDVR A  AL+ +N  EI GK + +E 
Sbjct: 293 VSNEEVRQIFGTYGEVKEIRETPNKKHHKFIEFYDVRAAEAALRSLNKSEIAGKRIKLEP 352

Query: 300 SRPGG 304
           SRPGG
Sbjct: 353 SRPGG 357

Probable RNA-binding protein that may play a role in growth regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q6EQX3|OML5_ORYSJ Protein MEI2-like 5 OS=Oryza sativa subsp. japonica GN=ML5 PE=2 SV=1

 Score =  104 bits (260), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 51/102 (50%), Positives = 67/102 (65%)

Query: 208 RPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQ 267
           R +   + +P  N      NQGT+V+FNL+  VS+  L +IF AFG V+E+RETP K+H 
Sbjct: 257 RKLDIHYSIPKENPSDKDMNQGTLVIFNLEPAVSNEELLQIFGAFGEVREIRETPHKRHH 316

Query: 268 RFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKF 309
           RFIEFYDVR A  AL+ +N  +I GK V +E SRPGG  + F
Sbjct: 317 RFIEFYDVRAAESALRSLNKSDIAGKRVKLEPSRPGGARRSF 358

Probable RNA-binding protein that may play a role in growth regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SJG8|AML2_ARATH Protein MEI2-like 2 OS=Arabidopsis thaliana GN=ML2 PE=2 SV=2

 Score =  104 bits (259), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 53/132 (40%), Positives = 76/132 (57%)

Query: 173 LATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIV 232
           L T C     V  S   + +    +      L+  R +   F +P  N      NQGT+V
Sbjct: 227 LYTACKSRGFVMISYYDIRAAHAAMRALQNTLLRKRTLDIHFSIPKENPSEKDMNQGTLV 286

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG 292
           +FN+D+ VS+  L ++F A+G ++E+RETP ++  RFIE+YDVRDA  ALK +N  EI G
Sbjct: 287 IFNVDTTVSNDELLQLFGAYGEIREIRETPNRRFHRFIEYYDVRDAETALKALNRSEIGG 346

Query: 293 KHVVIEFSRPGG 304
           K + +E SRPGG
Sbjct: 347 KCIKLELSRPGG 358

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SVV9|AML3_ARATH Protein MEI2-like 3 OS=Arabidopsis thaliana GN=ML3 PE=2 SV=2

 Score =  103 bits (256), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 83/274 (30%), Positives = 125/274 (45%), Gaps = 30/274 (10%)

Query: 57  GGVG--YAQYPTHPQLGVPLPPPS----TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVR 110
           GG+G       +HP +G  LP       +G    L LS +P  + +     D ++FG   
Sbjct: 57  GGIGNMLDDGDSHP-IGNMLPDDEEELFSGLMDDLNLSSLPATLDDL---EDYDLFGSGG 112

Query: 111 GVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHM-QLQQQSYGLKNPYS---SGLMLMNN 166
           G+++E      +   F  +  A+     +  Q++ Q    S   ++PY    S  + + N
Sbjct: 113 GLELETDPYDSLNKGFSRMGFADSNVDNVMPQNIFQNGVGSIAGEHPYGEHPSRTLFVRN 172

Query: 167 DNNN----------------NNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPV 210
            N+N                  L T C     V  S   + +    +      L+  R +
Sbjct: 173 INSNVEDSELQALFEQYGHIRTLYTACKQRGFVMVSYNDIRASRAAMRALQGKLLKKRKL 232

Query: 211 WAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFI 270
              F +P  N      NQGT+VVFNL   VS+  L+ IF  +G +KE+RETP K+H +F+
Sbjct: 233 DIHFSIPKDNPSEKDVNQGTLVVFNLAPSVSNRDLENIFGVYGEIKEIRETPNKRHHKFV 292

Query: 271 EFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG 304
           EF+DVR A  ALK +N  EI GK + +E SRPGG
Sbjct: 293 EFFDVRSADAALKALNRTEIAGKRIKLEHSRPGG 326

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8VWF5|AML5_ARATH Protein MEI2-like 5 OS=Arabidopsis thaliana GN=ML5 PE=1 SV=1

 Score =  102 bits (254), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 50/97 (51%), Positives = 63/97 (64%)

Query: 208 RPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQ 267
           R +   F +P  N      NQGT+VVFNLD  +S+  L  IF A G +KE+RETP K+H 
Sbjct: 232 RKLDIHFSIPKDNPSEKDMNQGTLVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKRHH 291

Query: 268 RFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG 304
           +F+EFYDVR A  ALK +N  EI GK + +E SRPGG
Sbjct: 292 KFVEFYDVRGAEAALKALNRCEIAGKRIKVEPSRPGG 328

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q64M78|OML4_ORYSJ Protein MEI2-like 4 OS=Oryza sativa subsp. japonica GN=ML4 PE=2 SV=1

 Score = 78.2 bits (191), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 43/110 (39%), Positives = 65/110 (59%)

Query: 208 RPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQ 267
           R +   + +P  N      NQGTIV+FN+D  +++  L +IF  +G +KE+R+TP K H 
Sbjct: 339 RKLDIHYSIPKDNPSEKDINQGTIVLFNVDLSLTNDDLHKIFGDYGEIKEIRDTPQKGHH 398

Query: 268 RFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSSC 317
           + IEFYDVR A  AL+ +N  +I GK + +E SR G   +   + +S  C
Sbjct: 399 KIIEFYDVRAAEAALRALNRNDIAGKKIKLETSRLGAARRLSQHMSSELC 448

Probable RNA-binding protein that may play a role in growth regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9LYN7|AML4_ARATH Protein MEI2-like 4 OS=Arabidopsis thaliana GN=ML4 PE=1 SV=1

 Score = 68.9 bits (167), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 36/103 (34%), Positives = 63/103 (61%), Gaps = 1/103 (0%)

Query: 204 LVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPL 263
           L+ GR +  ++ +P  N   + +++G + V NLDS +S+  L  IF ++G ++E+R T  
Sbjct: 271 LLRGRKLDIRYSIPKENP-KENSSEGALWVNNLDSSISNEELHGIFSSYGEIREVRRTMH 329

Query: 264 KKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHS 306
           +  Q +IEF+DVR A  AL+ +NG E+ G+ + +  + P G S
Sbjct: 330 ENSQVYIEFFDVRKAKVALQGLNGLEVAGRQLKLAPTCPEGTS 372

Probable RNA-binding protein that plays a role in meiosis and vegetative growth.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	408
148927338	677	terminal ear1-like 2 protein [Populus tr	0.850	0.512	0.472	4e-90
255547976	622	arginine/serine-rich splicing factor, pu	0.811	0.532	0.501	2e-87
225424576	658	PREDICTED: protein terminal ear1-like [V	0.879	0.545	0.471	1e-86
224100115	590	predicted protein [Populus trichocarpa]	0.825	0.571	0.496	4e-86
224107727	557	predicted protein [Populus trichocarpa]	0.681	0.499	0.584	1e-83
449500381	644	PREDICTED: protein terminal ear1-like [C	0.669	0.423	0.521	2e-81
449517014	750	PREDICTED: LOW QUALITY PROTEIN: protein	0.705	0.384	0.515	2e-77
449435442	659	PREDICTED: protein terminal ear1-like [C	0.705	0.437	0.512	1e-74
449450610	637	PREDICTED: protein terminal ear1-like [C	0.651	0.417	0.490	3e-73
297814854	603	hypothetical protein ARALYDRAFT_322753 [	0.637	0.431	0.464	2e-65

>gi|148927338|gb|ABR19818.1| terminal ear1-like 2 protein [Populus tremula x Populus alba]

 Score =  338 bits (866), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 210/444 (47%), Positives = 260/444 (58%), Gaps = 97/444 (21%)

Query: 1   MGETGISRFQGNLDPRAQEFRPTTL----FRPP-----------------------QVYY 33
           M E G  +F GNLDPRAQEFRP       F P                        QVYY
Sbjct: 1   MEENGSVQFPGNLDPRAQEFRPRRDNLHNFSPKFLPFGPPTPPLPPPPPPPSQLPHQVYY 60

Query: 34  PYGAASPPTLPPYPSNDVQVVPFGG-VGYAQYPTH-PQLGV-----PLPPPSTGPTRTLV 86
           PY                QV+PF   VG+AQY  H P   V     P  PP+  PTRTLV
Sbjct: 61  PYTP--------------QVLPFSDFVGFAQYDHHIPPAYVRVEPSPPLPPTGAPTRTLV 106

Query: 87  LSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQL 146
           LS VP +V+E++++R+LEVFGEVRGVQMER+  G VTVHFYDLRHAE A +EIREQHM  
Sbjct: 107 LSSVPSEVNESLIKRELEVFGEVRGVQMERVGYGTVTVHFYDLRHAERALREIREQHMLH 166

Query: 147 QQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVA 206
           Q +   L+N       + N+++ + N+A                    P  PPPARG++A
Sbjct: 167 QAR---LRN-----FFIQNSESISFNIA--------------------PTPPPPARGVIA 198

Query: 207 GRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKH 266
           G  VWAQFI+P+CN VPDG NQGT+VVFNLD  VS+ +LKEIFQAFG VKE+RETPLK+H
Sbjct: 199 GCVVWAQFIIPSCNEVPDGQNQGTLVVFNLDPNVSTRSLKEIFQAFGAVKEVRETPLKRH 258

Query: 267 QRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTI 326
           QRF+EFYDVRDAAKAL+EMNG+EIYGK V IEFSRPGGH K+FF A   + + +   + +
Sbjct: 259 QRFVEFYDVRDAAKALREMNGKEIYGKQVDIEFSRPGGHGKRFFNARPRTTSKNSFTTPV 318

Query: 327 YQT----RNSDCP------PPPL------SADPPSYSPRSFASQAPHFRKKSPSNSFKGN 370
           + +    R+S         PPPL         PP+ SPRSF S+      K PS    G+
Sbjct: 319 FDSTTNLRHSKVAAFVSPQPPPLLHRFSSGCSPPNVSPRSFLSETQSSAGKKPS----GD 374

Query: 371 PNNVN-VTCSIEPSVASLSLANAI 393
           P+  N +  SIE S+  LS+   +
Sbjct: 375 PSEGNPIEASIEASLGCLSMGGDV 398

Source: Populus tremula x Populus alba

Species: Populus tremula x Populus alba

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255547976|ref|XP_002515045.1| arginine/serine-rich splicing factor, putative [Ricinus communis] gi|223546096|gb|EEF47599.1| arginine/serine-rich splicing factor, putative [Ricinus communis]

 Score =  328 bits (842), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 210/419 (50%), Positives = 252/419 (60%), Gaps = 88/419 (21%)

Query: 1   MGETGISRFQGNLDPRAQEFRPT---------TLFR------------------------ 27
           M ETGI+RFQG+LDPRAQEFRP          TL                          
Sbjct: 1   MAETGIARFQGSLDPRAQEFRPRNNSLHLNTPTLIHHHHQQQQQQQQQLHIFTPPPPPPP 60

Query: 28  ---PPQVYYPYGAASPPTLPPYPSNDVQVVPFGGVGYAQY---PTHPQLGVP-----LPP 76
                Q+YYPY  A PP+L                G+ QY   P  PQ  +      LPP
Sbjct: 61  PPPAQQLYYPY--APPPSL----------------GFPQYQLAPPQPQAYISTTVPSLPP 102

Query: 77  PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAF 136
            S  PTRTLVLS VP +VSE+++RR+LEVFGEVRGVQMER+ +GIVTVHFYDLRHAE+A 
Sbjct: 103 QSAAPTRTLVLSSVPTEVSESVIRRELEVFGEVRGVQMERISDGIVTVHFYDLRHAEIAL 162

Query: 137 KEIREQHMQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPV 196
            EIRE+HMQ Q +   L+N +++       D NN         +   A +          
Sbjct: 163 VEIREKHMQQQSR---LRNLFAAL------DQNNFLAPPSLPPSPAAAAA---------- 203

Query: 197 LPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVK 256
               ARG +AG  VWAQF++P+CNAVPDG+N GTIVVFNLD  VS+S+LKEIFQAFG VK
Sbjct: 204 ----ARGFIAGCAVWAQFVIPSCNAVPDGHNHGTIVVFNLDPNVSTSSLKEIFQAFGAVK 259

Query: 257 ELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSS 316
           ELRETPLKK QRF+EFYD+RDAAKALKEMNG+EI+GK VVIEFSRPGG  +KFF  +S+S
Sbjct: 260 ELRETPLKKQQRFVEFYDIRDAAKALKEMNGKEIHGKQVVIEFSRPGGFGRKFFNGSSTS 319

Query: 317 CASSLNYSTIYQ---TRNSDCPPPPLSADPPSYSPRSFASQAPHFRKKSPSNSFKGNPN 372
            ASS + +       +R +  PPPP     P+ SPR F +Q      K  SNS KGNPN
Sbjct: 320 KASSFHNAININPKISRYAPPPPPPPPPVRPNISPRPFLAQTHSSSVKRSSNSIKGNPN 378

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225424576|ref|XP_002282117.1| PREDICTED: protein terminal ear1-like [Vitis vinifera]

 Score =  326 bits (835), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 197/418 (47%), Positives = 244/418 (58%), Gaps = 59/418 (14%)

Query: 1   MGETGISRFQGNLDPRAQEFRP--------TTLFRPPQVYYPYGAASPPTLPPYPSNDVQ 52
           MGETG SRF GNLDP AQEFRP         +L  P Q+YYPY    P     + ++   
Sbjct: 1   MGETGTSRFLGNLDPSAQEFRPRNPYIQNQMSLSVPTQIYYPYTHPHPQ----FVASSAY 56

Query: 53  VVPFGGVGYAQYPTHPQLGVPLPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGV 112
           V P  G         P L   + P S  PTR L+LS VP DVSE  VRR+LE FGEVR V
Sbjct: 57  VRPIAG--------KPPLSPLMSPLSATPTRALLLSSVPTDVSEVTVRRELEAFGEVRSV 108

Query: 113 QMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMNNDNNNNN 172
           Q+ER+ +GIV V FYDLRHA+    E+REQHMQ Q +   LK  Y S             
Sbjct: 109 QIERVCDGIVAVSFYDLRHAQACLTEVREQHMQQQSR---LKKHYDS------------- 152

Query: 173 LATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIV 232
           L T    +QV  E L++       LPPPARGL+AGR VWAQF++P    + D  NQGT+V
Sbjct: 153 LLTRKLASQV--EHLLV------PLPPPARGLIAGRAVWAQFMIPVSTCMLDDYNQGTLV 204

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG 292
           +FNLDS VS+S+L++IF+ FG +KELRETPLK+HQRF+EF+D+RDAA+AL+EMNG++I G
Sbjct: 205 IFNLDSEVSTSSLRDIFETFGSIKELRETPLKRHQRFVEFFDIRDAARALREMNGKKIQG 264

Query: 293 KHVVIEFSRPGGHSKKFFYANSSSCASSLNYST----------IYQTRNSDCPPPPLSAD 342
           K VVIEFSRPGGH  +FF A S++  SS   +T           Y T  S CPP      
Sbjct: 265 KRVVIEFSRPGGHGWRFFNAISTTALSSTYSTTNSTVISPSRLAYHTVTSRCPPALPCKL 324

Query: 343 PPSYS-----PRSFASQAPHFRKKSPSNSFKGNPNNVNVTCSIEPSVASLSLANAIED 395
           P   S     P S+ SQ  H  KKS     K + N  N+  S+     + S+ N IED
Sbjct: 325 PEKSSHFNVPPHSYLSQTHHSTKKSNVGINKRSSNAGNIKASMTSLRLTGSVVNGIED 382

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224100115|ref|XP_002311749.1| predicted protein [Populus trichocarpa] gi|222851569|gb|EEE89116.1| predicted protein [Populus trichocarpa]

 Score =  325 bits (832), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 204/411 (49%), Positives = 246/411 (59%), Gaps = 74/411 (18%)

Query: 1   MGETGISRFQGNLDPRAQEFRP--TTLFRPPQVYYPYGAASPPT------LPP--YPSND 50
           M E G  +F GNLDPRAQEFRP    L      + P+G   PP       LP   Y +  
Sbjct: 1   MEENGSVQFPGNLDPRAQEFRPRRDNLHNFSPKFLPFGPPPPPPPPPPPQLPHQVYYTYT 60

Query: 51  VQVVPFGG-VGYAQYPTH-PQLGV---PLPP--PSTGPTRTLVLSYVPGDVSETIVRRDL 103
            Q +PF   VG+ QY  H P   V   PLPP  P+  PTRTLVLS VP +V+E+++RR+L
Sbjct: 61  PQALPFSDFVGFVQYDHHIPPAYVSVEPLPPLPPTGAPTRTLVLSSVPSEVNESLIRREL 120

Query: 104 EVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLML 163
           EVFGEVRGVQMER+  G VTVHFYDLRHAE A +EIREQHM  Q +   L+N       +
Sbjct: 121 EVFGEVRGVQMERVGYGTVTVHFYDLRHAERALREIREQHMLHQAR---LRN-----FFI 172

Query: 164 MNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVP 223
            N+++ + N+A                    P  PPPARG++AG  VWAQFI+P+CN VP
Sbjct: 173 QNSESISFNIA--------------------PTPPPPARGVIAGCVVWAQFIIPSCNEVP 212

Query: 224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK 283
           DG NQGT+VVFNLD  VS+ +LKEIFQAFG VKE+RETPLK+HQRFIEFYDVRDAAKAL+
Sbjct: 213 DGQNQGTLVVFNLDPNVSTRSLKEIFQAFGAVKEVRETPLKRHQRFIEFYDVRDAAKALR 272

Query: 284 EMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTIYQTRNSDCPPPPLSADP 343
           EMNG+EIYGK V IEFSRPGGH KKFF A                         P +   
Sbjct: 273 EMNGKEIYGKQVDIEFSRPGGHGKKFFNAR------------------------PRATSK 308

Query: 344 PSYSPRSFASQAPHFRKKSPSNSFKGNPNNVN-VTCSIEPSVASLSLANAI 393
            S++   F S       K PS    G+P+  N +  SIE S+  LSL   +
Sbjct: 309 NSFTTPVFDSTTNLRHSKKPS----GDPSEGNPIEASIEASLGCLSLGGDV 355

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224107727|ref|XP_002314579.1| predicted protein [Populus trichocarpa] gi|222863619|gb|EEF00750.1| predicted protein [Populus trichocarpa]

 Score =  316 bits (810), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 183/313 (58%), Positives = 208/313 (66%), Gaps = 35/313 (11%)

Query: 1   MGETGISRFQGNLDPRAQEFRPTTLFRPPQVYYPYGAASPPTLPPYPSNDVQVVPFGGVG 60
           M ETG   F GNLDPRAQEFRP    R   +        P   PP P             
Sbjct: 1   MEETGFVPFPGNLDPRAQEFRP----RHNNLQDFTTKFPPFGPPPPPPPPQLPQLLHQYH 56

Query: 61  YAQYPTHPQLGVPLP-PPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLME 119
           +   P +  +G PLP PP+  PTRTLVLS VP DVSET++RR+LEVFGEVRGVQMER+ +
Sbjct: 57  HHVPPMYDTVGTPLPLPPTGAPTRTLVLSSVPSDVSETLIRRELEVFGEVRGVQMERVGD 116

Query: 120 GIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYD 179
           GIVTVHFYDLRHAE A +EIREQHM  Q +   L+N     L + N              
Sbjct: 117 GIVTVHFYDLRHAERALREIREQHMLHQAR---LRN-----LFIQN-------------- 154

Query: 180 NQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSG 239
                ESL +  + AP  PPPARGL+AG  VWAQFI+P+C AVPDG NQGT+VVFNLD  
Sbjct: 155 ----CESLSL--NIAP--PPPARGLIAGCVVWAQFIIPSCKAVPDGQNQGTLVVFNLDPN 206

Query: 240 VSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF 299
           VS+  LKE FQAFG VKELRETPLK+HQRF+EFYDVRDAAKAL EMNG+EIYGK V IEF
Sbjct: 207 VSTRCLKETFQAFGAVKELRETPLKRHQRFVEFYDVRDAAKALGEMNGKEIYGKQVDIEF 266

Query: 300 SRPGGHSKKFFYA 312
           SRPGG+ KKFF A
Sbjct: 267 SRPGGYGKKFFNA 279

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449500381|ref|XP_004161082.1| PREDICTED: protein terminal ear1-like [Cucumis sativus]

 Score =  309 bits (791), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 173/332 (52%), Positives = 217/332 (65%), Gaps = 59/332 (17%)

Query: 1   MGETGISRFQGNLDPRAQEFRPT------TLFRPP--QVYYPYGAASPPTLPPYPSNDVQ 52
           MGETG+ R Q +LDP AQEFRP        LF PP   VYY +G   PP+     +N++Q
Sbjct: 1   MGETGVIRHQKSLDPAAQEFRPGYVTNLPALFGPPVRHVYYSFGTPFPPS-----TNELQ 55

Query: 53  VVPFGGVGYAQYPTHP------------QLGVP-LPPPSTGPTRTLVLSYVPGDVSETIV 99
           V PF      + P  P             + VP + P S+ PTR+L+LS VP DVSE++V
Sbjct: 56  VEPFCNSVLTRSPNFPIDFNTAFVNPVEDIAVPEVQPLSSSPTRSLLLSAVPSDVSESVV 115

Query: 100 RRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS 159
           RRDLE FG+VRGVQMER+  GI+TVH+YDLRHAE AF+++R Q++  ++Q   ++N +S 
Sbjct: 116 RRDLECFGDVRGVQMERIRNGILTVHYYDLRHAEKAFRKMRSQNLMRRKQ---VRNQHSR 172

Query: 160 GLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTC 219
            L         NN  T                      P  AR L+ G  VWA+F++PT 
Sbjct: 173 FL--------QNNFDTP---------------------PRLARALIGGCDVWAEFVIPTS 203

Query: 220 NA-VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDA 278
           NA VPDGNNQGTIVVFNLD GVS+STLKEIF+ FGPVK++RETPLKKHQRF+EF+DVRDA
Sbjct: 204 NAAVPDGNNQGTIVVFNLDLGVSASTLKEIFERFGPVKDVRETPLKKHQRFVEFFDVRDA 263

Query: 279 AKALKEMNGQEIYGKHVVIEFSRPGGHSKKFF 310
           A A+KEMNG+EI+GK VV+EFSRPGG  +KFF
Sbjct: 264 AMAVKEMNGKEIHGKPVVVEFSRPGGSGRKFF 295

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449517014|ref|XP_004165541.1| PREDICTED: LOW QUALITY PROTEIN: protein terminal ear1-like [Cucumis sativus]

 Score =  296 bits (757), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 180/349 (51%), Positives = 221/349 (63%), Gaps = 61/349 (17%)

Query: 1   MGETGISRFQ---GNLDPRAQEFRP---TTLFRPP---QVYYPYGAASPPTLPPYPSNDV 51
           M ETG    Q   G+LDP AQEFRP   TTLF P    +V++PY    PP       +DV
Sbjct: 1   MAETGGVYGQFLAGSLDPTAQEFRPRYSTTLFLPQPPHRVFFPY----PPI------SDV 50

Query: 52  QVVPF--GGVGYAQYPTHPQLGVPLPPP-STGPTRTLVLSYVPGDVSETIVRRDLEVFGE 108
            ++PF   GV Y  + T     VP+  P S+  TR+LV+S VP DVSET+VRR+LEVFGE
Sbjct: 51  PLLPFCETGVTYPPFTTTESAYVPVRSPVSSVATRSLVVSSVPCDVSETMVRRELEVFGE 110

Query: 109 VRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMNNDN 168
           +RGVQMER+ EGIV +HFYD+RHAE A +EIR+QHM  Q +   L+N +++         
Sbjct: 111 IRGVQMERVKEGIVIIHFYDIRHAERALREIRDQHMHHQCR---LRNYFNN--------- 158

Query: 169 NNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQ 228
                              ++ NS  P  P PA GL+AG  VWAQFIVP       G NQ
Sbjct: 159 ------------NNNNNGFLLSNSSLP-RPSPAPGLIAGHAVWAQFIVPA------GKNQ 199

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
           GTIV+FNLDS VS+S L+EIF+ FG VKELRETPLKK QRF+EF+D+RDA KALKEMNG+
Sbjct: 200 GTIVIFNLDSTVSTSCLREIFERFGQVKELRETPLKKQQRFVEFFDIRDAGKALKEMNGK 259

Query: 289 EIYGKHVVIEFSRPGGHSKKFFYANSSS---CASSLNYSTIYQTRNSDC 334
           EI GK V+IEFSRPGGH  KFF AN ++   C S+  YS     R+S C
Sbjct: 260 EINGKSVLIEFSRPGGHGNKFFNANLTTPAICGSNNIYS-----RSSKC 303

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449435442|ref|XP_004135504.1| PREDICTED: protein terminal ear1-like [Cucumis sativus]

 Score =  286 bits (733), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 179/349 (51%), Positives = 218/349 (62%), Gaps = 61/349 (17%)

Query: 1   MGETGISRFQ---GNLDPRAQEFRP---TTLFRPP---QVYYPYGAASPPTLPPYPSNDV 51
           M ETG    Q   G+LDP AQEFRP   TTLF P    +V++PY    PP       +DV
Sbjct: 1   MAETGGVYGQFLAGSLDPTAQEFRPRYSTTLFLPQPPHRVFFPY----PPI------SDV 50

Query: 52  QVVPF--GGVGYAQYPTHPQLGVPLPPP-STGPTRTLVLSYVPGDVSETIVRRDLEVFGE 108
            ++PF   GV Y  + T     VP+  P S+  TR+LV+S VP DVSET+VRR+LEVFGE
Sbjct: 51  PLLPFCETGVTYPPFTTTESAYVPVRSPVSSVATRSLVVSSVPCDVSETMVRRELEVFGE 110

Query: 109 VRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMNNDN 168
           +RGVQMER+ EGIV +HFYD+RHAE A +EIR+QHM  Q +     N  ++         
Sbjct: 111 IRGVQMERVKEGIVIIHFYDIRHAERALREIRDQHMHHQCRLRNYLNNNNN--------- 161

Query: 169 NNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQ 228
                              ++ NS  P  P PA GL+AG  VWAQFIVP       G NQ
Sbjct: 162 ---------------NNGFLLSNSSLP-RPSPAPGLIAGHAVWAQFIVPA------GKNQ 199

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
           GTIV+FNLDS VS+S L+EIF+ FG VKELRETPLKK QRF+EF+D+RDA KALKEMNG+
Sbjct: 200 GTIVIFNLDSTVSTSCLREIFERFGQVKELRETPLKKQQRFVEFFDIRDAGKALKEMNGK 259

Query: 289 EIYGKHVVIEFSRPGGHSKKFFYANSSS---CASSLNYSTIYQTRNSDC 334
           EI GK V+IEFSRPGGH  KFF AN ++   C S+  YS     R+S C
Sbjct: 260 EINGKSVLIEFSRPGGHGNKFFNANLTTPAICGSNNIYS-----RSSKC 303

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449450610|ref|XP_004143055.1| PREDICTED: protein terminal ear1-like [Cucumis sativus]

 Score =  281 bits (720), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 163/332 (49%), Positives = 205/332 (61%), Gaps = 66/332 (19%)

Query: 1   MGETGISRFQGNLDPRAQEFRPT------TLFRPP--QVYYPYGAASPPTLPPYPSNDVQ 52
           MGETG+ R Q +LDP AQEFRP        LF PP   VYY +G   PP+     +N++Q
Sbjct: 1   MGETGVIRLQKSLDPAAQEFRPGYVTNLPALFGPPVRHVYYSFGTPFPPS-----TNELQ 55

Query: 53  VVPFGGVGYAQYPTHP------------QLGVP-LPPPSTGPTRTLVLSYVPGDVSETIV 99
           V PF      + P  P             + VP + P S+ PTR+L+LS VP DVSE++V
Sbjct: 56  VEPFCNSVLTRSPNFPIDFNTAFVNPVEDIAVPEVQPLSSSPTRSLLLSAVPSDVSESVV 115

Query: 100 RRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS 159
           RRDLE FG+VRGVQMER+  GI+TVH+YDLRHAE AF+++R Q++  ++Q    +N +S 
Sbjct: 116 RRDLECFGDVRGVQMERIRNGILTVHYYDLRHAEKAFRKMRSQNLMRRKQ---FRNQHSR 172

Query: 160 GLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTC 219
            L         NN  T                      P  AR L+ G  VWA+F++PT 
Sbjct: 173 FL--------QNNFDTP---------------------PRLARALIGGCDVWAEFVIPTS 203

Query: 220 N-AVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDA 278
           N AVPDGNNQGTIVVFNLD GV +STLKEIF+ FG         L +HQRF+EF+DVRDA
Sbjct: 204 NAAVPDGNNQGTIVVFNLDLGVCASTLKEIFERFGNF-------LSRHQRFVEFFDVRDA 256

Query: 279 AKALKEMNGQEIYGKHVVIEFSRPGGHSKKFF 310
           A A+KEMNG+EI+GK VV+EFSRPGG  +KFF
Sbjct: 257 AMAVKEMNGKEIHGKPVVVEFSRPGGSGRKFF 288

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297814854|ref|XP_002875310.1| hypothetical protein ARALYDRAFT_322753 [Arabidopsis lyrata subsp. lyrata] gi|297321148|gb|EFH51569.1| hypothetical protein ARALYDRAFT_322753 [Arabidopsis lyrata subsp. lyrata]

 Score =  255 bits (652), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 156/336 (46%), Positives = 187/336 (55%), Gaps = 76/336 (22%)

Query: 1   MGETGISRFQGNLDPRAQEFRPTTLFRPPQVYYPYGAASPP----------------TLP 44
           M ++ +  F GNLDPRAQEF P         Y+P+   SP                  +P
Sbjct: 1   MEDSRLFPFAGNLDPRAQEFIPLNP-TSSGFYFPFTPPSPLPPPLHPSSEPRVFTFFNIP 59

Query: 45  PYP-----------SNDVQVVPFGGVGYAQYPTHPQLGVPLPPPSTGPTRTLVLSYVPGD 93
           P+P            +      F GV  AQ          LPPPS  PTR+L L  VP D
Sbjct: 60  PHPVMFSPPPSQPPPSPPPRPCFNGVSAAQR---------LPPPSNSPTRSLSLISVPRD 110

Query: 94  VSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL 153
           V+E+ VRRDLEV+G+VRGVQMER+ EGIVTVHFYD+R A+ A +E+  +HMQ  QQ+ G 
Sbjct: 111 VTESTVRRDLEVYGDVRGVQMERISEGIVTVHFYDIRDAKRAVREVCGRHMQ--QQARGG 168

Query: 154 KNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQ 213
               S                                          ARG V+GRPVWAQ
Sbjct: 169 SVWSSPSTSS-------------------------------------ARGFVSGRPVWAQ 191

Query: 214 FIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFY 273
           F+VP  +AVP G NQGT+V+FNLD  VSS TL++ FQ +GP+KELRETP KKHQRFIEFY
Sbjct: 192 FVVPATSAVPGGCNQGTLVIFNLDPEVSSITLRQFFQVYGPIKELRETPYKKHQRFIEFY 251

Query: 274 DVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKF 309
           DVRDAA+A   MNG+EI GK VVIEFSRPGG   KF
Sbjct: 252 DVRDAARAFDRMNGEEIGGKQVVIEFSRPGGIKNKF 287

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	408
TAIR|locus:2090350	615	TEL1 "terminal EAR1-like 1" [A	0.267	0.177	0.715	4e-64
TAIR|locus:2008530	527	TEL2 "terminal EAR1-like 2" [A	0.269	0.208	0.636	2.6e-59
TAIR|locus:2013583	800	ML5 "MEI2-like protein 5" [Ara	0.223	0.113	0.538	6.9e-23
TAIR|locus:2045605	843	ML2 "MEI2-like 2" [Arabidopsis	0.247	0.119	0.475	2e-22
TAIR|locus:2117706	759	ML3 "MEI2-like 3" [Arabidopsis	0.247	0.133	0.485	1.4e-20
TAIR|locus:2156166	915	ML1 "MEI2-like protein 1" [Ara	0.460	0.205	0.242	4.8e-11
TAIR|locus:2182885	907	ML4 "MEI2-like 4" [Arabidopsis	0.458	0.206	0.247	8.2e-11
UNIPROTKB|E7ETC0	135	TIAL1 "Nucleolysin TIAR" [Homo	0.205	0.622	0.352	6.8e-07
DICTYBASE|DDB_G0279255	1698	DDB_G0279255 [Dictyostelium di	0.218	0.052	0.298	2.6e-06
GENEDB_PFALCIPARUM|PF13_0122	125	PF13_0122 "cyclophilin, putati	0.188	0.616	0.321	3.9e-06

TAIR|locus:2090350 TEL1 "terminal EAR1-like 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 421 (153.3 bits), Expect = 4.0e-64, Sum P(2) = 4.0e-64
 Identities = 78/109 (71%), Positives = 91/109 (83%)

Query:   201 ARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRE 260
             ARG V+GRPVWAQF+VP  +AVP G NQGT+V+FNLD  VSS TL++IFQ +GP+KELRE
Sbjct:   185 ARGFVSGRPVWAQFVVPATSAVPGGCNQGTLVIFNLDPEVSSITLRQIFQVYGPIKELRE 244

Query:   261 TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKF 309
             TP KKHQRF+EFYDVRDAA+A   MNG+EI GK VVIEFSRPGG   +F
Sbjct:   245 TPYKKHQRFVEFYDVRDAARAFDRMNGKEIGGKQVVIEFSRPGGIKNRF 293

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

TAIR|locus:2008530 TEL2 "terminal EAR1-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 380 (138.8 bits), Expect = 2.6e-59, Sum P(2) = 2.6e-59
 Identities = 70/110 (63%), Positives = 90/110 (81%)

Query:   201 ARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRE 260
             ARGLV+G  +WA F+ P  NAVP+GNNQG++V+ NL+  VSSSTL+ IFQ +G VK++RE
Sbjct:   155 ARGLVSGHSLWAHFVFPQLNAVPEGNNQGSLVIMNLEPTVSSSTLRHIFQVYGEVKQVRE 214

Query:   261 TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFF 310
             TP K+ QRF+EF+DVRDAAKAL+ MNG+ I GK +VI+FSRPGG +KK F
Sbjct:   215 TPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRPGGLTKKLF 264

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2013583 ML5 "MEI2-like protein 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 245 (91.3 bits), Expect = 6.9e-23, Sum P(2) = 6.9e-23
 Identities = 49/91 (53%), Positives = 61/91 (67%)

Query:   214 FIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFY 273
             F +P  N      NQGT+VVFNLD  +S+  L  IF A G +KE+RETP K+H +F+EFY
Sbjct:   238 FSIPKDNPSEKDMNQGTLVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKRHHKFVEFY 297

Query:   274 DVRDAAKALKEMNGQEIYGKHVVIEFSRPGG 304
             DVR A  ALK +N  EI GK + +E SRPGG
Sbjct:   298 DVRGAEAALKALNRCEIAGKRIKVEPSRPGG 328

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0016558 "protein import into peroxisome matrix" evidence=RCA

TAIR|locus:2045605 ML2 "MEI2-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 243 (90.6 bits), Expect = 2.0e-22, Sum P(2) = 2.0e-22
 Identities = 48/101 (47%), Positives = 68/101 (67%)

Query:   204 LVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPL 263
             L+  R +   F +P  N      NQGT+V+FN+D+ VS+  L ++F A+G ++E+RETP 
Sbjct:   258 LLRKRTLDIHFSIPKENPSEKDMNQGTLVIFNVDTTVSNDELLQLFGAYGEIREIRETPN 317

Query:   264 KKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG 304
             ++  RFIE+YDVRDA  ALK +N  EI GK + +E SRPGG
Sbjct:   318 RRFHRFIEYYDVRDAETALKALNRSEIGGKCIKLELSRPGG 358

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

TAIR|locus:2117706 ML3 "MEI2-like 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 242 (90.2 bits), Expect = 1.4e-20, Sum P(2) = 1.4e-20
 Identities = 49/101 (48%), Positives = 65/101 (64%)

Query:   204 LVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPL 263
             L+  R +   F +P  N      NQGT+VVFNL   VS+  L+ IF  +G +KE+RETP 
Sbjct:   226 LLKKRKLDIHFSIPKDNPSEKDVNQGTLVVFNLAPSVSNRDLENIFGVYGEIKEIRETPN 285

Query:   264 KKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG 304
             K+H +F+EF+DVR A  ALK +N  EI GK + +E SRPGG
Sbjct:   286 KRHHKFVEFFDVRSADAALKALNRTEIAGKRIKLEHSRPGG 326

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

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

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

TAIR|locus:2156166 ML1 "MEI2-like protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 162 (62.1 bits), Expect = 4.8e-11, Sum P(2) = 4.8e-11
 Identities = 46/190 (24%), Positives = 81/190 (42%)

Query:   204 LVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPL 263
             L+ G  +  ++ +   N      ++G ++V NLDS +S+  L  + +++G VKE+R T  
Sbjct:   277 LLRGTKLDIRYSISKENPSQKDTSKGALLVNNLDSSISNQELNRLVKSYGEVKEIRRTMH 336

Query:   264 KKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFXXXXXXXXXXXXX 323
                Q +IEF+DVR AA AL  +NG E+ GK + +  + P G   ++              
Sbjct:   337 DNSQIYIEFFDVRAAAAALGGLNGLEVAGKKLQLVPTYPEG--TRYTSQCAANDTEGCLP 394

Query:   324 XTIYQTRNXXXXXXXXXXXXXXXXXRSFASQAPHFRKKSPSNSFKGNPNNVNVTCSIEPS 383
              T Y   +                    + +  H    SP NSF     ++++     PS
Sbjct:   395 KTSYSNTSSGHIGRHFPGMISSTSSDGGSMRVIHNSIGSPVNSFIERHRSLSIPIGFPPS 454

Query:   384 VASLSLANAI 393
                +S +  +
Sbjct:   455 ANGISASKPV 464

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0005515 "protein binding" evidence=IPI

GO:0048507 "meristem development" evidence=IGI

GO:0045836 "positive regulation of meiosis" evidence=IGI

TAIR|locus:2182885 ML4 "MEI2-like 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 169 (64.5 bits), Expect = 8.2e-11, Sum P(2) = 8.2e-11
 Identities = 47/190 (24%), Positives = 86/190 (45%)

Query:   204 LVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPL 263
             L+ GR +  ++ +P  N   + +++G + V NLDS +S+  L  IF ++G ++E+R T  
Sbjct:   271 LLRGRKLDIRYSIPKENP-KENSSEGALWVNNLDSSISNEELHGIFSSYGEIREVRRTMH 329

Query:   264 KKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFXXXXXXXXXXXXX 323
             +  Q +IEF+DVR A  AL+ +NG E+ G+ + +  + P G S  F+             
Sbjct:   330 ENSQVYIEFFDVRKAKVALQGLNGLEVAGRQLKLAPTCPEGTS--FWPQFASDDGEGGLP 387

Query:   324 XTIYQTRNXXXXXXXXXXXXXXXXXRSFASQAPHFRKKSPSNSFKGNPNNVNVTCSIEPS 383
                +   +                    + +  H    SP NSF     +++V   + PS
Sbjct:   388 KMAFNNLSSAHMGRHFPGILASTSIDGGSIRGMHNSVGSPMNSFIERHQSLDVPIGLPPS 447

Query:   384 VASLSLANAI 393
                +S +  +
Sbjct:   448 ARVISASKPV 457

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0045836 "positive regulation of meiosis" evidence=IMP

GO:0045927 "positive regulation of growth" evidence=IMP

GO:0048507 "meristem development" evidence=IGI

UNIPROTKB|E7ETC0 TIAL1 "Nucleolysin TIAR" [Homo sapiens (taxid:9606)]

 Score = 121 (47.7 bits), Expect = 6.8e-07, P = 6.8e-07
 Identities = 31/88 (35%), Positives = 45/88 (51%)

Query:   224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAK 280
             DG  + T+ V NL   V+   + ++F   GP K  +   E        F+EFY+ RDAA 
Sbjct:     5 DGQPR-TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 63

Query:   281 ALKEMNGQEIYGKHVVIEFSRPGGHSKK 308
             AL  MNG++I GK V + ++      KK
Sbjct:    64 ALAAMNGRKILGKEVKVNWATTPSSQKK 91

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

DICTYBASE|DDB_G0279255 DDB_G0279255 [Dictyostelium discoideum (taxid:44689)]

 Score = 122 (48.0 bits), Expect = 2.6e-06, Sum P(2) = 2.6e-06
 Identities = 29/97 (29%), Positives = 52/97 (53%)

Query:   212 AQFIVPTCNAVPDGNNQGTIVV-FNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFI 270
             ++ IV  C       ++GT++  F+ D  + +  +   F  FG +K++R++P K  Q+F+
Sbjct:   978 SKLIVNYCFDKDQTVDKGTLIATFSNDDQIKN--IVNDFSKFGEIKDIRDSPNKPLQKFV 1035

Query:   271 EFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSK 307
             EFY++    KA+  +N  +I      + FS  GG SK
Sbjct:  1036 EFYNINSTLKAINNLNSDKIK-----VAFSHHGGSSK 1067

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GENEDB_PFALCIPARUM|PF13_0122 PF13_0122 "cyclophilin, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 114 (45.2 bits), Expect = 3.9e-06, P = 3.9e-06
 Identities = 27/84 (32%), Positives = 46/84 (54%)

Query:   224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPL----KKHQ--RFIEFYDVRD 277
             D N    + V  +D  +   +L +IF +FG ++ + E PL    KK++   F+E+ +V D
Sbjct:     3 DNNATDILFVGGIDETIDEKSLYDIFSSFGDIRNI-EVPLNMTTKKNRGFAFVEYVEVDD 61

Query:   278 AAKALKEMNGQEIYGKHVVIEFSR 301
             A  AL  MN  E+ GK + + +S+
Sbjct:    62 AKHALYNMNNFELNGKRIHVNYSK 85

GO:0003723 "RNA binding" evidence=ISS

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=ISS

GO:0006457 "protein folding" evidence=ISS

---

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	408
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	2e-36
cd12526	71	cd12526, RRM1_EAR1_like, RNA recognition motif 1 i	2e-30
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	3e-29
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	3e-29
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	4e-21
smart00360	73	smart00360, RRM, RNA recognition motif	4e-15
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-13
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	5e-12
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	6e-11
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-10
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-10
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	9e-10
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-09
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-09
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-09
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	5e-09
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	8e-09
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	1e-08
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	1e-08
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-08
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	5e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	1e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-07
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-07
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-07
cd12525	72	cd12525, RRM1_MEI2_fungi, RNA recognition motif 1	2e-07
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	2e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-07
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	2e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-07
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	3e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	4e-07
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	5e-07
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	5e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	7e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-06
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	1e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-06
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	1e-06
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	1e-06
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	2e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	2e-06
cd12528	81	cd12528, RRM2_MEI2_fungi, RNA recognition motif 2	2e-06
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	3e-06
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	3e-06
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-06
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	3e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	4e-06
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	4e-06
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	4e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	7e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	8e-06
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	8e-06
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	1e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-05
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	1e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-05
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	2e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	2e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-05
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	3e-05
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-05
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	3e-05
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	3e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	4e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-05
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	5e-05
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	5e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	5e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	7e-05
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	8e-05
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	8e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	8e-05
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	9e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	9e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-04
cd12694	86	cd12694, RRM2_hnRNPL_like, RNA recognition motif 2	1e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	1e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-04
cd12525	72	cd12525, RRM1_MEI2_fungi, RNA recognition motif 1	2e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	2e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-04
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	2e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-04
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	2e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	2e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-04
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	3e-04
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	3e-04
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	3e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	4e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	4e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	5e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	5e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-04
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	5e-04
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	6e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	6e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	6e-04
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	6e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	6e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	7e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	8e-04
cd12696	107	cd12696, RRM3_PTBP2, RNA recognition motif 3 in ve	8e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	8e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	9e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	0.001
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	0.001
cd12425	76	cd12425, RRM4_PTBP1_like, RNA recognition motif 4	0.001
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	0.001
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	0.001
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	0.001
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.002
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	0.002
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	0.002
cd12764	72	cd12764, RRM2_SRSF4, RNA recognition motif 2 in ve	0.002
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.002
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	0.002
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	0.002
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.003
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.004
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	0.004

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

 Score =  127 bits (320), Expect = 2e-36
 Identities = 51/71 (71%), Positives = 60/71 (84%)

Query: 228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           QGT+V+FNLD  VSS TL+ IFQ +G VKELRETP K+ QRF+EF+DVRDAAKAL+ MNG
Sbjct: 1   QGTLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNG 60

Query: 288 QEIYGKHVVIE 298
           +EI GK VVIE
Sbjct: 61  KEISGKPVVIE 71

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

>gnl|CDD|240970 cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal EAR1-like proteins

 Score =  111 bits (279), Expect = 2e-30
 Identities = 41/72 (56%), Positives = 51/72 (70%), Gaps = 1/72 (1%)

Query: 82  TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIRE 141
           +R L+LS VP  + ET +RRDLE +G VR VQM+ + EGIVTVHFYDLRHAE A ++IR 
Sbjct: 1   SRALLLSGVPPHIPETQLRRDLEQWGAVRAVQMDAMAEGIVTVHFYDLRHAEDALRDIRA 60

Query: 142 QHMQLQQQSYGL 153
           QH+  QQ     
Sbjct: 61  QHLF-QQHRQQQ 71

This subgroup corresponds to the RRM1 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

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

 Score =  108 bits (271), Expect = 3e-29
 Identities = 42/71 (59%), Positives = 53/71 (74%)

Query: 228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           QGT+VVFNLD  VS+  L +IF A+G +KE+RETP K+H +FIEFYDVR A  ALK +N 
Sbjct: 1   QGTLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNR 60

Query: 288 QEIYGKHVVIE 298
            EI GK + +E
Sbjct: 61  SEIAGKRIKLE 71

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

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

 Score =  108 bits (271), Expect = 3e-29
 Identities = 34/71 (47%), Positives = 50/71 (70%)

Query: 228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           QGT++VFNLDS +S   L+ +F  FG VK++RETPL+  Q+F+EFYD+R A  AL  +NG
Sbjct: 1   QGTLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNG 60

Query: 288 QEIYGKHVVIE 298
           +   G  + ++
Sbjct: 61  RPFLGGRLKVK 71

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

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

 Score = 86.1 bits (213), Expect = 4e-21
 Identities = 37/70 (52%), Positives = 51/70 (72%)

Query: 82  TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIRE 141
           +R+L +  VP DV+E+ +RR  EV+G+VRGVQ ER+ EGIVTVHFYD+R A+ A +E+  
Sbjct: 1   SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCG 60

Query: 142 QHMQLQQQSY 151
           +HMQ Q    
Sbjct: 61  RHMQQQALGG 70

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|214636 smart00360, RRM, RNA recognition motif

 Score = 69.5 bits (171), Expect = 4e-15
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 5/73 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
           T+ V NL    +   L+E+F  FG V+ +R    K+  +     F+EF    DA KAL+ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 285 MNGQEIYGKHVVI 297
           +NG+E+ G+ + +
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 65.8 bits (161), Expect = 7e-14
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMN 286
           + V NL    +   L+E+F  FG ++ +R    +    K   F+EF    DA KAL+ +N
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 287 GQEIYGKHVVIE 298
           G+E+ G+ + + 
Sbjct: 61  GKELDGRKLKVS 72

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

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

 Score = 63.0 bits (154), Expect = 6e-13
 Identities = 26/67 (38%), Positives = 39/67 (58%), Gaps = 4/67 (5%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMN 286
           + V NL    +   LK++F  FGP++ +R    ET   K   F+EF D  DA KAL+ +N
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 287 GQEIYGK 293
           G+E+ G+
Sbjct: 61  GKELGGR 67

(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|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 60.7 bits (148), Expect = 5e-12
 Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 4/75 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFI--EFYDVRDAAKALKEMNG 287
           T+ V N++S V    L+ +F+ FG ++ L      KH+ FI   +YD+R A +A + + G
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTA--CKHRGFIMVSYYDIRAARRAKRALQG 60

Query: 288 QEIYGKHVVIEFSRP 302
            E+ G+ + I FS P
Sbjct: 61  TELGGRKLDIHFSIP 75

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

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

 Score = 57.7 bits (140), Expect = 6e-11
 Identities = 26/67 (38%), Positives = 39/67 (58%), Gaps = 6/67 (8%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR----FIEFYDVRDAAKALKEMNGQ 288
           V NLD  V+   L E+F   GP+K  +   +++H      F+E+YD R AA AL+ MNG+
Sbjct: 3   VGNLDRTVTEDLLAELFSQIGPIKSCKL--IREHGNDPYAFVEYYDHRSAAAALQTMNGR 60

Query: 289 EIYGKHV 295
            I G+ +
Sbjct: 61  LILGQEI 67

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

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

 Score = 61.1 bits (147), Expect = 2e-10
 Identities = 39/157 (24%), Positives = 66/157 (42%), Gaps = 8/157 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
           T+ V NL   V+   L+E+F+ FGPVK +     RET   +   F+EF     A KA++E
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE 176

Query: 285 MNGQEIYGKHVVIEFSRPGGHSKKFFYANS-SSCASSLNYSTIYQTRNSDCPPPPLSADP 343
           +NG+E+ G+ + ++ ++P    +     N  +S A  L+         SD          
Sbjct: 177 LNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLK 236

Query: 344 PSYSPR--SFASQAPHFRKKSPSNSFKGNPNNVNVTC 378
            +       F S+    R   P +     P + +   
Sbjct: 237 TAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVG 273

Length = 306

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

 Score = 56.0 bits (136), Expect = 2e-10
 Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 5/73 (6%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEM 285
           + V  L   V+   LKEIF  +G VK++     RE  L +   ++EF    DA KA+K M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 286 NGQEIYGKHVVIE 298
           +G +I G+ V +E
Sbjct: 61  DGGQIDGQEVTVE 73

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

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

 Score = 54.2 bits (131), Expect = 9e-10
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 6/75 (8%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKEM 285
           ++V NL    + + LK++F  FG V E+   P K   +     F++F    DA KA+K +
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEV-TIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 286 NGQEIYGKHVVIEFS 300
           NG++I G+ V ++++
Sbjct: 61  NGKKIKGRPVAVDWA 75

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

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

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKEL---RETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           V NL    +   L++ F+ +GP++ +   R  P      F+EF D RDA  A++ ++G+ 
Sbjct: 4   VGNLGPRATKRELEDEFEKYGPLRSVWVARNPP---GFAFVEFEDPRDAEDAVRALDGRR 60

Query: 290 IYGKHVVIEFSRP 302
           I G  V +E SR 
Sbjct: 61  ICGNRVRVELSRG 73

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

>gnl|CDD|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 = 53.8 bits (130), Expect = 2e-09
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQR---FIEFYDVRDAAKALK 283
             + V  L +  +   L+ +F  FG V+E+   + P     R   F+ F  V DA  A++
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 284 EMNGQEIYGKHVVIEFSR 301
           ++NG+E+ G+ + +E ++
Sbjct: 62  DLNGKELEGRVIKVEKAK 79

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

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

 Score = 52.9 bits (128), Expect = 2e-09
 Identities = 16/56 (28%), Positives = 31/56 (55%)

Query: 245 LKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS 300
           L ++F  FG V++++    K    F+EF     A KA++ +NG    G+ + +++S
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

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

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 3/68 (4%)

Query: 235 NLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH 294
            L        ++  F+ +G    +RE  LK    F+EF D RDA  A+ E+NG+E+ G+ 
Sbjct: 6   RLPYRARERDVERFFKGYG---RIREINLKNGFGFVEFEDPRDADDAVYELNGKELCGER 62

Query: 295 VVIEFSRP 302
           V++E +R 
Sbjct: 63  VIVEHARG 70

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

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

 Score = 53.3 bits (129), Expect = 3e-09
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 230 TIVVFNLDSGVSSSTLK----EIFQAFGPVKEL--RETPLKKHQRFIEFYDVRDAAKALK 283
           T+ + NL+  +    LK     +F  FGPV ++   +T   + Q F+ F DV  A  AL+
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 284 EMNGQEIYGKHVVIEFSR 301
            + G   Y K + I++++
Sbjct: 61  ALQGFPFYDKPMRIQYAK 78

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

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

 Score = 52.2 bits (126), Expect = 5e-09
 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            + V NL   V+   LK++F  FG V        RET   +   F+E     +A  A+++
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NG +  G+ + +  +RP
Sbjct: 61  LNGTDFGGRTLTVNEARP 78

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

 Score = 51.5 bits (123), Expect = 8e-09
 Identities = 24/72 (33%), Positives = 44/72 (61%), Gaps = 3/72 (4%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           + V NL + V+   L++ F  FG ++ +++    K   FI F +   A KA++EMNG+E+
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKEL 60

Query: 291 YGKHVVIEFSRP 302
            G+++ I F++P
Sbjct: 61  EGENIEIVFAKP 72

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

 Score = 51.1 bits (122), Expect = 1e-08
 Identities = 23/56 (41%), Positives = 36/56 (64%)

Query: 246 KEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR 301
           K+I + FG   +L E  LK    F+EF D RDA  A+ E+NG+++ G+ V++E +R
Sbjct: 14  KDIQRFFGGYGKLLEIDLKNGYGFVEFEDSRDADDAVYELNGKDLCGERVIVEHAR 69

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

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
            ++V N+    +   L+E+F  FG VK +R  P K         F+EF   ++A  A++ 
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVR-LPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 285 MNGQEIYGKHVVIEFS 300
           +    +YG+H+V+E++
Sbjct: 61  LKSTHLYGRHLVLEYA 76

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

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 9/73 (12%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGP---VKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           V NL    +   L+E+F  +G    VK++++        F+ F +  DA KA++EMNG+E
Sbjct: 6   VRNLPLSTTEEQLRELFSEYGEVERVKKIKDYA------FVHFEERDDAVKAMEEMNGKE 59

Query: 290 IYGKHVVIEFSRP 302
           + G  + +  ++P
Sbjct: 60  LEGSPIEVSLAKP 72

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|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 = 49.9 bits (120), Expect = 4e-08
 Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           T+ V NL  G++   L+  F  FG ++E+R     K   F+ F     AA A+  +NG  
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFK-DKGYAFVRFDTHEAAATAIVAVNGTS 60

Query: 290 IYGKHV 295
           I G+ V
Sbjct: 61  INGQTV 66

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|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 49.5 bits (119), Expect = 5e-08
 Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLK--KHQRFIEFYDVRDAAKALKEMNG 287
           TI +FN+   V+   +K  F+  GP  ++R+  L        +EF    DA KA   +NG
Sbjct: 2   TIGLFNVSDTVNEEQIKAFFEKIGP--DVRKIELFPDHEGALVEFESPSDAGKASLSLNG 59

Query: 288 QEIYGKHVVI 297
            +  GK + I
Sbjct: 60  SQFGGKTIKI 69

This subfamily corresponds to the RRM4 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|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 48.3 bits (115), Expect = 1e-07
 Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 4/72 (5%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR----FIEFYDVRDAAKALKEMNGQ 288
           V NLD  V+   LK+IFQ  GPV+ ++  P K ++     F+E++   DA  AL+ +NG+
Sbjct: 3   VGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLNGR 62

Query: 289 EIYGKHVVIEFS 300
           +I    + + ++
Sbjct: 63  QIENNEIRVNWA 74

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEM 285
           + V N+    +   L EIF   GPV   R     +T   K   F EF D+  AA A++ +
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 286 NGQEIYGKHVVIEFS 300
           NG E  G+ + ++F+
Sbjct: 61  NGYEFNGRALRVDFA 75

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

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

 Score = 48.2 bits (115), Expect = 1e-07
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           T+ V   D G  ++  ++I + F P   L    ++K   F+EF D  DA KAL+ ++G  
Sbjct: 1   TLFVVGFDPG--TTREEDIEKLFEPFGPLVRCDIRKTFAFVEFEDSEDATKALEALHGSR 58

Query: 290 IYGKHVVIEFSR 301
           I G  + +EF +
Sbjct: 59  IDGSVLTVEFVK 70

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

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
           T+ V  L+   + S L+  F+ +GP+K +R    KK  +     FIEF   RD   A K 
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKY 62

Query: 285 MNGQEIYGKHVVIEFSR 301
            +G++I G+ V+++  R
Sbjct: 63  ADGKKIDGRRVLVDVER 79

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

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 7/69 (10%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPL----KKHQ--RFIEFYDVRDAAKALKE 284
           + V  L   V    L   F  FG +K++ + PL    +KH+   F+EF +  DAA A+  
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDI-QIPLDYETQKHRGFAFVEFEEPEDAAAAIDN 59

Query: 285 MNGQEIYGK 293
           MN  E++G+
Sbjct: 60  MNESELFGR 68

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

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 24/62 (38%), Positives = 43/62 (69%), Gaps = 1/62 (1%)

Query: 82  TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLM-EGIVTVHFYDLRHAEMAFKEIR 140
           TR L ++ VP DVS + ++   E  G+V+G+ +++L+ +GIV V F+DLR A  A+K+++
Sbjct: 1   TRYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKKLLSKGIVIVSFHDLRQAIKAYKDLQ 60

Query: 141 EQ 142
            +
Sbjct: 61  SK 62

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

 Score = 47.9 bits (115), Expect = 2e-07
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKH-QRFIEFYDVRDAAKALKEMNGQE 289
           + + NL   V+   L ++F  +G V+++         Q  ++F  V  A  A K +NG+ 
Sbjct: 4   VTISNLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRN 63

Query: 290 IYGK--HVVIEFSR 301
           IY     + I+FSR
Sbjct: 64  IYDGCCTLDIQFSR 77

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

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

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKE 284
           T+ V  L    +  TL+E+F  +G ++ LR      T   K   F+E+   RDA +A ++
Sbjct: 5   TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

Query: 285 MNGQEIYGKHVVIEFSR 301
            +   I G  + ++F R
Sbjct: 65  AHKLVIDGSEIFVDFER 81

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|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 47.8 bits (113), Expect = 2e-07
 Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 3/74 (4%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMN 286
           T+ V NL   V+   + ++F   GP K  +   E        F+EFY+ RDAA AL  MN
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60

Query: 287 GQEIYGKHVVIEFS 300
           G++I GK V + ++
Sbjct: 61  GRKILGKEVKVNWA 74

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKE---LRETPLKKHQRF--IEFYDVRDAAKALKE 284
           T+ V NL    +   L+E F   GP+K    +++   KK + F  + F    DA +AL+E
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 285 MNGQEIYGKHVVIEFSRP 302
               +  G+ + +EF++ 
Sbjct: 61  KKKTKFGGRKIHVEFAKK 78

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

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 47.3 bits (112), Expect = 3e-07
 Identities = 26/73 (35%), Positives = 46/73 (63%), Gaps = 5/73 (6%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAA-KALKEMNGQE 289
           + V NL + V+   L++ F  FG ++ +++  LK +  F+ F + RDAA +A+ EMNG+E
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKK--LKDYA-FVHFEE-RDAAVRAMDEMNGKE 59

Query: 290 IYGKHVVIEFSRP 302
           I G+ + I  ++P
Sbjct: 60  IEGEEIEIVLAKP 72

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 47.3 bits (113), Expect = 4e-07
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 8/80 (10%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR---FIEFYDVRDAAKA 281
            + + NLDS ++   L ++F  +G +K+      +  PLK   R   F+ F    +A KA
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 282 LKEMNGQEIYGKHVVIEFSR 301
           LK +NG+   GK +V+ ++ 
Sbjct: 61  LKSLNGKTALGKKLVVRWAH 80

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

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

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 16/58 (27%), Positives = 30/58 (51%)

Query: 82  TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEI 139
           +RTL +  +  +V +  +R   E FG++R +       G + V +YD+R A  A + +
Sbjct: 1   SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRAL 58

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

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

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 6/76 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEM 285
           TI V NLD   ++  L E F   G VK +R    ET   ++  F+EF +      ALK +
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYA-FVEFAEQTSVINALK-L 63

Query: 286 NGQEIYGKHVVIEFSR 301
           NG    G+ + +  S 
Sbjct: 64  NGAMFGGRPLKVNHSN 79

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

 Score = 46.4 bits (111), Expect = 7e-07
 Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 11/80 (13%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
           TI V NL        L+E+F+ FGP+  +     +ET   +   F+ F+   DA +A+++
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 285 MNGQEIYG-KHVV--IEFSR 301
           +NG   +G  +++  +E+++
Sbjct: 61  LNG---FGYDNLILSVEWAK 77

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

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

 Score = 45.2 bits (108), Expect = 1e-06
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 9/71 (12%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR------FIEFYDVRDAAKALKE 284
           + V NL   V+   L+E F  +G V+ +R   L +++       F+EF    DA  ALK+
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVR---LVRNKDRPRGFAFVEFASPEDAEAALKK 57

Query: 285 MNGQEIYGKHV 295
           +NG  + G+ +
Sbjct: 58  LNGLVLDGRTL 68

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

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 5/66 (7%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           V NL   ++   L+ IF+ FG ++ ++     ET   K   FI+F D  DA KAL+++NG
Sbjct: 3   VGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNG 62

Query: 288 QEIYGK 293
            E+ G+
Sbjct: 63  FELAGR 68

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

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 45.4 bits (107), Expect = 1e-06
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMN 286
           T+ V NL   V+ + + ++F   GP K  +   +T       F+EF++ R AA +L  MN
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60

Query: 287 GQEIYGKHVVIEFS 300
           G++I GK V + ++
Sbjct: 61  GRKIMGKEVKVNWA 74

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 4/78 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLK----KHQRFIEFYDVRDAAKALKEM 285
            + V  L   V+   L+++F+  G VK +R    +    K   ++E+ +   A++A+ +M
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 286 NGQEIYGKHVVIEFSRPG 303
           +G EI  K + +  S P 
Sbjct: 64  DGTEIKEKTISVAISNPP 81

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

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 3/70 (4%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           I V N+D   S   L+ +F+A+G V       + +   F+       A +A++E+NG+E+
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAV---LSCAVMRQFAFVHLRGEAAADRAIEELNGREL 59

Query: 291 YGKHVVIEFS 300
           +G+ +V+E S
Sbjct: 60  HGRKLVVEHS 69

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

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

 Score = 45.1 bits (107), Expect = 1e-06
 Identities = 17/68 (25%), Positives = 37/68 (54%), Gaps = 2/68 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKE--LRETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           T+ + NL+   + S L+E F+ FG + +  +++        FI++ D+    KA+++M+G
Sbjct: 4   TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDG 63

Query: 288 QEIYGKHV 295
           + +    V
Sbjct: 64  EYLGNNRV 71

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

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

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 18/59 (30%), Positives = 38/59 (64%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
           ++ V N+   V+ STL+ +F+ +G V+ ++   + +    + FYD+RDA +A++E+ G+
Sbjct: 3   SLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCGR 61

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

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 3/68 (4%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           I V N+ +  +S  L+ +F+ FG V E  +    K   F+      +A  A++ +NG+E+
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKV---KDYAFVHMEREEEALAAIEALNGKEV 59

Query: 291 YGKHVVIE 298
            G+ + +E
Sbjct: 60  KGRRINVE 67

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

>gnl|CDD|240972 cd12528, RRM2_MEI2_fungi, RNA recognition motif 2 in fungal Mei2-like proteins

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 3/57 (5%)

Query: 237 DSGVSSSTLKEIFQAFGPVKELRETPLK---KHQRFIEFYDVRDAAKALKEMNGQEI 290
           +S +  ++L+ +   FG +K  +  P +     +   EF+D RDA  A+ E+NG+ +
Sbjct: 17  NSDLVKNSLQNLLSTFGDLKAFKSLPSQQDNVKEFICEFFDTRDADNAVDELNGRVV 73

This subgroup corresponds to the RRM2 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 = 81

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

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 22/75 (29%), Positives = 29/75 (38%), Gaps = 9/75 (12%)

Query: 235 NLDSGVSSSTLKEIFQAFGPVKELRETPLK---------KHQRFIEFYDVRDAAKALKEM 285
           NL   V+   L  IF  F       +             K Q F+ F     A KAL  +
Sbjct: 8   NLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATKALNLV 67

Query: 286 NGQEIYGKHVVIEFS 300
           NG  + GK +VI+F 
Sbjct: 68  NGYVLKGKPMVIQFG 82

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

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           T+ V  LD  V+   L+ +F  FG +  ++  P  K   F++F     A  A++++ G  
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVK-IPPGKGCGFVQFVHRAAAEAAIQQLQGTI 61

Query: 290 IYGKHV 295
           I G  +
Sbjct: 62  IGGSRI 67

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

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

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 10/81 (12%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQR------FIEFYDVRDAA 279
           T+ V NL+   +  TLK+ F+  G V+ +    ++ P    +       F+EF     A 
Sbjct: 2   TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 280 KALKEMNGQEIYGKHVVIEFS 300
           KALK + G  + G  + ++ S
Sbjct: 62  KALKRLQGTVLDGHALELKLS 82

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

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

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 7/78 (8%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR------FIEFYDVRDAAKALK 283
           ++ V N+        L+ +F  +GP+ ++   PL  + R      +++F DVRDA  AL 
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVY-IPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 284 EMNGQEIYGKHVVIEFSR 301
            ++     G+ + I+F++
Sbjct: 61  YLDRTRFLGREIEIQFAQ 78

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 44.0 bits (104), Expect = 4e-06
 Identities = 18/77 (23%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALK 283
             I+V NL    +   ++ +F ++G +K +R  P K  Q      F+EF   ++A  A+ 
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEFSTAKEALNAMN 59

Query: 284 EMNGQEIYGKHVVIEFS 300
            +    + G+ +V++++
Sbjct: 60  ALKDTHLLGRRLVLQYA 76

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

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

 Score = 44.0 bits (104), Expect = 4e-06
 Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 3/56 (5%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
           V       S S ++EIF  +G VKE+    +  +  F+EF  +  A +A   ++G+
Sbjct: 4   VRPFPPDTSESAIREIFSPYGAVKEV---KMISNFAFVEFESLESAIRAKDSVHGK 56

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

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLK--KHQRF--IEFYDVRDAAKALKEM 285
           T+ V N       S ++++F+ +G +  +R   L+  K +RF  ++F     AA A+  +
Sbjct: 2   TLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALL 61

Query: 286 NGQEIYGKHVVIEFSRP 302
           NG+   G  +V++ S P
Sbjct: 62  NGKLGEGYKLVVKISDP 78

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

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

 Score = 43.4 bits (103), Expect = 7e-06
 Identities = 25/68 (36%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL---RETPLKKHQ--RFIEFYDVRDAAKALKEM 285
           + V NLD  V+   L E+F   GPV  +   ++   + HQ   F+EF    DA  A+K M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 286 NGQEIYGK 293
           N  ++YGK
Sbjct: 61  NMIKLYGK 68

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

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

 Score = 43.1 bits (102), Expect = 8e-06
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 5/76 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
           T+ V NL   V    LK  F+ FG V        RET   +   +++F    DA KA++ 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 285 MNGQEIYGKHVVIEFS 300
           M+G+E+ G+ + ++FS
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 43.0 bits (101), Expect = 8e-06
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           + +  L+       ++  F+ +G    +R+  LK+   F+EF D RDA  A+ E++G+E+
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYG---RIRDIDLKRGFGFVEFDDPRDADDAVYELDGKEL 58

Query: 291 YGKHVVIEFSR 301
             + V IE +R
Sbjct: 59  CNERVTIEHAR 69

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

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 4/75 (5%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKE----LRETPLKKHQRFIEFYDVRDAAKALKE 284
             ++V NLD GVS   +KE+F  FG +K+       +        + F    DA KA+K+
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60

Query: 285 MNGQEIYGKHVVIEF 299
            NG  + G+ + I+ 
Sbjct: 61  YNGVPLDGRPMKIQL 75

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

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 7/69 (10%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR------FIEFYDVRDAAKALKEMN 286
           V NL    +   L+ +F+ +G V ++   P  ++ R      F+ FYD RDA  A+  M+
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVY-IPRDRYTRESRGFAFVRFYDKRDAEDAMDAMD 61

Query: 287 GQEIYGKHV 295
           G+E+ G+ +
Sbjct: 62  GKELDGREL 70

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

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGP--VKELRETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           T++V +L   +S    +++ + FG   V+ +      K+  F  F + + A++AL  ++ 
Sbjct: 1   TLLVRHLPPELSEDDKEDLLKHFGASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLHQ 60

Query: 288 QEIYGKHVVIEF 299
            +I GK +V+E+
Sbjct: 61  LKILGKRLVVEY 72

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           VF L    +   L+E+F  +GP++++     ++T   +   F+ F  V DA +A + +NG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

Query: 288 QEIYGKHVVIEFS 300
            EI G+ + +++S
Sbjct: 64  MEIDGRRIRVDYS 76

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

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

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 22/70 (31%), Positives = 35/70 (50%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            +VV NL    S  +L+E+F+    ++  +     K   F+EF    DA +AL   N  E
Sbjct: 3   VLVVNNLSYSASEDSLQEVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTE 62

Query: 290 IYGKHVVIEF 299
           I G+ + +EF
Sbjct: 63  IEGRSIRLEF 72

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 9/71 (12%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLK-KHQR------FIEFYDVRDAAKAL 282
           T+ V NL   ++++ L +IF  +G V  ++ T +K K  R      FI F D  DA K +
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKV--VKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60

Query: 283 KEMNGQEIYGK 293
           K +N +E++G+
Sbjct: 61  KALNNKELFGR 71

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

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQ--RFIEFYDVRDAAKALKEMNG 287
           T+      +    S +K +F+  GPV+++     +  Q   FI F ++  A  A++ +NG
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVT-MLSRTVQPHAFITFENLEAAQLAIETLNG 59

Query: 288 QEIYGKHVVIE 298
             + G  + ++
Sbjct: 60  ASVDGNCIKVQ 70

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

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           + V NL    +S  L+ +F+ +G V    E  + K+  F+   +  DA  A+K +NG E 
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVT---ECDVVKNYGFVHMEEEEDAEDAIKALNGYEF 58

Query: 291 YGKHVVIE 298
            GK + +E
Sbjct: 59  MGKRINVE 66

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

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 19/83 (22%), Positives = 43/83 (51%), Gaps = 11/83 (13%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR--------FIEFYDVRDAAKA 281
            +++  L   ++    + +F A GPVK  +   + + +R        F+++    DA +A
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCK---IVRDKRTGYSYGFGFVDYQSAEDAQRA 58

Query: 282 LKEMNGQEIYGKHVVIEFSRPGG 304
           ++ +NG ++  K + + ++RPGG
Sbjct: 59  IRTLNGLQLQNKRIKVAYARPGG 81

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 235 NLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           NL    +   L+ +F  F   KE+R  P ++   F+EF     A  AL+ + G +I
Sbjct: 9   NLPEETTKEMLEMLFNQFPGFKEVRLVP-RRGIAFVEFETEEQATVALQALQGFKI 63

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGP----VKELRETPLKKHQR--FIEFYDVRDAAKALKE 284
           ++V NL + ++ + LKE F   G     VK LR T   K +R  FI +    +A KA   
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLR-TEDGKSRRIAFIGYKTEEEAQKAKDY 61

Query: 285 MNGQEIYGKHVVIEFS 300
            N   I    + +EF+
Sbjct: 62  FNNTYINTSKISVEFA 77

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

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

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 22/70 (31%), Positives = 39/70 (55%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           + V NL +  + + L+  F  +GP++ +          F+EF D RDAA A++E++G+ +
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 66

Query: 291 YGKHVVIEFS 300
            G  V +E S
Sbjct: 67  CGCRVRVELS 76

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

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

 Score = 41.5 bits (97), Expect = 3e-05
 Identities = 20/57 (35%), Positives = 37/57 (64%), Gaps = 3/57 (5%)

Query: 245 LKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR 301
           ++  F+ +G   ++ E  LK    F+EF D+RDA  A+ E+NG+++ G+ V++E +R
Sbjct: 16  VERFFKGYG---KILEVDLKNGYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHAR 69

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

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

 Score = 41.4 bits (97), Expect = 4e-05
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 9/76 (11%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
           T+ V NL   ++   LKE+F+      ++R  P  K        +IEF    +A KAL+E
Sbjct: 5   TLFVKNLPYNITVDELKEVFED---AVDIR-LPSGKDGSSKGIAYIEFKTEAEAEKALEE 60

Query: 285 MNGQEIYGKHVVIEFS 300
             G E+ G+ +V++++
Sbjct: 61  KQGAEVDGRSIVVDYT 76

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

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

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 5/70 (7%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEM 285
           I V +L   + + TL+  F  FG + + R     +T   K   F+ F    DA  A++ M
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 286 NGQEIYGKHV 295
           NGQ + G+ +
Sbjct: 62  NGQWLGGRAI 71

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

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

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 17/59 (28%), Positives = 29/59 (49%)

Query: 84  TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQ 142
           TL++  +   +S+  +R     FGEV+ ++   L      V FYD+R AE A   +  +
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNGR 61

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

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

 Score = 41.4 bits (98), Expect = 5e-05
 Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 10/81 (12%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFG--PVKELR-----ETPLKKHQRFIEFYDVRDAAKAL 282
           T+++  LD   +   + +   A    P+K++R      T   +   F+EF  + DA + +
Sbjct: 4   TLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWM 63

Query: 283 KEMNGQ---EIYGKHVVIEFS 300
             +N      I G+ V + ++
Sbjct: 64  DALNNLDPFVIDGRVVRVSYA 84

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

>gnl|CDD|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 = 41.1 bits (97), Expect = 5e-05
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 7/72 (9%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEM 285
           + V NL    +   L+E+F+AFG + E+     +ET   K   F+ F     A KA  E+
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 286 NGQEIYGK--HV 295
           +G    G+  HV
Sbjct: 62  DGSIFQGRLLHV 73

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

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

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 8/80 (10%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGP---VKEL--RETPLKKHQR---FIEFYDVRDAAKAL 282
           + V NL+  V+   L + F  FGP   VK +  R    ++  R   F+ F +  DA +AL
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 283 KEMNGQEIYGKHVVIEFSRP 302
            E++G+++ G  + + + + 
Sbjct: 64  DELDGKDVMGYELKLGWGKA 83

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

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 9/80 (11%)

Query: 225 GNNQGTIVVF--NLDSGVSSSTLKEIFQAFGPVKEL---RETPLKKHQRFIEFYDVRDAA 279
           G +  T  V+   LD  V+   L   F  +GPV  +   R    ++ Q  + F  V  A 
Sbjct: 2   GKSMPTNCVWLDGLDESVTEQYLTRHFSRYGPVVHVVIDR----QRGQALVFFDKVEAAQ 57

Query: 280 KALKEMNGQEIYGKHVVIEF 299
            A+ EM G+++ G+ + ++F
Sbjct: 58  AAVNEMKGRKLGGRKLQVDF 77

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

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

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 12/78 (15%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR--------FIEFYDVRDAAKA 281
            + V NL   V+   L+E+F   G VK+++      + R         + F    DA +A
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVK----INYDRSGRSEGTADVVFEKREDAERA 57

Query: 282 LKEMNGQEIYGKHVVIEF 299
           +K+ NG  + G+ + +E 
Sbjct: 58  IKQFNGVLLDGQPMQVEL 75

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

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

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 21/82 (25%), Positives = 35/82 (42%), Gaps = 15/82 (18%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRF---------IEFYDVRDAAK 280
           T+ V NL        L+E F+  G V ++R       Q           +EF     A K
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVR-----IAQDDDGRSKGFGHVEFATEEGAQK 55

Query: 281 ALKEMNGQEIYGKHVVIEFSRP 302
           AL E +G+E+ G+ + ++ +  
Sbjct: 56  AL-EKSGEELLGREIRVDLATE 76

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

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

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 11/77 (14%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR---------FIEFYDVRDAAKA 281
           I V NLD  +    L+ IF  FG V+ +R  P K+ ++         F+ F D   A  A
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIR-IPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 282 LKEMNGQEIYGKHVVIE 298
           L ++NG E+ G+ + + 
Sbjct: 62  L-QLNGTELGGRKISVS 77

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

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

 Score = 44.1 bits (104), Expect = 9e-05
 Identities = 26/93 (27%), Positives = 50/93 (53%), Gaps = 13/93 (13%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           V NL   ++   L++IF+ FG +++++     ET   K   FI+F+D  +A +AL+ MNG
Sbjct: 191 VGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNG 250

Query: 288 QEIYGKHVVIEFSRPGGHSKKFFYANSSSCASS 320
            E+ G+ + +      G+++   Y      A++
Sbjct: 251 FELAGRPIKV------GYAQDSTY--LLDAANT 275

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

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

 Score = 40.2 bits (95), Expect = 1e-04
 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 4/63 (6%)

Query: 235 NLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           NL   +    LKE+F  +G +   +    +    K   F+ F +   A KA++E+NG+E+
Sbjct: 8   NLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEV 67

Query: 291 YGK 293
            GK
Sbjct: 68  NGK 70

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|241138 cd12694, RRM2_hnRNPL_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKH--QRFIEFYDVRDAAKALKEMNGQEI 290
           + N    ++   +  I    G V  LR    +K+  Q  +EF  V  A +A   +NG +I
Sbjct: 8   ILNAIYPITVDVIYTICNPHGKV--LRIVIFRKNGVQAMVEFDSVDSAQRAKAALNGADI 65

Query: 291 YGK--HVVIEFSRPG 303
           Y     + IE+++P 
Sbjct: 66  YAGCCTLKIEYAKPD 80

This subfamily corresponds to the RRM2 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 = 86

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

 Score = 39.8 bits (94), Expect = 1e-04
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQR---FIEFYDVRDAAKALKEMNG 287
           V +L   V+ + L EIF   GPV  +R     + +      ++ F +  DA +AL  +N 
Sbjct: 4   VGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNF 63

Query: 288 QEIYGKHVVIEFS 300
             I GK + I +S
Sbjct: 64  DVIKGKPIRIMWS 76

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKE--LRETPLKKHQR--FIEFYDVRDAAKALKEMN 286
           ++V NL  G+    L+++F+AFG + +  L+ T   K ++  F+ +    +A KALK  N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 287 GQEIYGKHVVIEF 299
              I    + +E 
Sbjct: 63  NSFIDTSKITVEI 75

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 25/69 (36%), Positives = 33/69 (47%), Gaps = 5/69 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKE 284
            I + +L  G     LK+ F  FG VK +R     +T   KH  FI+F +   AA A K 
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 285 MNGQEIYGK 293
           MN   + GK
Sbjct: 61  MNNYLLMGK 69

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 43.5 bits (102), Expect = 1e-04
 Identities = 28/131 (21%), Positives = 48/131 (36%), Gaps = 1/131 (0%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG 292
           V NL +  +   +++ F  F P K  R   ++ +  F+ F D  DA KA+ E+NG+E+ G
Sbjct: 238 VRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRDYA-FVHFEDREDAVKAMDELNGKELEG 296

Query: 293 KHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTIYQTRNSDCPPPPLSADPPSYSPRSFA 352
             + +  ++P        Y   +        +          P     A    Y    +A
Sbjct: 297 SEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYA 356

Query: 353 SQAPHFRKKSP 363
                 R   P
Sbjct: 357 PSLHFPRMPGP 367

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

 Score = 41.6 bits (97), Expect = 1e-04
 Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 7/93 (7%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEM 285
           + +  L  G   ++L++ F  FG V +      RET   +   F+ F D   A  A+ EM
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 286 NGQEIYGKHVVIEFS--RPGGHSKKFFYANSSS 316
           +G+E+ G+H+ +  +  RP            S 
Sbjct: 97  DGKELNGRHIRVNPANDRPSAPRAYGGGGGYSG 129

Length = 144

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

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 9/65 (13%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKEMNG 287
           V  +   VS+S LKEIF+  G VK +      K         + F+D+R A KA K++  
Sbjct: 6   VTGVPKDVSTSNLKEIFEKMGDVKGI----FVKKLLSKGIVIVSFHDLRQAIKAYKDLQS 61

Query: 288 QEIYG 292
           +  +G
Sbjct: 62  KRAFG 66

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEM 285
           I V  +        + + F  FG +K L     R T   K    IE+   ++A  A++ +
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 286 NGQEIYGK--HVVIEFSRP 302
           NG+E+ G+   V   F + 
Sbjct: 69  NGKELLGQTISVDWAFVKG 87

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR---FIEFYDVRDAAKALKEMN 286
           TI V  +D  +S   LKE F   G V  +R    ++H     F+EF D   A  AL  ++
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALN-LS 60

Query: 287 GQEIYGKHVVIEFSR 301
           G  + G  + +  S+
Sbjct: 61  GTLLGGHPLRVSPSK 75

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

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

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVK--ELRETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           T+ V NL   +    ++++F  +GP+   +L+  P      FIEF D RDA  A++  +G
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 288 QEIYGKHVVIE 298
            +  G+ + +E
Sbjct: 61  YDFDGQRLRVE 71

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

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
           T+ V NLD+ V+   L E+F   GP++ ++  P   + +     F+ F        A++ 
Sbjct: 3   TLFVGNLDARVTEEILYELFLQAGPLEGVK-IPKDPNGKPKSFAFVTFKHEVSVPYAIQL 61

Query: 285 MNGQEIYGKHVVIE 298
           +NG  ++G+ + I+
Sbjct: 62  LNGIRLFGRELRIK 75

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

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 17/67 (25%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           V NL   +SS  L ++F  +G ++++R   T   +   F+ + D+ DA  A   ++G  +
Sbjct: 7   VRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSGFNV 66

Query: 291 YGKHVVI 297
             +++V+
Sbjct: 67  ANRYLVV 73

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|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 = 39.1 bits (92), Expect = 2e-04
 Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 3/69 (4%)

Query: 235 NLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK--EMNGQEIYG 292
           NL   V+ S L  +   FG V  +      K+Q  +E   V  A   +         I G
Sbjct: 6   NLPPDVTESDLIALVSPFGKVTNVLLLR-GKNQALVEMDSVESAKSMVDYYLTVPALIRG 64

Query: 293 KHVVIEFSR 301
           + V I++S 
Sbjct: 65  RRVYIQYSN 73

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 8/67 (11%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPV---KELRETPLKKHQR---FIEFYDVRDAAKALKEMN 286
           V NLD  +    L+E F  FG +   K + +   K   +   F+ F    +A KA+ EMN
Sbjct: 6   VKNLDDSIDDERLREEFSPFGTITSAKVMTDE--KGRSKGFGFVCFSSPEEATKAVTEMN 63

Query: 287 GQEIYGK 293
           G+ I GK
Sbjct: 64  GRIIGGK 70

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

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 230 TIVVFNLDSGVSSSTLKE----IFQAFGPVKEL--RETPLKKHQRFIEFYDVRDAAKALK 283
           TI + NL+  V    LK+    IF  FG + ++   +T   + Q F+ F D+  A  AL+
Sbjct: 1   TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALR 60

Query: 284 EMNGQEIYGKHVVIEFSR 301
            M G   Y K + I +S+
Sbjct: 61  SMQGFPFYDKPMRIAYSK 78

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
           T+ V  L   V    L E F   G V+++R    +  +R     ++EFYD      AL  
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-G 59

Query: 285 MNGQEIYGKHVVI 297
           + GQ + G+ +++
Sbjct: 60  LTGQRLLGQPIMV 72

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

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

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 4/64 (6%)

Query: 231 IVVFNLDSG-VSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           + V NL++  VS   L+EIF  +G +  +    L K   F++F +  DA  A+   NG+E
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGIS---LHKGYGFVQFDNEEDARAAVAGENGRE 59

Query: 290 IYGK 293
           I G+
Sbjct: 60  IAGQ 63

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 8/75 (10%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
            I V NL   +    ++++F  +GP+K +    LK  +R     F+EF D RDA  A++ 
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAID---LKNRRRGPPFAFVEFEDPRDAEDAVRG 57

Query: 285 MNGQEIYGKHVVIEF 299
            +G +  G  + +EF
Sbjct: 58  RDGYDFDGYRLRVEF 72

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

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

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 5/75 (6%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEM 285
           + V N+    +   LK+IF   GPV        RET   K   F E+ D   A  A++ +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 286 NGQEIYGKHVVIEFS 300
           NG E+ G+ + ++ +
Sbjct: 61  NGYELNGRQLRVDNA 75

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

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

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 5/63 (7%)

Query: 240 VSSSTLKEIFQAFGPVK--ELRETPLKKHQR---FIEFYDVRDAAKALKEMNGQEIYGKH 294
           +S   +K +F+AFG +K   L   P     +   FIE+ + + A  A+  MN  ++ G+ 
Sbjct: 12  LSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQQ 71

Query: 295 VVI 297
           + +
Sbjct: 72  LRV 74

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

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 4/71 (5%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKE 284
           G I + NLD  + +  L + F AFG +   +    E    K   F+ F     A +A+++
Sbjct: 3   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEK 62

Query: 285 MNGQEIYGKHV 295
           +NG  +  K V
Sbjct: 63  VNGMLLNDKKV 73

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

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

 Score = 42.5 bits (100), Expect = 3e-04
 Identities = 28/126 (22%), Positives = 50/126 (39%), Gaps = 19/126 (15%)

Query: 190 MNSYAPVLPPPARGLVAGRPVWAQFIVPTC-----NAVPDGNNQGTIVVF---NLDSGVS 241
             ++A  +P      + G+P +  +          N+  D      ++     N    ++
Sbjct: 54  CVNFATSVPI----YIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPIT 109

Query: 242 SSTLKEIFQAFGPVKELRETPLKKH---QRFIEFYDVRDAAKALKEMNGQEIYGK--HVV 296
              L +IF  +G V  LR     K+   Q  +EF  V  A  A   +NG +IY     + 
Sbjct: 110 LDVLYQIFNPYGKV--LRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLK 167

Query: 297 IEFSRP 302
           IE+++P
Sbjct: 168 IEYAKP 173

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

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 2/67 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           T+    + SG++   +++ F  FG + E+R  P K +  FI F     AA A+  +NG  
Sbjct: 2   TVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEKGYS-FIRFSTHESAAHAIVSVNGTT 60

Query: 290 IYGKHVV 296
           I G HVV
Sbjct: 61  IEG-HVV 66

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

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

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 11/49 (22%), Positives = 29/49 (59%), Gaps = 5/49 (10%)

Query: 245 LKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
           ++ +F+ +G ++E+     ++T   K   F++F    +A KA++ ++G+
Sbjct: 16  VRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGK 64

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

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 9/78 (11%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-------FIEFYDVRDAAKALK 283
           I+V N+    +   L+E+F  FG +K +R  P K           F++F   +DA +A K
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVR-LPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61

Query: 284 EM-NGQEIYGKHVVIEFS 300
            + +   +YG+ +V+E++
Sbjct: 62  ALCHSTHLYGRRLVLEWA 79

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 38.9 bits (90), Expect = 4e-04
 Identities = 25/85 (29%), Positives = 45/85 (52%), Gaps = 7/85 (8%)

Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDV 275
           A PD N    + VF L    +   L+E+F  +GP+ ++     ++ +R     F+ F +V
Sbjct: 4   ANPDPN--CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 61

Query: 276 RDAAKALKEMNGQEIYGKHVVIEFS 300
            DA +A +  NG E+ G+ + ++FS
Sbjct: 62  DDAKEAKERANGMELDGRRIRVDFS 86

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

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

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 23/88 (26%), Positives = 37/88 (42%), Gaps = 23/88 (26%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQR---------------- 268
           T+ V NL        LK++F+ FGP++ +R         K  ++                
Sbjct: 2   TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61

Query: 269 -FIEFYDVRDAAKALKEMNGQEIYGKHV 295
            ++ F +   A KALK +NG E  G H+
Sbjct: 62  AYVVFKEEESAEKALK-LNGTEFEGHHI 88

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 41.5 bits (97), Expect = 5e-04
 Identities = 27/91 (29%), Positives = 46/91 (50%), Gaps = 6/91 (6%)

Query: 224 DGNNQGTIVVFN-LDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRD 277
           D NN GT ++ N L   ++   L  +F+  GP+   R     +T       F++F    D
Sbjct: 102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEAD 161

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPGGHSKK 308
           + +A+K +NG  +  K + + ++RPGG S K
Sbjct: 162 SQRAIKNLNGITVRNKRLKVSYARPGGESIK 192

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

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

 Score = 41.7 bits (98), Expect = 5e-04
 Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 7/73 (9%)

Query: 225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAK 280
           G N   + V NLD  V+   L+E+F   G +   +    E  + +   F+ F +  +A +
Sbjct: 285 GVN---LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANR 341

Query: 281 ALKEMNGQEIYGK 293
           A+ EM+G+ + GK
Sbjct: 342 AVTEMHGRMLGGK 354

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

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 22/70 (31%), Positives = 36/70 (51%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           + V NL +G     L+  F  +GP++ +          F+EF D RDA  A++ ++G+ I
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 61

Query: 291 YGKHVVIEFS 300
            G  V +E S
Sbjct: 62  CGSRVRVELS 71

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

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

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEM 285
           + +++L +  +   L ++F  FG V   +      T   K   F+ + +   A  A+K M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 286 NGQEIYGKHVVIE 298
           NG ++ GK + ++
Sbjct: 61  NGFQVGGKRLKVQ 73

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

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

 Score = 38.1 bits (89), Expect = 6e-04
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 240 VSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH 294
           ++   L+ +F+A GP++       R T       F+++ D  DA KA+  +NG EI  K 
Sbjct: 12  MTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKR 71

Query: 295 VVIEF 299
           + + +
Sbjct: 72  LKVSY 76

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

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

 Score = 37.9 bits (88), Expect = 6e-04
 Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALK 283
           G + +  L    +  +L+++F  +G + E+     RET   +   F+ F +  DA  A+ 
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 284 EMNGQEIYGKHV 295
            MNG+ + G+ +
Sbjct: 61  AMNGKSVDGRQI 72

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

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

 Score = 37.7 bits (87), Expect = 6e-04
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 11/75 (14%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGP-----VKELRETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           V NL    S  T+K+ F  F P     VK++R+        F+ F    DA  A+  +NG
Sbjct: 6   VRNLMIETSEDTIKKTFGQFNPGCVERVKKIRDYA------FVHFTSREDAVHAMNNLNG 59

Query: 288 QEIYGKHVVIEFSRP 302
            E+ G  + +  ++P
Sbjct: 60  TELEGSCIEVTLAKP 74

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

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 38.0 bits (88), Expect = 6e-04
 Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 6/79 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEM 285
           T+ V  L    +  TLKE F   G +       R+T   K   F++F    DA  A + M
Sbjct: 2   TLFVKGLSEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 286 NGQEIYGKHVVIEFSRPGG 304
              EI G  V ++F++P G
Sbjct: 60  EDGEIDGNKVTLDFAKPKG 78

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

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

 Score = 37.8 bits (88), Expect = 7e-04
 Identities = 18/76 (23%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKE--LRETPLKKHQR--FIEFYDVRDAAKALKEM 285
           T+ V NL+  ++   L+  F+ +G V++  ++  P  +     F++F ++  A +A   M
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 286 NGQEIYGKHVVIEFSR 301
           +GQ I    + I + +
Sbjct: 64  SGQYIGRNQIKIGYGK 79

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

>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 20/58 (34%), Positives = 37/58 (63%), Gaps = 7/58 (12%)

Query: 244 TLKEIFQAFGPVKELR---ETPLKKHQ--RFIEFYDVRDAAK-ALKEMNGQEIYGKHV 295
           T+++ F  FGP+K +    +    KH+   F+E Y+V +AA+ AL++MNG  + G+++
Sbjct: 16  TIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVE-YEVPEAAQLALEQMNGVMLGGRNI 72

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|241140 cd12696, RRM3_PTBP2, RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)

 Score = 38.5 bits (89), Expect = 8e-04
 Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 229 GTIVVFNL-DSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNG 287
             ++V NL +  V+  +L  +F  +G V+ ++    KK    I+  D   +  A+  +NG
Sbjct: 14  TVLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQLAMSHLNG 73

Query: 288 QEIYGKHVVIEFSR 301
           Q++YGK + +  S+
Sbjct: 74  QKMYGKIIRVTLSK 87

This subgroup corresponds to the RRM3 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 107

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

 Score = 37.6 bits (87), Expect = 8e-04
 Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 7/78 (8%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR------FIEFYDVRDAAKALK 283
           ++ V N+     S  L+  F  +GP+ ++   PL  + R      +++F DVRDA  AL 
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVY-VPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 284 EMNGQEIYGKHVVIEFSR 301
            ++ + I G+ + I+F++
Sbjct: 61  NLDRKWICGRQIEIQFAQ 78

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 37.6 bits (88), Expect = 9e-04
 Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 5/68 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRET--PLKKHQR---FIEFYDVRDAAKALKE 284
           T+ + NL    +   LKE+F  FG VK  R     L  H +   F++F     A K L+ 
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

Query: 285 MNGQEIYG 292
            +  E  G
Sbjct: 62  ADNAEDSG 69

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 5/65 (7%)

Query: 231 IVVFNLDSGVSSSTLKEIFQ---AFGPVKELRETPL--KKHQRFIEFYDVRDAAKALKEM 285
           I V +L + V+   L   F    +F   K +R+      K   F+ F D  D  KA+KEM
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 286 NGQEI 290
           NG+ +
Sbjct: 69  NGKYV 73

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

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 10/75 (13%)

Query: 235 NLDSGVSSSTLKEIFQAFG----PVKELR--ETPLKKHQRFIEF--YDVRDAAKALKEMN 286
           NLD  V    L + F AFG      K +R  +T   K   FI +  ++  DAA  ++ MN
Sbjct: 8   NLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA--IEAMN 65

Query: 287 GQEIYGKHVVIEFSR 301
           GQ +  + + + ++ 
Sbjct: 66  GQYLCNRPITVSYAF 80

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

>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 235 NLDSGVSSSTLKEIF-QAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEM-NGQEIYG 292
           N+   V+   LKE+F Q  G VK  +  P  +    I+   V +A +AL  + N Q    
Sbjct: 6   NIPPSVTEEDLKELFTQTGGTVKAFKFFPKDRKMALIQMGSVEEAIEALIALHNYQLSES 65

Query: 293 KHVVIEFSRP 302
            H+ + FS+ 
Sbjct: 66  SHLRVSFSKS 75

This subfamily corresponds to the RRM4 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 18/79 (22%), Positives = 34/79 (43%), Gaps = 10/79 (12%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR----FIEFYDVRDAAKALKEM 285
           T+ V NL    +   L+++F      + L+   +         F+EF DV  A +AL  +
Sbjct: 4   TLFVANLGPNTTEEELRQLFSRQPGFRRLK---MHNKGGGPVCFVEFEDVSFATQALNSL 60

Query: 286 NGQEIYGKH---VVIEFSR 301
            G  +       + IE+++
Sbjct: 61  QGAVLSSSDRGGIRIEYAK 79

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

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 3/73 (4%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR---FIEFYDVRDAAKALKEMN 286
           +I V  L   V+   L E F   G + E+       H     FI+F   + AA+A++  N
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESEN 64

Query: 287 GQEIYGKHVVIEF 299
              +  K + +++
Sbjct: 65  HSMLKNKTMHVQY 77

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|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 20/92 (21%), Positives = 34/92 (36%), Gaps = 13/92 (14%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRD------- 277
            IVV+      S   +K  F +FG + E+R      T +      I++Y           
Sbjct: 4   EIVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPDRAAK 63

Query: 278 -AAKALKEMNGQEIYGKHVVIEFSRPGGHSKK 308
            A KA+++     I G    +E +      +K
Sbjct: 64  AALKAVRKAQDCRIGGAEFKVELNPNERKLEK 95

This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 110

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

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 9/90 (10%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKE 284
           G I V NLD  V +  L + F  FG +   +    E    +   F+ F     A  A+++
Sbjct: 89  GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQK 148

Query: 285 MNG-----QEIYGKHVVIEFSRPGGHSKKF 309
           +NG     +E+Y    + +  R     KKF
Sbjct: 149 VNGMLLNDKEVYVGRFIKKHEREAAPLKKF 178

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

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKE--LRETPLKKHQR---FIEFYDVRDAAKALKE 284
           T+ V NL   V+   L + F    P+K   +   P     R   F+ F  + DA +AL +
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +  ++++G+ + ++ +  
Sbjct: 61  LKNKKLHGRILRLDIAER 78

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

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 17/68 (25%), Positives = 25/68 (36%), Gaps = 1/68 (1%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           ++ V     G S   L + F AFGPV  +     K     +EF       K L E     
Sbjct: 4   SVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDSKEGVDKVLSE-PQHT 62

Query: 290 IYGKHVVI 297
           + G  + +
Sbjct: 63  LNGHRLRV 70

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|241208 cd12764, RRM2_SRSF4, RNA recognition motif 2 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 19/65 (29%), Positives = 34/65 (52%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           ++V NL S  S   LK+  +  G V        +K++  IEF    D  +AL++++G E+
Sbjct: 3   LIVENLSSRCSWQDLKDYMRQAGEVTYADAHKGRKNEGVIEFRSYSDMKRALEKLDGTEV 62

Query: 291 YGKHV 295
            G+ +
Sbjct: 63  NGRKI 67

This subgroup corresponds to the RRM2 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4), a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFRS4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, SRSF4 activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 9/76 (11%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR------FIEFYDVRDAAKAL 282
           G + + NL    +   L+++F  +GP+ E+   P+ K  +      F+ +     A KA 
Sbjct: 3   GRLFIRNLAYTCTEEDLEKLFSKYGPLSEV-HLPIDKLTKKPKGFAFVTYMIPEHAVKAF 61

Query: 283 KEMNGQEIYGK--HVV 296
            E++G    G+  H++
Sbjct: 62  AELDGTVFQGRLLHLL 77

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 11/77 (14%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGP-----VKELRETPLKKHQRFIEFYDVRDAAKALKEM 285
           + V NL    +  T+K  F  F P     VK+LR+        F+ F++  DA  A+  M
Sbjct: 4   LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRDYA------FVHFFNREDAVAAMSVM 57

Query: 286 NGQEIYGKHVVIEFSRP 302
           NG+ I G  + +  ++P
Sbjct: 58  NGKCIDGASIEVTLAKP 74

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

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

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 2/67 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           T+    + SG++   +++ F  FG + E+R  P K +  F+ F     AA A+  +NG  
Sbjct: 2   TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYS-FVRFNSHESAAHAIVSVNGTT 60

Query: 290 IYGKHVV 296
           I G HVV
Sbjct: 61  IEG-HVV 66

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 39.1 bits (91), Expect = 0.003
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRD 277
               +  T+ V  L        L E F   G V++++    +  +R     ++EFYDV  
Sbjct: 84  EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVES 143

Query: 278 AAKALKEMNGQEIYGKHVVIEFS 300
             KAL  + GQ + G+ ++++ S
Sbjct: 144 VIKAL-ALTGQMLLGRPIIVQSS 165

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

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

 Score = 39.0 bits (91), Expect = 0.004
 Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR----FIEFYDVRDAAKALKEMNGQ 288
           V NLD  V+   L+E+F  FG +           +     F+ F    DAAKA++EMNG+
Sbjct: 183 VKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGK 242

Query: 289 EI 290
           +I
Sbjct: 243 KI 244

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

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           VF L    +   L+E+F  +GP+  +     + T   +   F+ F  + D+ +A++  NG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 288 QEIYGKHVVIEFS 300
            E+ G+ + +++S
Sbjct: 64  MELDGRRIRVDYS 76

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	408
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.96
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.96
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.96
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.95
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.94
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.93
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.93
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.92
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.91
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.91
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.9
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.9
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.89
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.88
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.87
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.83
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.82
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.82
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.82
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.8
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.8
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.8
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.77
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.77
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.76
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.75
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.74
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.74
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.71
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.7
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.68
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.68
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.67
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.64
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.63
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.6
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.58
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.57
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.54
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.52
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.52
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.52
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.5
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.49
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.49
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.48
KOG0122	270	consensus Translation initiation factor 3, subunit	99.48
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.48
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.46
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.45
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.43
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.42
PLN03120	260	nucleic acid binding protein; Provisional	99.42
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.42
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.41
PLN03120	260	nucleic acid binding protein; Provisional	99.41
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.4
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.4
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.39
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.39
PLN03213	759	repressor of silencing 3; Provisional	99.38
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.38
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.37
KOG0122	270	consensus Translation initiation factor 3, subunit	99.36
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.33
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.33
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.33
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.32
PLN03121	243	nucleic acid binding protein; Provisional	99.32
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.32
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.31
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.3
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.3
PLN03213	759	repressor of silencing 3; Provisional	99.3
smart00362	72	RRM_2 RNA recognition motif.	99.29
smart00362	72	RRM_2 RNA recognition motif.	99.28
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.28
PLN03121	243	nucleic acid binding protein; Provisional	99.26
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.25
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.25
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.21
smart00360	71	RRM RNA recognition motif.	99.2
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.19
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.19
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.18
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.17
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.17
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.17
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.16
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.15
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.13
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.13
smart00360	71	RRM RNA recognition motif.	99.12
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.12
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.12
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.08
smart00361	70	RRM_1 RNA recognition motif.	99.08
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.05
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.04
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	99.03
KOG0226	290	consensus RNA-binding proteins [General function p	99.03
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.01
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.0
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.89
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.89
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.88
smart00361	70	RRM_1 RNA recognition motif.	98.86
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.83
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.83
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.82
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.8
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.73
KOG4210	285	consensus Nuclear localization sequence binding pr	98.7
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.7
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.66
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.61
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.6
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.56
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.55
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.52
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.51
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.44
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.39
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.38
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.34
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.34
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.34
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.3
KOG0151	877	consensus Predicted splicing regulator, contains R	98.3
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.28
KOG0151	877	consensus Predicted splicing regulator, contains R	98.28
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.23
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.22
KOG0226	290	consensus RNA-binding proteins [General function p	98.18
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.17
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.17
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.1
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.07
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.04
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.94
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.94
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.87
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.8
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.58
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.56
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.54
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.43
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.24
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.15
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.13
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.13
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.12
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.07
KOG2314	698	consensus Translation initiation factor 3, subunit	96.99
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.97
KOG3152	278	consensus TBP-binding protein, activator of basal	96.92
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.89
KOG2314	698	consensus Translation initiation factor 3, subunit	96.86
KOG3152	278	consensus TBP-binding protein, activator of basal	96.85
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.84
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.68
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.67
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.57
KOG4210	285	consensus Nuclear localization sequence binding pr	96.5
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.47
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.4
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.28
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.12
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.06
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.04
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.0
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.9
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.87
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.62
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.57
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	95.54
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.39
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.36
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.25
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.0
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.92
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.46
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.42
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.41
PF07145	18	PAM2: Ataxin-2 C-terminal region; InterPro: IPR009	94.34
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.98
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.75
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	93.71
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.62
KOG2591	684	consensus c-Mpl binding protein, contains La domai	93.4
KOG2135	526	consensus Proteins containing the RNA recognition	92.84
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	92.72
KOG2068	327	consensus MOT2 transcription factor [Transcription	92.59
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	92.41
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.01
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	90.99
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	90.91
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	90.83
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	90.82
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	90.09
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	89.49
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	89.07
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	88.39
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	87.78
KOG2318	650	consensus Uncharacterized conserved protein [Funct	87.36
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	87.19
KOG2068	327	consensus MOT2 transcription factor [Transcription	85.28
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	81.97

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=1.3e-29  Score=242.40  Aligned_cols=163  Identities=18%  Similarity=0.318  Sum_probs=136.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      .....++|||+|||+++||++|+++|+.||+|++|+|++     +++|||||+|.++++|++|++.|||..|.  ++  .
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~--gr--~  178 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVR--NK--R  178 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccC--Cc--e
Confidence            445678999999999999999999999999999999875     45899999999999999999999998875  55  3


Q ss_pred             eeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEE
Q 046223          153 LKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIV  232 (408)
Q Consensus       153 ~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~  232 (408)
                      |++.|+...                                                             .......+||
T Consensus       179 i~V~~a~p~-------------------------------------------------------------~~~~~~~~lf  197 (346)
T TIGR01659       179 LKVSYARPG-------------------------------------------------------------GESIKDTNLY  197 (346)
T ss_pred             eeeeccccc-------------------------------------------------------------ccccccceeE
Confidence            444332200                                                             0001136899


Q ss_pred             EcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEEecCCCC
Q 046223          233 VFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG--KHVVIEFSRPGGH  305 (408)
Q Consensus       233 V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~a~~~~~  305 (408)
                      |+||+..+|+++|+++|++||+|+.++     .+++.+|||||+|.+.++|++|++.||+..+.|  +.|+|.+++....
T Consensus       198 V~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       198 VTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             EeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcccc
Confidence            999999999999999999999998872     367778999999999999999999999998876  7899999987643

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).

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

Probab=99.97  E-value=2.1e-29  Score=234.72  Aligned_cols=217  Identities=23%  Similarity=0.333  Sum_probs=164.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .....||||.||.|+.|+||.-+|++.|+|.+++++.     .+||||||.|.+.++|++||+.||+.+|. .||.|.+-
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir-~GK~igvc  159 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIR-PGKLLGVC  159 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCcccc-CCCEeEEE
Confidence            3567899999999999999999999999999999886     56999999999999999999999999987 56644444


Q ss_pred             ccccCccccccCCCCCCCcccCCCCh-----hHHHH------HHhhhhccCCCCCC-------------------CcCCC
Q 046223          155 NPYSSGLMLMNNDNNNNNLATGCYDN-----QVVAE------SLMIMNSYAPVLPP-------------------PARGL  204 (408)
Q Consensus       155 ~~~s~~~s~~~~~~~~~~~~~~~~~~-----~~~~~------~~~~~~~~~~~~~~-------------------~~~~~  204 (408)
                      +..           .+.+++.+.+..     +++.+      .+..++.|..+...                   ..+.+
T Consensus       160 ~Sv-----------an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl  228 (506)
T KOG0117|consen  160 VSV-----------ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKL  228 (506)
T ss_pred             Eee-----------ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhc
Confidence            322           245566555542     22222      12223333333221                   12334


Q ss_pred             CCCCC-ccccccCCcCCCCCC------CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHH
Q 046223          205 VAGRP-VWAQFIVPTCNAVPD------GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRD  277 (408)
Q Consensus       205 ~~g~~-~~~~~~~p~~~~~~~------~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~  277 (408)
                      ..|+. +|.+.....|+....      ....+.|||+||+.++|+|.|+++|.+||.|+.|+   +-+.||||.|.+.++
T Consensus       229 ~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVk---k~rDYaFVHf~eR~d  305 (506)
T KOG0117|consen  229 MPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVK---KPRDYAFVHFAERED  305 (506)
T ss_pred             cCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEee---cccceeEEeecchHH
Confidence            44443 355555555544221      23467899999999999999999999999999986   347899999999999


Q ss_pred             HHHHHHHhCCceeCCeEEEEEEecCCCCCCCccc
Q 046223          278 AAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFY  311 (408)
Q Consensus       278 A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~  311 (408)
                      |.+|++.+||++|+|..|.|.+|+|...++..+.
T Consensus       306 avkAm~~~ngkeldG~~iEvtLAKP~~k~k~~r~  339 (506)
T KOG0117|consen  306 AVKAMKETNGKELDGSPIEVTLAKPVDKKKKERK  339 (506)
T ss_pred             HHHHHHHhcCceecCceEEEEecCChhhhccchh
Confidence            9999999999999999999999999876655543

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.96  E-value=8.1e-29  Score=241.24  Aligned_cols=76  Identities=24%  Similarity=0.402  Sum_probs=71.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      .+|||+||+.++++++|+++|++||.|.+++     .++.++|||||+|.+.++|.+|++.|||..|+||.|+|.|+..+
T Consensus       270 ~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       270 YCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNK  349 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCC
Confidence            4799999999999999999999999999983     37889999999999999999999999999999999999999776


Q ss_pred             C
Q 046223          304 G  304 (408)
Q Consensus       304 ~  304 (408)
                      .
T Consensus       350 ~  350 (352)
T TIGR01661       350 A  350 (352)
T ss_pred             C
Confidence            5

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

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

Probab=99.96  E-value=4.5e-28  Score=243.32  Aligned_cols=170  Identities=17%  Similarity=0.307  Sum_probs=137.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ...++|||+||+++++|++|+++|++||+|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  ||.|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~--GR~IkV~  182 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLG--GRNIKVG  182 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEe--cceeeec
Confidence            3567899999999999999999999999999999875     57999999999999999999999998876  6743333


Q ss_pred             ccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEc
Q 046223          155 NPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVF  234 (408)
Q Consensus       155 ~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~  234 (408)
                        .....  .                                   .      .......       .........+|||+
T Consensus       183 --rp~~~--p-----------------------------------~------a~~~~~~-------~~~~~~~~~rLfVg  210 (612)
T TIGR01645       183 --RPSNM--P-----------------------------------Q------AQPIIDM-------VQEEAKKFNRIYVA  210 (612)
T ss_pred             --ccccc--c-----------------------------------c------ccccccc-------ccccccccceEEee
Confidence              11100  0                                   0      0000000       00111234799999


Q ss_pred             CCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          235 NLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       235 nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ||+.++++++|+++|+.||.|.+++     .++.++|||||+|.+.++|.+|++.|||..|+|+.|+|.++..+
T Consensus       211 nLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       211 SVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             cCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCC
Confidence            9999999999999999999999883     35678999999999999999999999999999999999999764

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.

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

Probab=99.96  E-value=9e-27  Score=233.73  Aligned_cols=210  Identities=19%  Similarity=0.263  Sum_probs=145.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ...+|||+|||.+++|++|+++|++||.|.+|++++    +++|||||+|.+.++|++||+.||+..|. .++.+  .+.
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~-~Gr~l--~V~  133 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIR-PGRLL--GVC  133 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeec-CCccc--ccc
Confidence            357999999999999999999999999999999875    57999999999999999999999998874 23422  222


Q ss_pred             ccCccccccCCCCCCCcccCCCChhHHHHHHhh-hhc----------cCCCCCC-C------------------------
Q 046223          157 YSSGLMLMNNDNNNNNLATGCYDNQVVAESLMI-MNS----------YAPVLPP-P------------------------  200 (408)
Q Consensus       157 ~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~----------~~~~~~~-~------------------------  200 (408)
                      .+.         .+.++..+.+......+.+.. ...          +..+... .                        
T Consensus       134 ~S~---------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~  204 (578)
T TIGR01648       134 ISV---------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMP  204 (578)
T ss_pred             ccc---------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhc
Confidence            211         123333444332222221111 000          0000000 0                        


Q ss_pred             cCCCCCCCCccccccCCcCCCCC-CCCCCceEEEcCCCCCCcHHHHHHHHhcC--CCceeeccCCCCccEEEEEECCHHH
Q 046223          201 ARGLVAGRPVWAQFIVPTCNAVP-DGNNQGTIVVFNLDSGVSSSTLKEIFQAF--GPVKELRETPLKKHQRFIEFYDVRD  277 (408)
Q Consensus       201 ~~~~~~g~~~~~~~~~p~~~~~~-~~~~~~~l~V~nLp~~~t~~~L~~~F~~~--G~v~~v~~~~~~~g~afV~F~~~~~  277 (408)
                      .+-.+.|+.+.+....+.....+ .....++|||+||+.++++++|+++|++|  |.|++|.   ..++||||+|++.++
T Consensus       205 gki~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~---~~rgfAFVeF~s~e~  281 (578)
T TIGR01648       205 GRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVK---KIRDYAFVHFEDRED  281 (578)
T ss_pred             cceEecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEE---eecCeEEEEeCCHHH
Confidence            00011222222222222221111 12345789999999999999999999999  9999986   347899999999999


Q ss_pred             HHHHHHHhCCceeCCeEEEEEEecCCCC
Q 046223          278 AAKALKEMNGQEIYGKHVVIEFSRPGGH  305 (408)
Q Consensus       278 A~~A~~~l~g~~~~g~~l~v~~a~~~~~  305 (408)
                      |++|++.|||.+|+|+.|+|.|+++...
T Consensus       282 A~kAi~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       282 AVKAMDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             HHHHHHHhCCCEECCEEEEEEEccCCCc
Confidence            9999999999999999999999988654

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

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

Probab=99.95  E-value=7.5e-28  Score=211.03  Aligned_cols=176  Identities=21%  Similarity=0.375  Sum_probs=143.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ..-.|||+.|..+++.++|++.|.+||+|.+.+++|     ++||||||.|.+.++|++||..|||+-|.  +|  .||-
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG--~R--~IRT  136 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLG--RR--TIRT  136 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeec--cc--eeec
Confidence            355799999999999999999999999999999988     78999999999999999999999998875  66  4565


Q ss_pred             cccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCc--cccccCCcCCCCCCCCCCceEEE
Q 046223          156 PYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPV--WAQFIVPTCNAVPDGNNQGTIVV  233 (408)
Q Consensus       156 ~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~--~~~~~~p~~~~~~~~~~~~~l~V  233 (408)
                      .|+..+                ..                        ..++.++  ...+       .....++++|||
T Consensus       137 NWATRK----------------p~------------------------e~n~~~ltfdeV~-------NQssp~NtsVY~  169 (321)
T KOG0148|consen  137 NWATRK----------------PS------------------------EMNGKPLTFDEVY-------NQSSPDNTSVYV  169 (321)
T ss_pred             cccccC----------------cc------------------------ccCCCCccHHHHh-------ccCCCCCceEEe
Confidence            555422                11                        0011111  0000       011234699999


Q ss_pred             cCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCCCCC
Q 046223          234 FNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKK  308 (408)
Q Consensus       234 ~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~  308 (408)
                      |||+..+||++|++.|+.||.|.+||.. +.+||+||.|++.|+|.+||..+||++++|..+++.|-+.......
T Consensus       170 G~I~~~lte~~mr~~Fs~fG~I~EVRvF-k~qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~~~  243 (321)
T KOG0148|consen  170 GNIASGLTEDLMRQTFSPFGPIQEVRVF-KDQGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDGIN  243 (321)
T ss_pred             CCcCccccHHHHHHhcccCCcceEEEEe-cccceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCCCC
Confidence            9999999999999999999999999854 6799999999999999999999999999999999999987764433

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

Probab=99.94  E-value=1.3e-26  Score=215.18  Aligned_cols=168  Identities=21%  Similarity=0.361  Sum_probs=137.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      .+.+.-.||||.||..++|.||+++|++||.|.+|.+++     .++|||||.|.+.++|.+|+.+|++++.. -|-...
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktl-pG~~~p  108 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTL-PGMHHP  108 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhccccc-CCCCcc
Confidence            345667899999999999999999999999999999987     45999999999999999999999986543 222233


Q ss_pred             eeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEE
Q 046223          153 LKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIV  232 (408)
Q Consensus       153 ~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~  232 (408)
                      +.+-|++..                                                            .+.-...++||
T Consensus       109 vqvk~Ad~E------------------------------------------------------------~er~~~e~KLF  128 (510)
T KOG0144|consen  109 VQVKYADGE------------------------------------------------------------RERIVEERKLF  128 (510)
T ss_pred             eeecccchh------------------------------------------------------------hhccccchhhh
Confidence            444332200                                                            00001248899


Q ss_pred             EcCCCCCCcHHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHHhCCc-eeCC--eEEEEEEecCCCC
Q 046223          233 VFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQ-EIYG--KHVVIEFSRPGGH  305 (408)
Q Consensus       233 V~nLp~~~t~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~-~~~g--~~l~v~~a~~~~~  305 (408)
                      ||-|+..+||.|++++|++||.|+++    ...+.+||||||+|.+.|.|..|++.|||. ++.|  ..|.|+||++++.
T Consensus       129 vg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkd  208 (510)
T KOG0144|consen  129 VGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKD  208 (510)
T ss_pred             hhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCC
Confidence            99999999999999999999999999    367789999999999999999999999997 5555  5899999998765


Q ss_pred             C
Q 046223          306 S  306 (408)
Q Consensus       306 ~  306 (408)
                      +
T Consensus       209 k  209 (510)
T KOG0144|consen  209 K  209 (510)
T ss_pred             c
Confidence            5

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

Probab=99.94  E-value=2e-25  Score=224.96  Aligned_cols=197  Identities=20%  Similarity=0.262  Sum_probs=140.2

Q ss_pred             CCCCCCEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           78 STGPTRTLVLSYVPG-DVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~-~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ...++.+|||+||+. .+|+++|+++|+.||.|..|++++..+|||||+|.+.++|++|++.|||..|.  |+  .|++.
T Consensus       271 ~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~--g~--~l~v~  346 (481)
T TIGR01649       271 GGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLF--GK--PLRVC  346 (481)
T ss_pred             CCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEC--Cc--eEEEE
Confidence            345788999999998 69999999999999999999999877899999999999999999999998876  66  45555


Q ss_pred             ccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcC-CCCCCCCCCceEEEcC
Q 046223          157 YSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTC-NAVPDGNNQGTIVVFN  235 (408)
Q Consensus       157 ~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~-~~~~~~~~~~~l~V~n  235 (408)
                      ++....+.....       +..++...    . ...+..  ....           .+..+.. ....-...+.+|||+|
T Consensus       347 ~s~~~~~~~~~~-------~~~~~~~~----~-~~d~~~--~~~~-----------r~~~~~~~~~~~~~~ps~~L~v~N  401 (481)
T TIGR01649       347 PSKQQNVQPPRE-------GQLDDGLT----S-YKDYSS--SRNH-----------RFKKPGSANKNNIQPPSATLHLSN  401 (481)
T ss_pred             EcccccccCCCC-------CcCcCCCc----c-cccccC--Cccc-----------cCCCcccccccccCCCCcEEEEec
Confidence            554332111000       00000000    0 000000  0000           0000000 0000112458999999


Q ss_pred             CCCCCcHHHHHHHHhcCCC--ceeeccC---CCCccEEEEEECCHHHHHHHHHHhCCceeCCeE------EEEEEecCC
Q 046223          236 LDSGVSSSTLKEIFQAFGP--VKELRET---PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH------VVIEFSRPG  303 (408)
Q Consensus       236 Lp~~~t~~~L~~~F~~~G~--v~~v~~~---~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~------l~v~~a~~~  303 (408)
                      ||.++++++|+++|+.||.  |..++..   ...+++|||+|.+.++|.+|+..|||..|.|+.      |+|.|++++
T Consensus       402 Lp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       402 IPLSVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             CCCCCCHHHHHHHHHhcCCccceEEEEecCCCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence            9999999999999999998  7766322   224799999999999999999999999999985      999999764

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).

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

Probab=99.94  E-value=7.3e-26  Score=228.19  Aligned_cols=173  Identities=23%  Similarity=0.260  Sum_probs=133.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccCc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSG  160 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~~  160 (408)
                      ++++|||+|||+++||++|+++|+.||.|.+|.+++ ++|||||+|.+.++|++|++.|+...+.+.|+  .+++.|+..
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~-~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~--~l~v~~s~~   77 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP-GKRQALVEFEDEESAKACVNFATSVPIYIRGQ--PAFFNYSTS   77 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC-CCCEEEEEeCchHHHHHHHHHhhcCCceEcCe--EEEEEecCC
Confidence            589999999999999999999999999999998884 78999999999999999999864433444577  466656542


Q ss_pred             cccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCCCCC
Q 046223          161 LMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGV  240 (408)
Q Consensus       161 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp~~~  240 (408)
                      ..+...          .                            ..     .      ..........+|||+||++.+
T Consensus        78 ~~~~~~----------~----------------------------~~-----~------~~~~~~~~~~~v~v~nl~~~v  108 (481)
T TIGR01649        78 QEIKRD----------G----------------------------NS-----D------FDSAGPNKVLRVIVENPMYPI  108 (481)
T ss_pred             cccccC----------C----------------------------CC-----c------ccCCCCCceEEEEEcCCCCCC
Confidence            110000          0                            00     0      000001123579999999999


Q ss_pred             cHHHHHHHHhcCCCceeeccC-CCCccEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEEecCCCC
Q 046223          241 SSSTLKEIFQAFGPVKELRET-PLKKHQRFIEFYDVRDAAKALKEMNGQEIYG--KHVVIEFSRPGGH  305 (408)
Q Consensus       241 t~~~L~~~F~~~G~v~~v~~~-~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~a~~~~~  305 (408)
                      |+++|+++|+.||.|.+|... ....++|||+|.+.++|.+|++.|||..|.|  +.|+|+|++....
T Consensus       109 t~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l  176 (481)
T TIGR01649       109 TLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTRL  176 (481)
T ss_pred             CHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCCc
Confidence            999999999999999998432 2334799999999999999999999999964  5899999987553

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).

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

Probab=99.94  E-value=8.3e-26  Score=227.65  Aligned_cols=171  Identities=25%  Similarity=0.326  Sum_probs=135.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      .+...++|||+|||.++++++|+++|++||.|..|++++     +++|||||+|.+.++|++|+. |+|..|.  |+.| 
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~--g~~i-  160 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLL--GRPI-  160 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEEC--Ceee-
Confidence            456789999999999999999999999999999999975     469999999999999999996 8998876  5533 


Q ss_pred             eeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEE
Q 046223          153 LKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIV  232 (408)
Q Consensus       153 ~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~  232 (408)
                       .+.++...             .....                      .   ...      ..     ........+||
T Consensus       161 -~v~~~~~~-------------~~~~~----------------------~---~~~------~~-----~~~~p~~~~l~  190 (457)
T TIGR01622       161 -IVQSSQAE-------------KNRAA----------------------K---AAT------HQ-----PGDIPNFLKLY  190 (457)
T ss_pred             -EEeecchh-------------hhhhh----------------------h---ccc------cc-----CCCCCCCCEEE
Confidence             33222100             00000                      0   000      00     00011258999


Q ss_pred             EcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          233 VFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       233 V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      |+||+..+++++|+++|+.||.|..|.     .++.++|||||+|.+.++|.+|++.|||..|.|+.|+|.|+..
T Consensus       191 v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       191 VGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             EcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            999999999999999999999999883     3457899999999999999999999999999999999999863

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=99.94  E-value=8.3e-26  Score=233.07  Aligned_cols=158  Identities=23%  Similarity=0.294  Sum_probs=133.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      +|||+|||.++||++|+++|++||.|.+|++.+     +++|||||+|.+.++|++|++.||+..|.  |+  .+++.|+
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~--gk--~i~i~~s   77 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLG--GK--PIRIMWS   77 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--Ce--eEEeecc
Confidence            799999999999999999999999999999975     46899999999999999999999998776  66  3455443


Q ss_pred             CccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCCC
Q 046223          159 SGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDS  238 (408)
Q Consensus       159 ~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp~  238 (408)
                      ...                                                       +    ........+|||+||+.
T Consensus        78 ~~~-------------------------------------------------------~----~~~~~~~~~vfV~nLp~   98 (562)
T TIGR01628        78 QRD-------------------------------------------------------P----SLRRSGVGNIFVKNLDK   98 (562)
T ss_pred             ccc-------------------------------------------------------c----cccccCCCceEEcCCCc
Confidence            200                                                       0    00011236799999999


Q ss_pred             CCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          239 GVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       239 ~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ++++++|+++|++||.|.+|+    ..++++|||||+|.+.++|.+|++.|||..+.|+.|.|.....+.
T Consensus        99 ~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~  168 (562)
T TIGR01628        99 SVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKH  168 (562)
T ss_pred             cCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEecccccc
Confidence            999999999999999998873    356789999999999999999999999999999999998765543

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

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

Probab=99.93  E-value=1.7e-24  Score=221.07  Aligned_cols=193  Identities=16%  Similarity=0.199  Sum_probs=135.4

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHhhcc------------CCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcC
Q 046223           74 LPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVF------------GEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIRE  141 (408)
Q Consensus        74 ~p~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~------------G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng  141 (408)
                      ..+......++|||||||+++|+++|+++|..+            +.|..+.+. +.+|||||+|.+.++|.+|| .|+|
T Consensus       167 ~~~~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~-~~kg~afVeF~~~e~A~~Al-~l~g  244 (509)
T TIGR01642       167 YQQQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN-KEKNFAFLEFRTVEEATFAM-ALDS  244 (509)
T ss_pred             cCccCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEEC-CCCCEEEEEeCCHHHHhhhh-cCCC
Confidence            344567788999999999999999999999985            244445444 57999999999999999999 5999


Q ss_pred             ccccccccccceeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCC
Q 046223          142 QHMQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNA  221 (408)
Q Consensus       142 ~~i~~~gr~l~~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~  221 (408)
                      ..|.  |+.|.+...  .... .          .....                +. .....   ..........+. ..
T Consensus       245 ~~~~--g~~l~v~r~--~~~~-~----------~~~~~----------------~~-~~~~~---~~~~~~~~~~~~-~~  288 (509)
T TIGR01642       245 IIYS--NVFLKIRRP--HDYI-P----------VPQIT----------------PE-VSQKN---PDDNAKNVEKLV-NS  288 (509)
T ss_pred             eEee--CceeEecCc--cccC-C----------ccccC----------------CC-CCCCC---Cccccccccccc-cc
Confidence            7765  564444321  0000 0          00000                00 00000   000000000000 00


Q ss_pred             CCCCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          222 VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       222 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      ........+|||+|||..+++++|+++|+.||.|..+.     .++.++|||||+|.+.++|.+|++.|||..|+|+.|.
T Consensus       289 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~  368 (509)
T TIGR01642       289 TTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLH  368 (509)
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            11123458999999999999999999999999998872     3677899999999999999999999999999999999


Q ss_pred             EEEecCCC
Q 046223          297 IEFSRPGG  304 (408)
Q Consensus       297 v~~a~~~~  304 (408)
                      |.++....
T Consensus       369 v~~a~~~~  376 (509)
T TIGR01642       369 VQRACVGA  376 (509)
T ss_pred             EEECccCC
Confidence            99997543

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=99.93  E-value=4.7e-25  Score=227.46  Aligned_cols=223  Identities=15%  Similarity=0.212  Sum_probs=146.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ....+|||+||+.++++++|+++|++||.|.+|++..    +++|||||+|.+.++|++|++.|||..+.  ++.+.+..
T Consensus        86 ~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~--~~~i~v~~  163 (562)
T TIGR01628        86 SGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLN--DKEVYVGR  163 (562)
T ss_pred             cCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEec--CceEEEec
Confidence            3456899999999999999999999999999998875    46999999999999999999999998765  55433322


Q ss_pred             cccCccccccCCCCCCCcccCCCChhHHHHHHhhh-hccCCC-------C-CCC----------------------cCCC
Q 046223          156 PYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIM-NSYAPV-------L-PPP----------------------ARGL  204 (408)
Q Consensus       156 ~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~-------~-~~~----------------------~~~~  204 (408)
                      .................+..+.+......+.+... ..+..-       . ...                      ....
T Consensus       164 ~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~  243 (562)
T TIGR01628       164 FIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKK  243 (562)
T ss_pred             cccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcE
Confidence            11110000000111122223333322222211111 001000       0 000                      0000


Q ss_pred             CC----CCCccccccCCcCCC--------------CCCCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCC
Q 046223          205 VA----GRPVWAQFIVPTCNA--------------VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETP  262 (408)
Q Consensus       205 ~~----g~~~~~~~~~p~~~~--------------~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~  262 (408)
                      ..    |+.+.+.........              ........+|||+||+..+++++|+++|++||.|.+++    .++
T Consensus       244 i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g  323 (562)
T TIGR01628       244 IGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKG  323 (562)
T ss_pred             ecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCC
Confidence            11    221111111110000              00123457899999999999999999999999999883    467


Q ss_pred             CCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          263 LKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       263 ~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      .++|||||+|.+.++|.+|++.|||+.++|+.|.|.++..+.
T Consensus       324 ~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~  365 (562)
T TIGR01628       324 VSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKE  365 (562)
T ss_pred             CcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcH
Confidence            889999999999999999999999999999999999998654

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

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

Probab=99.92  E-value=7.9e-25  Score=181.68  Aligned_cols=164  Identities=20%  Similarity=0.248  Sum_probs=138.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ....|||||||+..++++.|+++|-+.|.|..+++.+     ..+|||||+|.++|+|+-|++.||..++.  ||+|++.
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLY--grpIrv~   84 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLY--GRPIRVN   84 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhc--CceeEEE
Confidence            4567999999999999999999999999999999876     46999999999999999999999976665  7854444


Q ss_pred             ccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEc
Q 046223          155 NPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVF  234 (408)
Q Consensus       155 ~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~  234 (408)
                      ..  .                 .                                           .......+.+|||+
T Consensus        85 ka--s-----------------~-------------------------------------------~~~nl~vganlfvg  102 (203)
T KOG0131|consen   85 KA--S-----------------A-------------------------------------------HQKNLDVGANLFVG  102 (203)
T ss_pred             ec--c-----------------c-------------------------------------------cccccccccccccc
Confidence            31  0                 0                                           00011224789999


Q ss_pred             CCCCCCcHHHHHHHHhcCCCceee------ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCCCC
Q 046223          235 NLDSGVSSSTLKEIFQAFGPVKEL------RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSK  307 (408)
Q Consensus       235 nLp~~~t~~~L~~~F~~~G~v~~v------~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  307 (408)
                      ||...++|..|.+.|+.||.+...      ..++..+|||||.|.+.|.+.+|+..|||..++.++|.|.++..+..+.
T Consensus       103 NLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  103 NLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             ccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCCc
Confidence            999999999999999999988764      2567889999999999999999999999999999999999998766543

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

Probab=99.91  E-value=3.7e-24  Score=186.71  Aligned_cols=160  Identities=23%  Similarity=0.396  Sum_probs=135.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ....+|.|.-||.++|+|||+.+|...|+|++++++|     .+.||+||.|.+++||++||..|||-.  ++.|  .++
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLr--LQ~K--TIK  114 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLR--LQNK--TIK  114 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhccee--eccc--eEE
Confidence            3456799999999999999999999999999999988     569999999999999999999999955  4567  456


Q ss_pred             ccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEc
Q 046223          155 NPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVF  234 (408)
Q Consensus       155 ~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~  234 (408)
                      |.|+.+.+                                                             +......|||+
T Consensus       115 VSyARPSs-------------------------------------------------------------~~Ik~aNLYvS  133 (360)
T KOG0145|consen  115 VSYARPSS-------------------------------------------------------------DSIKDANLYVS  133 (360)
T ss_pred             EEeccCCh-------------------------------------------------------------hhhcccceEEe
Confidence            65544211                                                             11223789999


Q ss_pred             CCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEEecCCC
Q 046223          235 NLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG--KHVVIEFSRPGG  304 (408)
Q Consensus       235 nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~a~~~~  304 (408)
                      +||..+|..||+++|+.||.|...     ..++.++|.+||.|+..++|+.|++.|||.+-.|  ..|.|+|+....
T Consensus       134 GlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPs  210 (360)
T KOG0145|consen  134 GLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPS  210 (360)
T ss_pred             cCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcc
Confidence            999999999999999999998655     3578899999999999999999999999987766  589999997654

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

Probab=99.91  E-value=7.9e-23  Score=208.80  Aligned_cols=187  Identities=19%  Similarity=0.275  Sum_probs=131.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ...++|||+|||.++|+++|+++|+.||.|..+.+++     .++|||||+|.+.++|..|++.|||..|.  |+.  |.
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~--~~~--l~  368 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTG--DNK--LH  368 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEEC--CeE--EE
Confidence            3468999999999999999999999999999998875     36999999999999999999999998876  664  44


Q ss_pred             ccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEc
Q 046223          155 NPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVF  234 (408)
Q Consensus       155 ~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~  234 (408)
                      +.++......    .......+....                     .....+        ..............+|+|.
T Consensus       369 v~~a~~~~~~----~~~~~~~~~~~~---------------------~~~~~~--------~~~~~~~~~~~~s~v~~l~  415 (509)
T TIGR01642       369 VQRACVGANQ----ATIDTSNGMAPV---------------------TLLAKA--------LSQSILQIGGKPTKVVQLT  415 (509)
T ss_pred             EEECccCCCC----CCcccccccccc---------------------cccccc--------chhhhccccCCCceEEEec
Confidence            4333210000    000000000000                     000000        0000000112345889999


Q ss_pred             CCCCC----------CcHHHHHHHHhcCCCceeeccC--------CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          235 NLDSG----------VSSSTLKEIFQAFGPVKELRET--------PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       235 nLp~~----------~t~~~L~~~F~~~G~v~~v~~~--------~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      ||...          ...++|+++|++||.|+.|...        +.+.|+|||+|.+.++|++|+..|||.+|+|+.|.
T Consensus       416 N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~  495 (509)
T TIGR01642       416 NLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVV  495 (509)
T ss_pred             cCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            99642          1236899999999999998421        24578999999999999999999999999999999


Q ss_pred             EEEecCC
Q 046223          297 IEFSRPG  303 (408)
Q Consensus       297 v~~a~~~  303 (408)
                      |.|....
T Consensus       496 ~~~~~~~  502 (509)
T TIGR01642       496 AAFYGED  502 (509)
T ss_pred             EEEeCHH
Confidence            9998653

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

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

Probab=99.90  E-value=5.8e-24  Score=188.47  Aligned_cols=147  Identities=22%  Similarity=0.370  Sum_probs=129.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccCcccc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLML  163 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~~~s~  163 (408)
                      .|||||||.++++.+|+.+|++||+|.++.|+   |.||||..++...|+.||+.|+|..|+  |.  .|.|.-++.   
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv---KNYgFVHiEdktaaedairNLhgYtLh--g~--nInVeaSks---   73 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIV---KNYGFVHIEDKTAAEDAIRNLHGYTLH--GV--NINVEASKS---   73 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeee---cccceEEeecccccHHHHhhcccceec--ce--EEEEEeccc---
Confidence            58999999999999999999999999999998   789999999999999999999998887  43  233321110   


Q ss_pred             ccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCCCCCcHH
Q 046223          164 MNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSS  243 (408)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp~~~t~~  243 (408)
                                                                                  +.....+|+|+||...++..
T Consensus        74 ------------------------------------------------------------Ksk~stkl~vgNis~tctn~   93 (346)
T KOG0109|consen   74 ------------------------------------------------------------KSKASTKLHVGNISPTCTNQ   93 (346)
T ss_pred             ------------------------------------------------------------cCCCccccccCCCCccccCH
Confidence                                                                        01224889999999999999


Q ss_pred             HHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          244 TLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       244 ~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ||++.|++||.|.+++   .-++|+||.|+-.++|..|++.|++++|.|++++|+++.++
T Consensus        94 ElRa~fe~ygpviecd---ivkdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen   94 ELRAKFEKYGPVIECD---IVKDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             HHhhhhcccCCceeee---eecceeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence            9999999999999986   45899999999999999999999999999999999998754

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

Probab=99.90  E-value=5.3e-23  Score=196.18  Aligned_cols=184  Identities=20%  Similarity=0.251  Sum_probs=138.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ..||||++||++++.++|.++|+.+|.|..+.++.     .++|||||.|.-.+|+++|++.+++..|.  ||  .+++.
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~--Gr--~l~v~   80 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFE--GR--ILNVD   80 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCccc--ce--ecccc
Confidence            37999999999999999999999999999988775     56999999999999999999999998876  66  35555


Q ss_pred             ccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCC
Q 046223          157 YSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNL  236 (408)
Q Consensus       157 ~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nL  236 (408)
                      ++.++--..      .  ..+-..+    +.              .     .+  .....+.  ...-......|.|.||
T Consensus        81 ~A~~R~r~e------~--~~~~e~~----~v--------------e-----K~--~~q~~~~--k~~v~~~k~rLIIRNL  125 (678)
T KOG0127|consen   81 PAKKRARSE------E--VEKGENK----AV--------------E-----KP--IEQKRPT--KAKVDLPKWRLIIRNL  125 (678)
T ss_pred             cccccccch------h--cccccch----hh--------------h-----cc--cccCCcc--hhhccCccceEEeecC
Confidence            444221000      0  0000000    00              0     00  0000000  0000122578999999


Q ss_pred             CCCCcHHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          237 DSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       237 p~~~t~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      |+.+.+.+|+.+|+.||.|.+|    +..++-+|||||+|.+..+|.+|++.+||.+|+||.|-|.||-.+.
T Consensus       126 Pf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  126 PFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             CcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            9999999999999999999999    4566678999999999999999999999999999999999997654

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

Probab=99.89  E-value=2e-21  Score=195.78  Aligned_cols=217  Identities=18%  Similarity=0.238  Sum_probs=137.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      .++|||+|||.++||++|+++|+.||.|..|.+.+     +++|||||+|.+.++|.+|++.|||..|.  |+  .|+|.
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~--g~--~i~v~  261 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELA--GR--PIKVG  261 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEEC--CE--EEEEE
Confidence            78999999999999999999999999999998875     45899999999999999999999997765  67  45565


Q ss_pred             ccCccccccCCCCC----------CCcccCCCChhHHHHHHhhhhcc-CCCCCCCcC-----------CCCC-CCC----
Q 046223          157 YSSGLMLMNNDNNN----------NNLATGCYDNQVVAESLMIMNSY-APVLPPPAR-----------GLVA-GRP----  209 (408)
Q Consensus       157 ~s~~~s~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~-----------~~~~-g~~----  209 (408)
                      |+.... .......          ..............+.+...... ....++...           +... ..+    
T Consensus       262 ~a~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (457)
T TIGR01622       262 YAQDST-YLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYA  340 (457)
T ss_pred             EccCCC-ccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccccccccccccccc
Confidence            643111 0000000          00000000000000000000000 000000000           0000 000    


Q ss_pred             --ccccccCCcCCC-CCCCCCCceEEEcCCCCCCc----------HHHHHHHHhcCCCceeeccC-CCCccEEEEEECCH
Q 046223          210 --VWAQFIVPTCNA-VPDGNNQGTIVVFNLDSGVS----------SSTLKEIFQAFGPVKELRET-PLKKHQRFIEFYDV  275 (408)
Q Consensus       210 --~~~~~~~p~~~~-~~~~~~~~~l~V~nLp~~~t----------~~~L~~~F~~~G~v~~v~~~-~~~~g~afV~F~~~  275 (408)
                        .......+.... ........+|+|.||-...+          .+||++.|++||.|+.|... ....|++||+|.+.
T Consensus       341 ~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~~~G~~fV~F~~~  420 (457)
T TIGR01622       341 TGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFSSV  420 (457)
T ss_pred             ccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCCCCceeEEEEECCH
Confidence              000000000000 00224568999999955433          36899999999999998543 67789999999999


Q ss_pred             HHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          276 RDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       276 ~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ++|.+|++.|||++|+|+.|.|.|....
T Consensus       421 e~A~~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       421 DAALAAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             HHHHHHHHHhcCcccCCeEEEEEEEcHH
Confidence            9999999999999999999999998653

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=99.88  E-value=7e-22  Score=172.55  Aligned_cols=222  Identities=19%  Similarity=0.215  Sum_probs=144.7

Q ss_pred             CCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccc
Q 046223           72 VPLPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQL  146 (408)
Q Consensus        72 ~~~p~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~  146 (408)
                      ...|..+.-...+|||++||..+|..||+.+|++||.|..-+|.-     .+||.|||.|...++|++||+.|||+.-.+
T Consensus       117 yARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g  196 (360)
T KOG0145|consen  117 YARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSG  196 (360)
T ss_pred             eccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCC
Confidence            344545555667899999999999999999999999887755432     579999999999999999999999987653


Q ss_pred             cccccceeccccCccccccCCCC-------CCCcccCCCChhHHHHHHhhh--hccCC-CCCCCcCCCCCCCCccccccC
Q 046223          147 QQQSYGLKNPYSSGLMLMNNDNN-------NNNLATGCYDNQVVAESLMIM--NSYAP-VLPPPARGLVAGRPVWAQFIV  216 (408)
Q Consensus       147 ~gr~l~~~~~~s~~~s~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~g~~~~~~~~~  216 (408)
                        ..=.+.|-|+..-+.......       ..+...+-++.+...-.+...  ..+.. ..+|...+...|-   +...+
T Consensus       197 --~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l---~~~~l  271 (360)
T KOG0145|consen  197 --CTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGL---AGVNL  271 (360)
T ss_pred             --CCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCcccccccee---eeecc
Confidence              333455556542211000000       000000001100000000000  00000 0000000101110   00111


Q ss_pred             CcCCCCCCCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeC
Q 046223          217 PTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY  291 (408)
Q Consensus       217 p~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~  291 (408)
                      |     .......+|||-||..+++|.-|+++|..||.|..|+     .+.+.+|||||.+.+.++|..|+..|||..++
T Consensus       272 p-----~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg  346 (360)
T KOG0145|consen  272 P-----GGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLG  346 (360)
T ss_pred             C-----CCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCcccc
Confidence            1     1223468999999999999999999999999998882     35788999999999999999999999999999


Q ss_pred             CeEEEEEEecCC
Q 046223          292 GKHVVIEFSRPG  303 (408)
Q Consensus       292 g~~l~v~~a~~~  303 (408)
                      +|.|.|.|...+
T Consensus       347 ~rvLQVsFKtnk  358 (360)
T KOG0145|consen  347 DRVLQVSFKTNK  358 (360)
T ss_pred             ceEEEEEEecCC
Confidence            999999997543

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

Probab=99.87  E-value=2.5e-21  Score=184.77  Aligned_cols=219  Identities=16%  Similarity=0.181  Sum_probs=143.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      .-.|.|+|||+.+.+.+|+.+|+.||.|.+|.|.+    +..|||||.|.+..+|.+|++.+||..|.  ||  .+-++|
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~--gR--~VAVDW  192 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKID--GR--PVAVDW  192 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceec--Cc--eeEEee
Confidence            55799999999999999999999999999999986    33799999999999999999999999987  78  466667


Q ss_pred             cCccccccCCCCCCCcccCC-CChhHHH------------H-----HHhhh--hccCCCCCCCcCCCCCCCCccc-----
Q 046223          158 SSGLMLMNNDNNNNNLATGC-YDNQVVA------------E-----SLMIM--NSYAPVLPPPARGLVAGRPVWA-----  212 (408)
Q Consensus       158 s~~~s~~~~~~~~~~~~~~~-~~~~~~~------------~-----~~~~~--~~~~~~~~~~~~~~~~g~~~~~-----  212 (408)
                      +..+-..+...........+ .+.+...            +     +....  ....-...-.......+..+..     
T Consensus       193 AV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~  272 (678)
T KOG0127|consen  193 AVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSG  272 (678)
T ss_pred             ecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccc
Confidence            66443222110000000000 0000000            0     00000  0000000000000000000000     


Q ss_pred             -cccCCcC-C--CCCCCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHH
Q 046223          213 -QFIVPTC-N--AVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALK  283 (408)
Q Consensus       213 -~~~~p~~-~--~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~  283 (408)
                       ....... .  ..++.....+|||.||++++|+++|.+.|++||+|..+     ..++.++|.|||.|.+..+|++||.
T Consensus       273 ~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~  352 (678)
T KOG0127|consen  273 KKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIE  352 (678)
T ss_pred             cCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHH
Confidence             0000000 0  01223345899999999999999999999999999888     4788999999999999999999999


Q ss_pred             Hh-----CC-ceeCCeEEEEEEecCCC
Q 046223          284 EM-----NG-QEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       284 ~l-----~g-~~~~g~~l~v~~a~~~~  304 (408)
                      ..     .| ..|.||.|+|..|-.+.
T Consensus       353 ~Aspa~e~g~~ll~GR~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  353 AASPASEDGSVLLDGRLLKVTLAVTRK  379 (678)
T ss_pred             hcCccCCCceEEEeccEEeeeeccchH
Confidence            77     24 67899999999987653

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

Probab=99.83  E-value=2.5e-20  Score=169.89  Aligned_cols=166  Identities=19%  Similarity=0.306  Sum_probs=133.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ..||||.|.+++.|+.|+..|..||.|++|.+..     ++||||||+|+-.|.|+.|++.|||..+.  ||.|++...-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlG--GRNiKVgrPs  191 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLG--GRNIKVGRPS  191 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhcccccc--CccccccCCC
Confidence            4699999999999999999999999999999876     67999999999999999999999998765  7744333210


Q ss_pred             cCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCC
Q 046223          158 SSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLD  237 (408)
Q Consensus       158 s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp  237 (408)
                      .-            ..+ ..+-+.+..+                                       ...-.+|||..+.
T Consensus       192 Nm------------pQA-QpiID~vqee---------------------------------------Ak~fnRiYVaSvH  219 (544)
T KOG0124|consen  192 NM------------PQA-QPIIDMVQEE---------------------------------------AKKFNRIYVASVH  219 (544)
T ss_pred             CC------------ccc-chHHHHHHHH---------------------------------------HHhhheEEeeecC
Confidence            00            000 0000000011                                       1123789999999


Q ss_pred             CCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          238 SGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       238 ~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .+++|+||+.+|+.||+|.+|.     ..+..+||+||+|.+..+-..|+..||-+.++|+-|+|-.+-.
T Consensus       220 pDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  220 PDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             CCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            9999999999999999999992     4556799999999999999999999999999999999987643

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

Probab=99.82  E-value=1.1e-19  Score=174.87  Aligned_cols=150  Identities=21%  Similarity=0.326  Sum_probs=127.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec--CccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccCc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL--MEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSG  160 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~--~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~~  160 (408)
                      ..||||   +++||..|+++|+.+|.|.+|++.+.  +-|||||.|.+.++|++|++.||...+.  |+  .+++.|+..
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~--~~--~~rim~s~r   74 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLK--GK--PIRIMWSQR   74 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccC--Cc--EEEeehhcc
Confidence            368999   99999999999999999999888763  6899999999999999999999998876  66  344433320


Q ss_pred             cccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCCCCC
Q 046223          161 LMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGV  240 (408)
Q Consensus       161 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp~~~  240 (408)
                                                                             .           ...|||.||+.++
T Consensus        75 -------------------------------------------------------d-----------~~~~~i~nl~~~~   88 (369)
T KOG0123|consen   75 -------------------------------------------------------D-----------PSLVFIKNLDESI   88 (369)
T ss_pred             -------------------------------------------------------C-----------CceeeecCCCccc
Confidence                                                                   0           1229999999999


Q ss_pred             cHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCCC
Q 046223          241 SSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHS  306 (408)
Q Consensus       241 t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~  306 (408)
                      +..+|.++|+.||.|.+|+   ....++|| ||+|+++++|.+|++.|||..+.|++|.|.....+..+
T Consensus        89 ~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er  156 (369)
T KOG0123|consen   89 DNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEER  156 (369)
T ss_pred             CcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhh
Confidence            9999999999999999992   23338999 99999999999999999999999999999988765443

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

Probab=99.82  E-value=1.1e-18  Score=151.08  Aligned_cols=207  Identities=17%  Similarity=0.246  Sum_probs=145.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHH----HhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRR----DLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~----~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ..++.||||.||...+..++|+.    +|++||+|.+|...+  +.+|.|||.|.+.+.|..|++.|+|..+.  ||  .
T Consensus         6 ~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFy--gK--~   81 (221)
T KOG4206|consen    6 VNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFY--GK--P   81 (221)
T ss_pred             cCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCccc--Cc--h
Confidence            34566999999999999999887    999999999998876  77999999999999999999999998887  77  5


Q ss_pred             eeccccCccccccCC-CCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceE
Q 046223          153 LKNPYSSGLMLMNND-NNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTI  231 (408)
Q Consensus       153 ~~~~~s~~~s~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l  231 (408)
                      +++.|+...+.+-.. .........+...+...         ..+ .+......... + .....|..........+..|
T Consensus        82 mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~---------~~~-~~~~~ng~~~~-~-~~~~~p~p~~~~~~ppn~il  149 (221)
T KOG4206|consen   82 MRIQYAKSDSDIIAQAPGTFVEKEKKINGEILA---------RIK-QPLDTNGHFYN-M-NRMNLPPPFLAQMAPPNNIL  149 (221)
T ss_pred             hheecccCccchhhccCceeccccCcccccccc---------ccC-Ccccccccccc-c-ccccCCCCccccCCCCceEE
Confidence            788888866622111 00000000000000000         000 00000000000 0 00000000011224557899


Q ss_pred             EEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeC-CeEEEEEEec
Q 046223          232 VVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY-GKHVVIEFSR  301 (408)
Q Consensus       232 ~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~l~v~~a~  301 (408)
                      |+.|||..++.+.|..+|.+|...++|+......+.|||+|.+...|..|...|.|..+. ...++|.+++
T Consensus       150 f~~niP~es~~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  150 FLTNIPSESESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             EEecCCcchhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            999999999999999999999999999877778999999999999999999999999887 7888888875

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

Probab=99.82  E-value=7.7e-20  Score=180.13  Aligned_cols=164  Identities=20%  Similarity=0.347  Sum_probs=132.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--------cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           85 LVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        85 lfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      |||.||++++|.++|..+|...|.|.++.|..        .+.|||||+|.+.++|+.|++.|+|..|.  |..|.++. 
T Consensus       518 lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvld--GH~l~lk~-  594 (725)
T KOG0110|consen  518 LFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLD--GHKLELKI-  594 (725)
T ss_pred             hhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceec--CceEEEEe-
Confidence            99999999999999999999999999987765        23599999999999999999999999877  66444443 


Q ss_pred             ccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCC
Q 046223          157 YSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNL  236 (408)
Q Consensus       157 ~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nL  236 (408)
                       +..+.                                        ....|.            ..........|+|.||
T Consensus       595 -S~~k~----------------------------------------~~~~gK------------~~~~kk~~tKIlVRNi  621 (725)
T KOG0110|consen  595 -SENKP----------------------------------------ASTVGK------------KKSKKKKGTKILVRNI  621 (725)
T ss_pred             -ccCcc----------------------------------------cccccc------------ccccccccceeeeecc
Confidence             22000                                        000000            0011112478999999


Q ss_pred             CCCCcHHHHHHHHhcCCCceeecc-----CCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          237 DSGVSSSTLKEIFQAFGPVKELRE-----TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       237 p~~~t~~~L~~~F~~~G~v~~v~~-----~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      |+..+..+++++|..||.|.+|+.     .+-.+|||||+|-+..+|.+|+++|.++.+.||+|.++||+...
T Consensus       622 pFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  622 PFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             chHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            999999999999999999999942     23358999999999999999999999999999999999998654

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

Probab=99.80  E-value=2.1e-19  Score=157.68  Aligned_cols=82  Identities=24%  Similarity=0.427  Sum_probs=75.6

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ..+.++|||-.||.+..+.||..+|-.||.|.+.     +.++.+|.|+||.|++..+|+.||.+|||..|+=++|+|.+
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQL  361 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQL  361 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhh
Confidence            3467999999999999999999999999999877     57889999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 046223          300 SRPGGHS  306 (408)
Q Consensus       300 a~~~~~~  306 (408)
                      .+++...
T Consensus       362 KRPkdan  368 (371)
T KOG0146|consen  362 KRPKDAN  368 (371)
T ss_pred             cCccccC
Confidence            8887644

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

Probab=99.80  E-value=2.8e-19  Score=157.32  Aligned_cols=136  Identities=24%  Similarity=0.367  Sum_probs=110.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      ....|||||+||+.+|||+-|..||.+.|.|..++++.+                    +              +++.++
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~--------------------e--------------~~v~wa   48 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD--------------------E--------------LKVNWA   48 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehh--------------------h--------------hccccc
Confidence            456799999999999999999999999999999998853                    1              222221


Q ss_pred             CccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCCC
Q 046223          159 SGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDS  238 (408)
Q Consensus       159 ~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp~  238 (408)
                      .                                                        .|...+.+.......+||+.|..
T Consensus        49 ~--------------------------------------------------------~p~nQsk~t~~~hfhvfvgdls~   72 (321)
T KOG0148|consen   49 T--------------------------------------------------------APGNQSKPTSNQHFHVFVGDLSP   72 (321)
T ss_pred             c--------------------------------------------------------CcccCCCCccccceeEEehhcch
Confidence            1                                                        00000111122246899999999


Q ss_pred             CCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          239 GVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       239 ~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      .++.++|++.|.+||+|.+++     .++++|||+||.|-+.++|++||..|||.+|++|.|+..||..+.
T Consensus        73 eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen   73 EIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             hcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence            999999999999999998772     578999999999999999999999999999999999999996543

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

Probab=99.80  E-value=3e-19  Score=166.42  Aligned_cols=80  Identities=25%  Similarity=0.438  Sum_probs=72.6

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ..+...|||.+||.+.-+.||-..|..||.|.+.     +.++.++.|+||.|++..+|.+||..|||..++.++++|..
T Consensus       421 GpeGanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQl  500 (510)
T KOG0144|consen  421 GPEGANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQL  500 (510)
T ss_pred             CCCccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEe
Confidence            3456789999999999999999999999999877     46788999999999999999999999999999999999998


Q ss_pred             ecCCC
Q 046223          300 SRPGG  304 (408)
Q Consensus       300 a~~~~  304 (408)
                      .+.+.
T Consensus       501 k~~~~  505 (510)
T KOG0144|consen  501 KRDRN  505 (510)
T ss_pred             eeccC
Confidence            76554

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

Probab=99.77  E-value=5e-19  Score=170.09  Aligned_cols=176  Identities=24%  Similarity=0.357  Sum_probs=135.9

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           76 PPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        76 ~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      ...++..||||+-.|...+++.+|+++|+.+|.|..|+++.     .++|.|||+|.|.+....|| .|.|+.+.  |- 
T Consensus       173 ~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrll--g~-  248 (549)
T KOG0147|consen  173 SPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLL--GV-  248 (549)
T ss_pred             CchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCccc--Cc-
Confidence            35678899999999999999999999999999999999885     56999999999999999999 69998876  22 


Q ss_pred             cceeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCce
Q 046223          151 YGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGT  230 (408)
Q Consensus       151 l~~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~  230 (408)
                       .+.+..+.                          +.........   +.    ..+.    .+..|          -..
T Consensus       249 -pv~vq~sE--------------------------aeknr~a~~s---~a----~~~k----~~~~p----------~~r  280 (549)
T KOG0147|consen  249 -PVIVQLSE--------------------------AEKNRAANAS---PA----LQGK----GFTGP----------MRR  280 (549)
T ss_pred             -eeEecccH--------------------------HHHHHHHhcc---cc----cccc----ccccc----------hhh
Confidence             33332111                          0000000000   00    0000    00111          133


Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCceee----c-cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL----R-ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       231 l~V~nLp~~~t~~~L~~~F~~~G~v~~v----~-~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ||||||.+++++++|+.+|+.||.|+.|    + .+|.++|||||+|.+.++|.+|++.|||.+|.|+.|+|.....+
T Consensus       281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            9999999999999999999999999999    2 38999999999999999999999999999999999999876543

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

Probab=99.77  E-value=6.6e-17  Score=163.12  Aligned_cols=75  Identities=21%  Similarity=0.262  Sum_probs=65.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ..++|||+||+.++++++|+++|+.||+|.+|++.+     +++|||||+|.+.++|.+|++.|||..|.  |+.  |+|
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elg--Gr~--LrV  278 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLG--GQY--LRV  278 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeC--CeE--EEE
Confidence            457899999999999999999999999999999876     46999999999999999999999998765  774  444


Q ss_pred             cccC
Q 046223          156 PYSS  159 (408)
Q Consensus       156 ~~s~  159 (408)
                      .++.
T Consensus       279 ~kAi  282 (612)
T TIGR01645       279 GKCV  282 (612)
T ss_pred             EecC
Confidence            4433

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.

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

Probab=99.76  E-value=5.5e-18  Score=163.23  Aligned_cols=161  Identities=16%  Similarity=0.237  Sum_probs=130.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccCcc
Q 046223           85 LVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGL  161 (408)
Q Consensus        85 lfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~~~  161 (408)
                      |||.||+.++|..+|+++|+.||+|.+|++..   -++|| ||+|+++++|++|++.+||..+.  ++.+-+........
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~--~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLN--GKKIYVGLFERKEE  155 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccC--CCeeEEeeccchhh
Confidence            99999999999999999999999999999987   35999 99999999999999999998776  44333322111100


Q ss_pred             ccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCCCCCc
Q 046223          162 MLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVS  241 (408)
Q Consensus       162 s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp~~~t  241 (408)
                                                                  ...+..          . ....-..++|.|+..+++
T Consensus       156 --------------------------------------------r~~~~~----------~-~~~~~t~v~vk~~~~~~~  180 (369)
T KOG0123|consen  156 --------------------------------------------REAPLG----------E-YKKRFTNVYVKNLEEDST  180 (369)
T ss_pred             --------------------------------------------hccccc----------c-hhhhhhhhheeccccccc
Confidence                                                        000000          0 111236789999999999


Q ss_pred             HHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          242 SSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       242 ~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      +++|.++|..||.|..+    ...+.+++|+||.|++.++|..|++.|||..+.+..+.|..+..+
T Consensus       181 ~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk  246 (369)
T KOG0123|consen  181 DEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKK  246 (369)
T ss_pred             hHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCCccceeecccccc
Confidence            99999999999999988    356668999999999999999999999999999999999988764

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

Probab=99.75  E-value=6.5e-18  Score=157.22  Aligned_cols=165  Identities=20%  Similarity=0.238  Sum_probs=128.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ...+|||++|+++++|+.|++.|.+||+|.++.+++     +++||+||+|.+.+...+++..-   ...+++|.+....
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~---~h~~dgr~ve~k~   81 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNAR---THKLDGRSVEPKR   81 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeeccc---ccccCCcccccee
Confidence            678999999999999999999999999999998887     56999999999999988887532   1222355333332


Q ss_pred             cccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcC
Q 046223          156 PYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFN  235 (408)
Q Consensus       156 ~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~n  235 (408)
                      ..+.                  .+                       .                .........++|||++
T Consensus        82 av~r------------------~~-----------------------~----------------~~~~~~~~tkkiFvGG  104 (311)
T KOG4205|consen   82 AVSR------------------ED-----------------------Q----------------TKVGRHLRTKKIFVGG  104 (311)
T ss_pred             ccCc------------------cc-----------------------c----------------cccccccceeEEEecC
Confidence            1111                  00                       0                0000011357999999


Q ss_pred             CCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCCC
Q 046223          236 LDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHS  306 (408)
Q Consensus       236 Lp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~  306 (408)
                      |+.+++++++++.|.+||.|..+     ..+...+||+||.|.+++++.+++. .+-..|+|+.+.|..|.++...
T Consensus       105 ~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  105 LPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             cCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccchhhc
Confidence            99999999999999999988777     4567789999999999999998876 7788999999999999887543

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

Probab=99.74  E-value=1.2e-17  Score=160.62  Aligned_cols=221  Identities=14%  Similarity=0.113  Sum_probs=135.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      -+.||||||..+++|++|+.+|+.||.|..|.+.+     .++|||||+|.+.++|++|++.|||  |.+.||.+++.+.
T Consensus       278 ~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lng--felAGr~ikV~~v  355 (549)
T KOG0147|consen  278 MRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNG--FELAGRLIKVSVV  355 (549)
T ss_pred             hhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhcc--ceecCceEEEEEe
Confidence            33499999999999999999999999999998876     4699999999999999999999999  5566885554432


Q ss_pred             ccCccc-cccCCCCCCC------cccCCCC-hhHHHHHHhhhhccCCCCC---------CCcCCCCCCCCccccccCCcC
Q 046223          157 YSSGLM-LMNNDNNNNN------LATGCYD-NQVVAESLMIMNSYAPVLP---------PPARGLVAGRPVWAQFIVPTC  219 (408)
Q Consensus       157 ~s~~~s-~~~~~~~~~~------~~~~~~~-~~~~~~~~~~~~~~~~~~~---------~~~~~~~~g~~~~~~~~~p~~  219 (408)
                      -..... ....+....+      +..+..+ .+...+........ .+..         ........+.........|..
T Consensus       356 ~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~-~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~  434 (549)
T KOG0147|consen  356 TERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRS-LPSTAISALLLLAKLASAAQFNGVVRVRSVDPAD  434 (549)
T ss_pred             eeecccccccccccccchhhccccccccccHHHHHHHHhccCCcc-ccchhhhHHHhccccchHHhhcCCcCccccCccc
Confidence            111000 0000000000      0000000 00001100000000 0000         000000000000011111111


Q ss_pred             CCCCCCCCCceEEEcCCCC--CCc--------HHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCce
Q 046223          220 NAVPDGNNQGTIVVFNLDS--GVS--------SSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE  289 (408)
Q Consensus       220 ~~~~~~~~~~~l~V~nLp~--~~t--------~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~  289 (408)
                      ....-.....++.+.|+=.  ..|        .+|+.+.+++||.|..|.....+-|+.||.|.+.+.|..|+++|||++
T Consensus       435 ~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgrW  514 (549)
T KOG0147|consen  435 ASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGRW  514 (549)
T ss_pred             cccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhhh
Confidence            1111114456777887732  112        368889999999999997666677999999999999999999999999


Q ss_pred             eCCeEEEEEEecCCCC
Q 046223          290 IYGKHVVIEFSRPGGH  305 (408)
Q Consensus       290 ~~g~~l~v~~a~~~~~  305 (408)
                      |.|+.|.+.|-.....
T Consensus       515 F~gr~Ita~~~~~~~Y  530 (549)
T KOG0147|consen  515 FAGRMITAKYLPLERY  530 (549)
T ss_pred             hccceeEEEEeehhhh
Confidence            9999999999765443

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

Probab=99.74  E-value=5.8e-17  Score=135.06  Aligned_cols=179  Identities=20%  Similarity=0.236  Sum_probs=127.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ...+++|||+|||.++.|.||+++|-+||.|..|.+..  ..-.||||+|++..+|+.||..-+|..+.  +.  .|+|.
T Consensus         3 gr~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdyd--g~--rLRVE   78 (241)
T KOG0105|consen    3 GRNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYD--GC--RLRVE   78 (241)
T ss_pred             CcccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccC--cc--eEEEE
Confidence            34678999999999999999999999999999998864  23689999999999999999999997776  33  58887


Q ss_pred             ccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCC
Q 046223          157 YSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNL  236 (408)
Q Consensus       157 ~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nL  236 (408)
                      |...-.       ......+.+.                         ..|+..+..-   ...-.+.......|.|.+|
T Consensus        79 fprggr-------~s~~~~G~y~-------------------------gggrgGgg~g---g~rgppsrrSe~RVvVsGL  123 (241)
T KOG0105|consen   79 FPRGGR-------SSSDRRGSYS-------------------------GGGRGGGGGG---GRRGPPSRRSEYRVVVSGL  123 (241)
T ss_pred             eccCCC-------cccccccccC-------------------------CCCCCCCCCC---cccCCcccccceeEEEecC
Confidence            754110       0000001000                         0001000000   0000112234578999999


Q ss_pred             CCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeC--CeEEEEE
Q 046223          237 DSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY--GKHVVIE  298 (408)
Q Consensus       237 p~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~--g~~l~v~  298 (408)
                      |.+.+++||++...+-|.|.....  ...|++.|+|-..|+-+-|++.|+...+.  |...-+.
T Consensus       124 p~SgSWQDLKDHmReaGdvCfadv--~rDg~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yir  185 (241)
T KOG0105|consen  124 PPSGSWQDLKDHMREAGDVCFADV--QRDGVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIR  185 (241)
T ss_pred             CCCCchHHHHHHHHhhCCeeeeee--ecccceeeeeeehhhHHHHHHhhccccccCcCcEeeEE
Confidence            999999999999999999876642  34569999999999999999999877654  4443333

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

Probab=99.71  E-value=5.8e-16  Score=132.88  Aligned_cols=217  Identities=15%  Similarity=0.175  Sum_probs=123.8

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecC------ccEEEEEECCHHHHHHHHHHhcCcccccc
Q 046223           74 LPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLM------EGIVTVHFYDLRHAEMAFKEIREQHMQLQ  147 (408)
Q Consensus        74 ~p~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~------kG~afV~F~~~~~A~~Ai~~lng~~i~~~  147 (408)
                      ........-|||||.+||.|+...||+.+|..|-..+...+...+      +-+|||.|.+..+|..|+.+|||..|+.+
T Consensus        26 ~~~~~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE  105 (284)
T KOG1457|consen   26 LLADEPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPE  105 (284)
T ss_pred             cccccccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccc
Confidence            333444567999999999999999999999999877775544322      46999999999999999999999998865


Q ss_pred             ccccceeccccC--ccccccCC--CCCC--CcccCCCChhHH-----HHHHhhhhccCCCCCCCcCCCCCCCC-cccccc
Q 046223          148 QQSYGLKNPYSS--GLMLMNND--NNNN--NLATGCYDNQVV-----AESLMIMNSYAPVLPPPARGLVAGRP-VWAQFI  215 (408)
Q Consensus       148 gr~l~~~~~~s~--~~s~~~~~--~~~~--~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~g~~-~~~~~~  215 (408)
                      .- ..+++.+++  .++.-+..  .+..  -+..-.......     +.......-+....+-.+..+..... ......
T Consensus       106 ~~-stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~  184 (284)
T KOG1457|consen  106 TG-STLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALS  184 (284)
T ss_pred             cC-ceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhh
Confidence            32 234444433  22111000  0000  000000000000     00000000000000000000000000 000000


Q ss_pred             -----CCcCC-----C---CCCCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeecc-CCCCccEEEEEECCHHHHHHH
Q 046223          216 -----VPTCN-----A---VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRE-TPLKKHQRFIEFYDVRDAAKA  281 (408)
Q Consensus       216 -----~p~~~-----~---~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~-~~~~~g~afV~F~~~~~A~~A  281 (408)
                           .|..+     .   ........+|||.||..+++|++|+.+|+.|-....++. .......||++|++.+.|..|
T Consensus       185 a~~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~a  264 (284)
T KOG1457|consen  185 APDSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDA  264 (284)
T ss_pred             hhhhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHH
Confidence                 00000     0   011223468999999999999999999999975544432 223456899999999999999


Q ss_pred             HHHhCCceeC
Q 046223          282 LKEMNGQEIY  291 (408)
Q Consensus       282 ~~~l~g~~~~  291 (408)
                      +..|+|..|.
T Consensus       265 m~~lqg~~~s  274 (284)
T KOG1457|consen  265 MNHLQGNLLS  274 (284)
T ss_pred             HHHhhcceec
Confidence            9999987653

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

Probab=99.70  E-value=9.8e-16  Score=142.18  Aligned_cols=218  Identities=19%  Similarity=0.182  Sum_probs=146.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccE-EEEEECCHHHHHHHHHHhcCccccccccccceeccccCcc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGI-VTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGL  161 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~-afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~~~  161 (408)
                      -.++|+|+-+-|+-|-|..+|++||.|..|....++.|| |+|+|.|.+.|..|..+|+|+.|.....  .+|+.|++-.
T Consensus       151 Lr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcC--tLrId~Sklt  228 (492)
T KOG1190|consen  151 LRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCC--TLRIDFSKLT  228 (492)
T ss_pred             EEEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccchhhhhhccchhhHHHHHHhccCCcccCcee--EEEeehhhcc
Confidence            457899999999999999999999999998887788777 9999999999999999999999987666  5777787644


Q ss_pred             cc--ccCC-----CCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEc
Q 046223          162 ML--MNND-----NNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVF  234 (408)
Q Consensus       162 s~--~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~  234 (408)
                      .+  -...     ..+-++..+....  ..+.+.....+..++.+.......+   .................+..|.|.
T Consensus       229 ~LnvKynndkSRDyTnp~LP~gd~~p--~l~~~~~aa~~~~~~~~g~p~aip~---~~~~a~~a~~~~~~~~~n~vllvs  303 (492)
T KOG1190|consen  229 DLNVKYNNDKSRDYTNPDLPVGDGQP--SLDQLMAAAFGSVPAVHGAPLAIPS---GAAGANAADGKIESPSANVVLLVS  303 (492)
T ss_pred             cceeeccccccccccCCCCCCCcccc--ccchhhhccccccccccCCcccCCc---cchhhcccccccccCCCceEEEEe
Confidence            31  1111     1111112221100  0000000000111111000000000   000000000000001125788999


Q ss_pred             CCCC-CCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCCCC
Q 046223          235 NLDS-GVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSK  307 (408)
Q Consensus       235 nLp~-~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  307 (408)
                      ||.. .+|.+.|..+|+-||+|.+|+.....+.-|+|+|.+...|+-|++.|+|..|.|++|+|.+++......
T Consensus       304 nln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vql  377 (492)
T KOG1190|consen  304 NLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQL  377 (492)
T ss_pred             cCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccC
Confidence            9976 589999999999999999997666667899999999999999999999999999999999998765443

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

Probab=99.68  E-value=1.1e-16  Score=140.08  Aligned_cols=166  Identities=22%  Similarity=0.333  Sum_probs=127.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccCccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLM  162 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~~~s  162 (408)
                      ..||||+|++.+.+.+|..+|..||.|..|.+.   .||+||+|.|..+|..|+..|||..|.+..    +.+.|...  
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk---~gf~fv~fed~rda~Dav~~l~~~~l~~e~----~vve~~r~--   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK---NGFGFVEFEDPRDADDAVHDLDGKELCGER----LVVEHARG--   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee---cccceeccCchhhhhcccchhcCceeccee----eeeecccc--
Confidence            358999999999999999999999999999885   799999999999999999999999887321    44443320  


Q ss_pred             cccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCC-CCCccccccCCcCCCCCCCCCCceEEEcCCCCCCc
Q 046223          163 LMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVA-GRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVS  241 (408)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp~~~t  241 (408)
                                    .....                    ..... ++..|...-      .......+.|+|.|+...+.
T Consensus        73 --------------~~~~~--------------------g~~~~g~r~~~~~~~------~~p~~s~~r~~~~~~~~r~~  112 (216)
T KOG0106|consen   73 --------------KRRGR--------------------GRPRGGDRRSDSRRY------RPPSRTHFRLIVRNLSLRVS  112 (216)
T ss_pred             --------------ccccc--------------------CCCCCCCccchhhcc------CCcccccceeeeccchhhhh
Confidence                          00000                    00000 111111111      11234468899999999999


Q ss_pred             HHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          242 SSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       242 ~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      +.+|.+.|+.+|.+.....   ..+++||+|+..++|.+|+..|+|..+.|+.|.+...
T Consensus       113 ~qdl~d~~~~~g~~~~~~~---~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  113 WQDLKDHFRPAGEVTYVDA---RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             HHHHhhhhcccCCCchhhh---hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            9999999999999955432   6899999999999999999999999999999999443

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

Probab=99.68  E-value=7.4e-16  Score=148.77  Aligned_cols=249  Identities=28%  Similarity=0.369  Sum_probs=169.9

Q ss_pred             CCCCccccCCCCCCCCCCCCCCCCCCCC----CCCcCCCCCCCCCCCCCCCCCCCCCCccCCcCCccCCCCCCCCCCCCC
Q 046223            1 MGETGISRFQGNLDPRAQEFRPTTLFRP----PQVYYPYGAASPPTLPPYPSNDVQVVPFGGVGYAQYPTHPQLGVPLPP   76 (408)
Q Consensus         1 ~~~~~~~~~~~~~~~~a~~~~p~~p~~~----~~~~~p~~~~ppppppp~~~~~~~~~p~~~~~~~~~~~~p~~~~~~p~   76 (408)
                      |++.++=...|++++.|++|-+..-..+    .+...++.+++++++ +.+-+.        .-|.++  .+++...+|.
T Consensus         1 ~~d~~lf~~~G~~el~~~~~~~~~~~~~~~n~~~~~~~~~P~~~s~~-~~~~l~--------a~f~~~--~~p~~~~np~   69 (549)
T KOG4660|consen    1 LEDCDLFSSGGGMELDADSFDNLSVRNSDRNSAGFVFPEHPPGESRT-FVSELS--------ALFEPF--NKPLRPDNPS   69 (549)
T ss_pred             CCccccccCCCCCCcccccccchhhcccccCCCccccCCCCCCCCCC-ChhhHH--------hhhhcc--CCCCCcCCCC
Confidence            5566777788999999999988443221    111112111111111 111110        111111  2222235666


Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      .....+++|+|-|||.+|++++|..+|+.||+|+.|+.....+|.+||+|.|+.+|+.|+++|++.+|.++..    +..
T Consensus        70 ~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~----k~~  145 (549)
T KOG4660|consen   70 EKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRI----KRP  145 (549)
T ss_pred             cccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhh----cCC
Confidence            7778899999999999999999999999999999999888889999999999999999999999999873322    121


Q ss_pred             ccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCC
Q 046223          157 YSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNL  236 (408)
Q Consensus       157 ~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nL  236 (408)
                      ..                                       ....+....+...|.++..+..+..+.......+|+- |
T Consensus       146 ~~---------------------------------------~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l  185 (549)
T KOG4660|consen  146 GG---------------------------------------ARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-L  185 (549)
T ss_pred             Cc---------------------------------------ccccchhcccchhhhhccchhhcCCCCCCcCCcceee-e
Confidence            11                                       1112233344555666555554444444444555544 8


Q ss_pred             CCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCCC
Q 046223          237 DSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHS  306 (408)
Q Consensus       237 p~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~  306 (408)
                      ....+..-++..|..+|.+.. +.++.-...-|++|.+..++..+...+ |..+.+....+.++.+.+..
T Consensus       186 ~P~~s~~~~~~~~~~~~~~~~-~~~~~~~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~~g~~  253 (549)
T KOG4660|consen  186 SPTRSSILLEHISSVDGSSPG-RETPLLNHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGPGGVW  253 (549)
T ss_pred             ccchhhhhhhcchhccCcccc-ccccchhhhhhhhhccccchhhcccCC-ceecCCCCceEEecCCCccc
Confidence            888888888888899999887 777777778899999999997776644 77788888888888886554

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

Probab=99.67  E-value=7.8e-16  Score=129.43  Aligned_cols=79  Identities=25%  Similarity=0.452  Sum_probs=72.4

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ..++|||+||++++++++|+++|++||.|.++.     .++.++|||||+|++.++|++|++.||+..|+|+.|+|++++
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~  112 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN  112 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence            358999999999999999999999999999883     467789999999999999999999999999999999999997


Q ss_pred             CCCC
Q 046223          302 PGGH  305 (408)
Q Consensus       302 ~~~~  305 (408)
                      .+..
T Consensus       113 ~~~~  116 (144)
T PLN03134        113 DRPS  116 (144)
T ss_pred             cCCC
Confidence            6543

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

Probab=99.64  E-value=2.1e-15  Score=149.16  Aligned_cols=202  Identities=17%  Similarity=0.223  Sum_probs=130.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ..+..+.|+|+|||..+..++|.++|..||+|..|.+. ...-.|+|+|.+..+|++|++.|....+.    .-.+.+.+
T Consensus       381 ~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp-~~G~~aiv~fl~p~eAr~Afrklaysr~k----~~plyle~  455 (725)
T KOG0110|consen  381 AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP-PGGTGAIVEFLNPLEARKAFRKLAYSRFK----SAPLYLEW  455 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhcccccceeecC-cccceeeeeecCccchHHHHHHhchhhhc----cCcccccc
Confidence            34556789999999999999999999999999999665 33344999999999999999999887654    11233322


Q ss_pred             cCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCC--CCCCcC-CCCCCCCccccccCCcC--C-CCCCCCCCceE
Q 046223          158 SSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPV--LPPPAR-GLVAGRPVWAQFIVPTC--N-AVPDGNNQGTI  231 (408)
Q Consensus       158 s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~-~~~~g~~~~~~~~~p~~--~-~~~~~~~~~~l  231 (408)
                      +....... + ++.......               ....  .-+..+ ....+............  . .........+|
T Consensus       456 aP~dvf~~-~-pka~~~~~e---------------~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~l  518 (725)
T KOG0110|consen  456 APEDVFTE-D-PKADDLSAE---------------SRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKL  518 (725)
T ss_pred             ChhhhccC-C-ccccccccc---------------cccccccCcceecccccccccccCCccccccchhhhhccccchhh
Confidence            22110000 0 000000000               0000  000000 00011100000000000  0 00111222339


Q ss_pred             EEcCCCCCCcHHHHHHHHhcCCCceeec----cC----CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          232 VVFNLDSGVSSSTLKEIFQAFGPVKELR----ET----PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       232 ~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~----~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ||.||++++|.++|...|...|.|..+.    ..    -.+.|||||+|.+.++|++|++.|+|+.|+|+.|.|+++.
T Consensus       519 fvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  519 FVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            9999999999999999999999999882    11    1245999999999999999999999999999999999997

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

Probab=99.63  E-value=9.8e-15  Score=135.60  Aligned_cols=188  Identities=18%  Similarity=0.260  Sum_probs=140.2

Q ss_pred             CCEEEEcCCC-CCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccCc
Q 046223           82 TRTLVLSYVP-GDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSG  160 (408)
Q Consensus        82 ~rtlfV~nLp-~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~~  160 (408)
                      +..|.|.||. ..||.+.|..+|.-||+|..|+|..+.+--|+|+|.|...|+.|++.|+|..|+  ||  +|++.|++.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~--gk--~lrvt~SKH  372 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLY--GK--KLRVTLSKH  372 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceec--Cc--eEEEeeccC
Confidence            5788999995 568999999999999999999999888899999999999999999999999988  56  588888875


Q ss_pred             cccc--cCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCC-CCCCCCceEEEcCCC
Q 046223          161 LMLM--NNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAV-PDGNNQGTIVVFNLD  237 (408)
Q Consensus       161 ~s~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~-~~~~~~~~l~V~nLp  237 (408)
                      ..+.  .......++...                |.  ..+.           .++..|..... .-..+..+|.+.|+|
T Consensus       373 ~~vqlp~egq~d~glT~d----------------y~--~spL-----------hrfkkpgsKN~~ni~PpsatlHlsnip  423 (492)
T KOG1190|consen  373 TNVQLPREGQEDQGLTKD----------------YG--NSPL-----------HRFKKPGSKNYQNIFPPSATLHLSNIP  423 (492)
T ss_pred             ccccCCCCCCcccccccc----------------CC--CCch-----------hhccCcccccccccCCchhheeeccCC
Confidence            5322  111111100000                00  0000           01111111110 112335799999999


Q ss_pred             CCCcHHHHHHHHhcCCCceee-ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCe-EEEEEEecC
Q 046223          238 SGVSSSTLKEIFQAFGPVKEL-RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK-HVVIEFSRP  302 (408)
Q Consensus       238 ~~~t~~~L~~~F~~~G~v~~v-~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~-~l~v~~a~~  302 (408)
                      .+++||||++.|..-|...+. ...++.+.+|++.++++|+|..|+..+|...+++. -|+|.|++.
T Consensus       424 ~svsee~lk~~f~~~g~~vkafkff~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  424 PSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             cccchhHHHHhhhcCCceEEeeeecCCCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            999999999999998876544 66777889999999999999999999999998865 899999875

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

Probab=99.60  E-value=7.4e-14  Score=127.47  Aligned_cols=196  Identities=14%  Similarity=0.206  Sum_probs=131.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEE--------EEEee----cCccEEEEEECCHHHHHHHHHHhcCccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRG--------VQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQL  146 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~--------v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~  146 (408)
                      ...+..|||+|||.++|.+++.++|++||-|..        |++.+    .-+|-|+|.|...+++..|++.|++..|. 
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r-  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELR-  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCccccc-
Confidence            345677999999999999999999999998766        66666    33899999999999999999999999886 


Q ss_pred             cccccceeccccCccccccCCCCCCCcc-cCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCC
Q 046223          147 QQQSYGLKNPYSSGLMLMNNDNNNNNLA-TGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDG  225 (408)
Q Consensus       147 ~gr~l~~~~~~s~~~s~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~  225 (408)
                       |+  .++|.-+.-.   .....+.... .++....  .+..+..+...            +   |    .|........
T Consensus       210 -g~--~~rVerAkfq---~Kge~~~~~k~k~k~~~~--kk~~k~q~k~~------------d---w----~pd~~~~sk~  262 (382)
T KOG1548|consen  210 -GK--KLRVERAKFQ---MKGEYDASKKEKGKCKDK--KKLKKQQQKLL------------D---W----RPDRDDPSKA  262 (382)
T ss_pred             -Cc--EEEEehhhhh---hccCcCcccccccccccH--HHHHHHHHhhc------------c---c----CCCccccccc
Confidence             55  4555322210   0000000000 0000000  00000000000            0   0    1111111123


Q ss_pred             CCCceEEEcCCCC----CCc-------HHHHHHHHhcCCCceeec-cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCe
Q 046223          226 NNQGTIVVFNLDS----GVS-------SSTLKEIFQAFGPVKELR-ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK  293 (408)
Q Consensus       226 ~~~~~l~V~nLp~----~~t-------~~~L~~~F~~~G~v~~v~-~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~  293 (408)
                      ...++|.|.|+=.    ..+       ++||.+-+.+||.|..|. ......|.+-|.|.+.++|..||+.|+|+.|+||
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgR  342 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGR  342 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecce
Confidence            3468899999842    222       467888899999999983 4557899999999999999999999999999999


Q ss_pred             EEEEEEecC
Q 046223          294 HVVIEFSRP  302 (408)
Q Consensus       294 ~l~v~~a~~  302 (408)
                      +|.......
T Consensus       343 ql~A~i~DG  351 (382)
T KOG1548|consen  343 QLTASIWDG  351 (382)
T ss_pred             EEEEEEeCC
Confidence            999887644

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

Probab=99.58  E-value=3.9e-15  Score=123.44  Aligned_cols=77  Identities=27%  Similarity=0.463  Sum_probs=73.0

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      .++|||+||+..+++.||+.+|..||.|..|+......|||||+|++..+|+.|+..|+|+.|+|..|+|+++.-..
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCc
Confidence            58999999999999999999999999999998777889999999999999999999999999999999999997554

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

Probab=99.57  E-value=9.5e-15  Score=122.83  Aligned_cols=76  Identities=16%  Similarity=0.202  Sum_probs=66.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ...+++|||+||++++||++|+++|++||.|.+|.+..     +++|||||+|.+.++|++|++.||+..|.  ++.  +
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~--Gr~--l  106 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELN--GRH--I  106 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEEC--CEE--E
Confidence            44577899999999999999999999999999998875     46999999999999999999999998876  664  4


Q ss_pred             ecccc
Q 046223          154 KNPYS  158 (408)
Q Consensus       154 ~~~~s  158 (408)
                      ++.++
T Consensus       107 ~V~~a  111 (144)
T PLN03134        107 RVNPA  111 (144)
T ss_pred             EEEeC
Confidence            44443

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

Probab=99.54  E-value=1.7e-13  Score=128.30  Aligned_cols=214  Identities=16%  Similarity=0.171  Sum_probs=133.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhc-cCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEV-FGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~-~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      -.|.+||.|||+++.+++|+++|.. .|+|+.|.+..    +.+|+|.|+|+++|.+++|++.||...+.  ||.|.++.
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~--GR~l~vKE  120 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVN--GRELVVKE  120 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhcccc--CceEEEec
Confidence            4567999999999999999999975 89999998875    77999999999999999999999987765  88766665


Q ss_pred             cccCccc----cccCCCCCCCcccCCCChhHHHHHHhhhhccCC---CCC-CCcCCCCCC---CCc--------------
Q 046223          156 PYSSGLM----LMNNDNNNNNLATGCYDNQVVAESLMIMNSYAP---VLP-PPARGLVAG---RPV--------------  210 (408)
Q Consensus       156 ~~s~~~s----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~~~~~g---~~~--------------  210 (408)
                      +-...+-    +.+ +..  ..+.+..+.+.-...+...-.-..   ... ........+   ...              
T Consensus       121 d~d~q~~~~~~~~r-~g~--~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lf  197 (608)
T KOG4212|consen  121 DHDEQRDQYGRIVR-DGG--GGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLF  197 (608)
T ss_pred             cCchhhhhhhheee-ccC--cccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcc
Confidence            3221000    000 000  000000000000000000000000   000 000000000   000              


Q ss_pred             --cccccCCcCCCCCCCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHH
Q 046223          211 --WAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKE  284 (408)
Q Consensus       211 --~~~~~~p~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~  284 (408)
                        ...|..+..  .-.......+||.||.+.+....|++.|.-.|.|+.|    ...+.++|++.++|.+.-+|..||..
T Consensus       198 gl~~~Flr~~h--~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsm  275 (608)
T KOG4212|consen  198 GLSASFLRSLH--IFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISM  275 (608)
T ss_pred             cchhhhhhhcc--CCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHh
Confidence              000000000  0011124689999999999999999999999999888    45678899999999999999999999


Q ss_pred             hCCceeCCeEEEEEEec
Q 046223          285 MNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       285 l~g~~~~g~~l~v~~a~  301 (408)
                      |++.-+..++..+.+.+
T Consensus       276 l~~~g~~~~~~~~Rl~~  292 (608)
T KOG4212|consen  276 LDRQGLFDRRMTVRLDR  292 (608)
T ss_pred             hccCCCccccceeeccc
Confidence            99877777777777643

>PF00076 RRM_1: RNA recognition motif

Probab=99.52  E-value=5.6e-14  Score=103.16  Aligned_cols=66  Identities=33%  Similarity=0.600  Sum_probs=61.4

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       231 l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      |||+|||.++|+++|+++|+.||.|..+.    ..+..+++|||+|.+.++|++|++.|+|..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            79999999999999999999999998882    3567889999999999999999999999999999986

(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 ....

>PF00076 RRM_1: RNA recognition motif

Probab=99.52  E-value=3.9e-14  Score=103.97  Aligned_cols=61  Identities=26%  Similarity=0.441  Sum_probs=57.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec----CccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           85 LVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL----MEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        85 lfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~----~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      |||+|||.++|+++|+++|++||.|..+.+...    .+|+|||+|.+.++|++|++.|+|..+.
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~   65 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKIN   65 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEEC
Confidence            799999999999999999999999999988863    5999999999999999999999998775

(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 ....

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

Probab=99.52  E-value=2.1e-14  Score=119.11  Aligned_cols=75  Identities=19%  Similarity=0.276  Sum_probs=68.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      -.+.||||||+.++++.||+.+|..||.|.+|.|.+...|||||+|+|..||+.|+..|+|+.|.  |.  .++|+++.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~c--G~--r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDIC--GS--RIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCcccc--Cc--eEEEEeec
Confidence            46789999999999999999999999999999999988999999999999999999999999987  32  47776654

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

Probab=99.50  E-value=1.2e-13  Score=125.15  Aligned_cols=80  Identities=19%  Similarity=0.312  Sum_probs=72.5

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ....++|+|+|||+...|-||+.+|.+||.|.+|.   ....+||||||+|++.+||++|.++|||..+.||+|+|..|.
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            34458999999999999999999999999999882   345689999999999999999999999999999999999998


Q ss_pred             CCC
Q 046223          302 PGG  304 (408)
Q Consensus       302 ~~~  304 (408)
                      .+-
T Consensus       173 arV  175 (376)
T KOG0125|consen  173 ARV  175 (376)
T ss_pred             hhh
Confidence            763

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

Probab=99.49  E-value=4.8e-13  Score=127.61  Aligned_cols=164  Identities=16%  Similarity=0.221  Sum_probs=115.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ....|-+.+|||++|++||.++|+.++ |+.+.+.+   +..|-|||+|.+.|++++|++. +-..|.  .|  -|.| |
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg--~R--YIEV-f   81 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALKK-DRESMG--HR--YIEV-F   81 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHHh-hHHHhC--Cc--eEEE-E
Confidence            345677899999999999999999998 88887776   5689999999999999999973 333322  33  1222 2


Q ss_pred             cCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCC
Q 046223          158 SSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLD  237 (408)
Q Consensus       158 s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp  237 (408)
                      ....       ...+                                      |.-....    .........|.+.+||
T Consensus        82 ~~~~-------~e~d--------------------------------------~~~~~~g----~~s~~~d~vVRLRGLP  112 (510)
T KOG4211|consen   82 TAGG-------AEAD--------------------------------------WVMRPGG----PNSSANDGVVRLRGLP  112 (510)
T ss_pred             ccCC-------cccc--------------------------------------ccccCCC----CCCCCCCceEEecCCC
Confidence            1100       0000                                      0000000    0011235789999999


Q ss_pred             CCCcHHHHHHHHhcCCCcee-e----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          238 SGVSSSTLKEIFQAFGPVKE-L----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       238 ~~~t~~~L~~~F~~~G~v~~-v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      +.+|++||.++|+..-.|.. +    ...++..|-|||+|++.+.|++|+. -|...|+.|-|.|-.+.
T Consensus       113 fscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  113 FSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRSS  180 (510)
T ss_pred             ccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehhH
Confidence            99999999999987643333 1    3455678999999999999999987 57777888888887664

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

Probab=99.49  E-value=5.1e-14  Score=110.69  Aligned_cols=77  Identities=22%  Similarity=0.339  Sum_probs=71.4

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      .+++|||+||++.++||+|.++|++.|+|..|     +.+...+||+||+|.+.++|..|++.++|+.++.+.|+|.|..
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            36999999999999999999999999999998     5666789999999999999999999999999999999999976


Q ss_pred             CC
Q 046223          302 PG  303 (408)
Q Consensus       302 ~~  303 (408)
                      .-
T Consensus       115 GF  116 (153)
T KOG0121|consen  115 GF  116 (153)
T ss_pred             cc
Confidence            43

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.48  E-value=1.2e-13  Score=132.65  Aligned_cols=79  Identities=27%  Similarity=0.546  Sum_probs=72.3

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||+++|+++|+++|+.||.|++|+     .+++++|||||+|.++++|++|++.|||..+.+++|+|.++
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a  184 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA  184 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence            3468999999999999999999999999998883     46778899999999999999999999999999999999999


Q ss_pred             cCCC
Q 046223          301 RPGG  304 (408)
Q Consensus       301 ~~~~  304 (408)
                      ++..
T Consensus       185 ~p~~  188 (346)
T TIGR01659       185 RPGG  188 (346)
T ss_pred             cccc
Confidence            7643

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

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

Probab=99.48  E-value=1.1e-13  Score=120.78  Aligned_cols=79  Identities=32%  Similarity=0.577  Sum_probs=74.4

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ..+..+|.|.||+.++++++|+++|.+||.|..+     +.+|.++|||||.|.+.++|++||+.|||.-++.-.|+|+|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            3467899999999999999999999999999988     57999999999999999999999999999999999999999


Q ss_pred             ecCC
Q 046223          300 SRPG  303 (408)
Q Consensus       300 a~~~  303 (408)
                      ++|+
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9885

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.48  E-value=1.4e-13  Score=134.11  Aligned_cols=77  Identities=19%  Similarity=0.440  Sum_probs=71.5

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..+|||+|||.++++++|+++|+.||.|.+|+     .+++++|||||+|.+.++|++|++.|||..|.|+.|+|+|+++
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            48999999999999999999999999999883     4577899999999999999999999999999999999999976


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      ..
T Consensus        83 ~~   84 (352)
T TIGR01661        83 SS   84 (352)
T ss_pred             cc
Confidence            54

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

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

Probab=99.46  E-value=7.4e-12  Score=115.34  Aligned_cols=225  Identities=16%  Similarity=0.157  Sum_probs=153.0

Q ss_pred             CCCCCCEEEEc--CCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           78 STGPTRTLVLS--YVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        78 ~~~~~rtlfV~--nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ...++..|.+.  |-=+.+|-+-|+.+....|+|..|.|.+++.=.|.|+|++.+.|++|.+.|||..|.-+..  .|++
T Consensus       116 s~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCC--TLKI  193 (494)
T KOG1456|consen  116 SATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCC--TLKI  193 (494)
T ss_pred             CCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccce--eEEE
Confidence            34455666655  4456799999999999999999999998877789999999999999999999999987776  4667


Q ss_pred             cccCccc--cccCCCCCCCcccCCC----ChhHHHHHHhhhhccCCCCCCCcCCCCCCCCc----cccccCCcC------
Q 046223          156 PYSSGLM--LMNNDNNNNNLATGCY----DNQVVAESLMIMNSYAPVLPPPARGLVAGRPV----WAQFIVPTC------  219 (408)
Q Consensus       156 ~~s~~~s--~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~----~~~~~~p~~------  219 (408)
                      +|+++..  |.+.+....++....+    +...-.-.......+..-.+...++...+-..    ......|..      
T Consensus       194 eyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~  273 (494)
T KOG1456|consen  194 EYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYR  273 (494)
T ss_pred             EecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccc
Confidence            7888766  6666655554432221    11100000000000000000000000000000    000000100      


Q ss_pred             -----CCCCCCCCCceEEEcCCCCC-CcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCe
Q 046223          220 -----NAVPDGNNQGTIVVFNLDSG-VSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK  293 (408)
Q Consensus       220 -----~~~~~~~~~~~l~V~nLp~~-~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~  293 (408)
                           .......+...+.|.+|... ++-+.|.++|..||.|+.|++.....|.|.|++.|..+.++|+..||+..+.|.
T Consensus       274 ~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~  353 (494)
T KOG1456|consen  274 DGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGG  353 (494)
T ss_pred             cCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccc
Confidence                 01123445788999999874 678899999999999999988878889999999999999999999999999999


Q ss_pred             EEEEEEecCCC
Q 046223          294 HVVIEFSRPGG  304 (408)
Q Consensus       294 ~l~v~~a~~~~  304 (408)
                      +|.|.+++...
T Consensus       354 kl~v~~SkQ~~  364 (494)
T KOG1456|consen  354 KLNVCVSKQNF  364 (494)
T ss_pred             eEEEeeccccc
Confidence            99999987653

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

Probab=99.45  E-value=4.2e-13  Score=135.54  Aligned_cols=137  Identities=16%  Similarity=0.179  Sum_probs=94.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcc--CCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVF--GEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~--G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      ..++|||+||+.++||++|+++|++|  |+|+.|.++   ++||||+|.+.++|++|++.|||..|.  |+  .|++.|+
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~---rgfAFVeF~s~e~A~kAi~~lnG~~i~--Gr--~I~V~~A  304 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI---RDYAFVHFEDREDAVKAMDELNGKELE--GS--EIEVTLA  304 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee---cCeEEEEeCCHHHHHHHHHHhCCCEEC--CE--EEEEEEc
Confidence            45789999999999999999999999  999999875   689999999999999999999999876  66  4666665


Q ss_pred             CccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCCC
Q 046223          159 SGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDS  238 (408)
Q Consensus       159 ~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp~  238 (408)
                      .....    ....     +.                      .++. .++....+... ......-.....+++++|+++
T Consensus       305 kp~~~----~~~~-----~~----------------------~rg~-gg~~~~~~~~~-~~~g~~~sp~s~~~~~g~~~~  351 (578)
T TIGR01648       305 KPVDK----KSYV-----RY----------------------TRGT-GGRGKERQAAR-QSLGQVYDPASRSLAYEDYYY  351 (578)
T ss_pred             cCCCc----cccc-----cc----------------------cccc-CCCcccccccc-cccCcccCccccccccccccc
Confidence            42210    0000     00                      0000 00000000000 000001122358999999999


Q ss_pred             CCcHHHHHHHHhcCCCcee
Q 046223          239 GVSSSTLKEIFQAFGPVKE  257 (408)
Q Consensus       239 ~~t~~~L~~~F~~~G~v~~  257 (408)
                      +.+++.+.++|..+|.|..
T Consensus       352 ~~~~~~~~~~f~~~g~~~~  370 (578)
T TIGR01648       352 HPPYAPSLHFPRMPGPIRG  370 (578)
T ss_pred             cccccchhhccccCccccC
Confidence            9999999999999998754

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.

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

Probab=99.43  E-value=1.1e-12  Score=119.06  Aligned_cols=73  Identities=19%  Similarity=0.212  Sum_probs=65.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....+.|+|+|||+..-|-||+.+|++||.|.+|.|+.   -+||||||+|++.+||++|.++|||..+.  ||.|.+
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VE--GRkIEV  168 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVE--GRKIEV  168 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceee--ceEEEE
Confidence            33457899999999999999999999999999999885   57999999999999999999999999987  884333

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

Probab=99.42  E-value=7.3e-12  Score=115.37  Aligned_cols=177  Identities=19%  Similarity=0.195  Sum_probs=129.4

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      +...++-.|.|++|-..++|.+|.+.++.||.|..|..+. .+..|.|+|+|++.|++++...-...+...|.  ..-..
T Consensus        26 hk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P-~~r~alvefedi~~akn~Vnfaa~n~i~i~gq--~Al~N  102 (494)
T KOG1456|consen   26 HKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMP-HKRQALVEFEDIEGAKNCVNFAADNQIYIAGQ--QALFN  102 (494)
T ss_pred             CCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEecc-ccceeeeeeccccchhhheehhccCcccccCc--hhhcc
Confidence            5566778999999999999999999999999999988774 57789999999999999997544333332222  11112


Q ss_pred             ccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEc--
Q 046223          157 YSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVF--  234 (408)
Q Consensus       157 ~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~--  234 (408)
                      |+...                                                   ....+.   .+....++.|.+.  
T Consensus       103 yStsq---------------------------------------------------~i~R~g---~es~~pN~VLl~TIl  128 (494)
T KOG1456|consen  103 YSTSQ---------------------------------------------------CIERPG---DESATPNKVLLFTIL  128 (494)
T ss_pred             cchhh---------------------------------------------------hhccCC---CCCCCCCeEEEEEee
Confidence            22100                                                   000000   1112234555544  


Q ss_pred             CCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeC--CeEEEEEEecCCCCCCCcc
Q 046223          235 NLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY--GKHVVIEFSRPGGHSKKFF  310 (408)
Q Consensus       235 nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~--g~~l~v~~a~~~~~~~~~~  310 (408)
                      |--+.+|.+-|..++...|.|..|....+..-.|.|+|++.+.|++|.+.|||..|.  ..+|+|+||++.+.+..+.
T Consensus       129 Np~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~kn  206 (494)
T KOG1456|consen  129 NPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKN  206 (494)
T ss_pred             cCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcceeeeeec
Confidence            555679999999999999999999655566667999999999999999999999875  4799999999977654433

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.42  E-value=7.6e-13  Score=119.17  Aligned_cols=74  Identities=22%  Similarity=0.306  Sum_probs=66.9

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeecc--CCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRE--TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~--~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+||++.+|+++|+++|+.||.|++|+.  .+..+|||||+|++.++|+.|+. |||..|.|+.|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            489999999999999999999999999999942  23357999999999999999996 999999999999999753

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

Probab=99.42  E-value=2.4e-12  Score=118.14  Aligned_cols=66  Identities=21%  Similarity=0.293  Sum_probs=59.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      +.-..|||..+.++.+|+||+.+|+.||+|..|.+.+     .+|||+||+|.+..+-..||..||-..+.
T Consensus       208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLG  278 (544)
T KOG0124|consen  208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLG  278 (544)
T ss_pred             HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcc
Confidence            3456899999999999999999999999999999976     67999999999999999999999875443

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

Probab=99.41  E-value=3.9e-13  Score=114.33  Aligned_cols=77  Identities=29%  Similarity=0.485  Sum_probs=71.7

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      .+...+|.|-||.+.++.++|..+|++||.|-+|     +.+..++|||||.|.+..+|+.|+++|+|..|+|+.|.|++
T Consensus        10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~   89 (256)
T KOG4207|consen   10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQM   89 (256)
T ss_pred             cccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehh
Confidence            3445789999999999999999999999999988     46888999999999999999999999999999999999999


Q ss_pred             ec
Q 046223          300 SR  301 (408)
Q Consensus       300 a~  301 (408)
                      |+
T Consensus        90 ar   91 (256)
T KOG4207|consen   90 AR   91 (256)
T ss_pred             hh
Confidence            86

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.41  E-value=7.6e-13  Score=119.18  Aligned_cols=69  Identities=25%  Similarity=0.271  Sum_probs=61.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec--CccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL--MEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~--~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      .++|||+||++++||++|+++|+.||+|.+|.|.+.  .+|||||+|.+.++|+.|+. |+|..|.  ||.|.+
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~--gr~V~V   74 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIV--DQSVTI   74 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeC--CceEEE
Confidence            689999999999999999999999999999999863  58999999999999999995 9999886  664333

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

Probab=99.40  E-value=1.2e-12  Score=99.25  Aligned_cols=76  Identities=16%  Similarity=0.233  Sum_probs=66.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ...++-|||.|||+++|.++..++|.+||.|..|++-.  ..+|.|||.|+++.+|++|++.|+|..+.  ++  .+.+.
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~--~r--yl~vl   90 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVD--NR--YLVVL   90 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccC--Cc--eEEEE
Confidence            34678999999999999999999999999999999854  56999999999999999999999998765  55  45555


Q ss_pred             cc
Q 046223          157 YS  158 (408)
Q Consensus       157 ~s  158 (408)
                      |-
T Consensus        91 yy   92 (124)
T KOG0114|consen   91 YY   92 (124)
T ss_pred             ec
Confidence            53

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.40  E-value=1.3e-12  Score=96.03  Aligned_cols=66  Identities=32%  Similarity=0.597  Sum_probs=58.4

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       231 l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      |||+|||.++++++|+++|+.||.|..+.    ..+..+++|||+|.+.++|.+|++.++|..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999998883    2255689999999999999999999999999999985

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 ....

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

Probab=99.39  E-value=1.5e-12  Score=98.68  Aligned_cols=78  Identities=21%  Similarity=0.440  Sum_probs=70.8

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec--cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~--~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      .++.|||.|||+++|.|++.++|.+||.|..|+  .+..-+|.|||.|++..+|.+|++.|+|..++++-+.|-+-.+..
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPED   96 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHH
Confidence            358999999999999999999999999999995  344568999999999999999999999999999999999877654

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.39  E-value=1.4e-12  Score=95.91  Aligned_cols=61  Identities=21%  Similarity=0.335  Sum_probs=54.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec----CccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           85 LVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL----MEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        85 lfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~----~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      |||+|||+++++++|+++|+.||.|..|.+...    .+|+|||+|.+.++|++|++.++|..|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~   65 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEID   65 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEEC
Confidence            799999999999999999999999999999874    4899999999999999999999887765

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 ....

>PLN03213 repressor of silencing 3; Provisional

Probab=99.38  E-value=1.3e-12  Score=124.26  Aligned_cols=75  Identities=21%  Similarity=0.301  Sum_probs=68.8

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee---ccCCCCccEEEEEECCH--HHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL---RETPLKKHQRFIEFYDV--RDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v---~~~~~~~g~afV~F~~~--~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ...+||||||++.++++||+.+|+.||.|..|   +.++  +|||||+|.+.  .++.+||..|||..|.|+.|+|..|+
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            35899999999999999999999999999988   4454  99999999987  78999999999999999999999998


Q ss_pred             CC
Q 046223          302 PG  303 (408)
Q Consensus       302 ~~  303 (408)
                      +.
T Consensus        87 P~   88 (759)
T PLN03213         87 EH   88 (759)
T ss_pred             HH
Confidence            63

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

Probab=99.38  E-value=1.4e-12  Score=127.66  Aligned_cols=185  Identities=15%  Similarity=0.260  Sum_probs=123.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ....+||++||..++++++.++.+.||.+....++.     .++||||.+|.+......|++.|||+.+.  ++.|....
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lg--d~~lvvq~  365 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLG--DKKLVVQR  365 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhc--CceeEeeh
Confidence            445799999999999999999999999999977765     56999999999999999999999998765  55433333


Q ss_pred             cccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcC
Q 046223          156 PYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFN  235 (408)
Q Consensus       156 ~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~n  235 (408)
                      .+.....+.      ....   +.              ..        .+.        .++.............|.+.|
T Consensus       366 A~~g~~~~~------~~~~---~~--------------~~--------~~~--------~i~~~~~q~~g~~t~Vl~L~n  406 (500)
T KOG0120|consen  366 AIVGASNAN------VNFN---IS--------------QS--------QVP--------GIPLLMTQMAGIPTEVLCLTN  406 (500)
T ss_pred             hhccchhcc------ccCC---cc--------------cc--------ccc--------cchhhhcccCCCcchhhhhhh
Confidence            222211000      0000   00              00        000        000000011122234455554


Q ss_pred             CCC--CC-cH-------HHHHHHHhcCCCceeec--------cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q 046223          236 LDS--GV-SS-------STLKEIFQAFGPVKELR--------ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVI  297 (408)
Q Consensus       236 Lp~--~~-t~-------~~L~~~F~~~G~v~~v~--------~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  297 (408)
                      +=.  ++ .+       |+++..|++||.|..|.        ......|..||+|.+.+++++|+++|+|++|.||.|..
T Consensus       407 ~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvt  486 (500)
T KOG0120|consen  407 VVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVA  486 (500)
T ss_pred             cCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEE
Confidence            411  11 11       45666778999999982        22345678999999999999999999999999999999


Q ss_pred             EEecCCCCC
Q 046223          298 EFSRPGGHS  306 (408)
Q Consensus       298 ~~a~~~~~~  306 (408)
                      .|..+....
T Consensus       487 sYydeDkY~  495 (500)
T KOG0120|consen  487 SYYDEDKYH  495 (500)
T ss_pred             EecCHHHhh
Confidence            998765443

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

Probab=99.37  E-value=1.1e-12  Score=103.22  Aligned_cols=71  Identities=17%  Similarity=0.210  Sum_probs=62.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      -..+.|||||||+..++|++|.++|+++|+|+.|.|--     ..-|||||+|.+.++|+.|++.++|..++  .|.|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLd--dr~i  108 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLD--DRPI  108 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCccc--ccce
Confidence            35688999999999999999999999999999987632     34799999999999999999999998876  6643

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

Probab=99.36  E-value=1.6e-12  Score=113.53  Aligned_cols=77  Identities=19%  Similarity=0.262  Sum_probs=69.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .+..+|=|.||+.+++|++|+++|..||.|..|.+.+     .+||||||.|.+.++|.+||+.|||.-++    .|.|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd----~LILr  262 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYD----NLILR  262 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccc----eEEEE
Confidence            3677899999999999999999999999999999887     56999999999999999999999998776    56788


Q ss_pred             ccccCc
Q 046223          155 NPYSSG  160 (408)
Q Consensus       155 ~~~s~~  160 (408)
                      +.|+++
T Consensus       263 vEwskP  268 (270)
T KOG0122|consen  263 VEWSKP  268 (270)
T ss_pred             EEecCC
Confidence            888763

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

Probab=99.33  E-value=1.2e-12  Score=112.22  Aligned_cols=80  Identities=28%  Similarity=0.522  Sum_probs=74.5

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ..++||||+|...++|.-|...|-.||.|.+|     ...++.+|||||+|...|+|.+|+..||+.+|.||.|+|.+|+
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            35899999999999999999999999999999     3677899999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 046223          302 PGGHS  306 (408)
Q Consensus       302 ~~~~~  306 (408)
                      |.+.+
T Consensus        89 P~kik   93 (298)
T KOG0111|consen   89 PEKIK   93 (298)
T ss_pred             Ccccc
Confidence            87544

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

Probab=99.33  E-value=1.9e-12  Score=112.80  Aligned_cols=75  Identities=28%  Similarity=0.364  Sum_probs=67.7

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      -.+||||||++.+..++|++.|++||+|++.     +.++++||||||+|.|.++|.+|++..| -.|+||+..+++|.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccccchhhh
Confidence            4789999999999999999999999999887     5789999999999999999999998554 568999999999865


Q ss_pred             C
Q 046223          303 G  303 (408)
Q Consensus       303 ~  303 (408)
                      .
T Consensus        91 g   91 (247)
T KOG0149|consen   91 G   91 (247)
T ss_pred             c
Confidence            3

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

Probab=99.33  E-value=8.2e-12  Score=112.09  Aligned_cols=79  Identities=30%  Similarity=0.528  Sum_probs=73.7

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      .++-+||||+-|+++++|.+|+..|++||.|+.|     ..+++++|||||+|+++.+...|.+..+|.+|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            4567999999999999999999999999999999     37899999999999999999999999999999999999999


Q ss_pred             ecCC
Q 046223          300 SRPG  303 (408)
Q Consensus       300 a~~~  303 (408)
                      -+..
T Consensus       178 ERgR  181 (335)
T KOG0113|consen  178 ERGR  181 (335)
T ss_pred             cccc
Confidence            7644

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

Probab=99.32  E-value=1.5e-11  Score=114.72  Aligned_cols=136  Identities=19%  Similarity=0.228  Sum_probs=95.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ..+|||+||+.++|+++|+++|.+||.|..|.+..     .++|||||+|.+.++|..|++.++|..|.  |+.  +++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~--~~~--~~v~  190 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELE--GRP--LRVQ  190 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeEC--Cce--eEee
Confidence            69999999999999999999999999998887764     56999999999999999999999998776  674  4443


Q ss_pred             ccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCC
Q 046223          157 YSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNL  236 (408)
Q Consensus       157 ~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nL  236 (408)
                      +....            ...+......                ........         ..............++++++
T Consensus       191 ~~~~~------------~~~~~~~~~~----------------~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~  233 (306)
T COG0724         191 KAQPA------------SQPRSELSNN----------------LDASFAKK---------LSRGKALLLEKSDNLYVGNL  233 (306)
T ss_pred             ccccc------------cccccccccc----------------cchhhhcc---------ccccccccccccceeecccc
Confidence            32100            0000000000                00000000         00001112334588999999


Q ss_pred             CCCCcHHHHHHHHhcCCCceee
Q 046223          237 DSGVSSSTLKEIFQAFGPVKEL  258 (408)
Q Consensus       237 p~~~t~~~L~~~F~~~G~v~~v  258 (408)
                      +..++..++...|..+|.+..+
T Consensus       234 ~~~~~~~~~~~~~~~~~~~~~~  255 (306)
T COG0724         234 PLKTAEEELADLFKSRGDIVRA  255 (306)
T ss_pred             ccccchhHHHHhccccccceee
Confidence            9999999999999999999666

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.32  E-value=5.1e-12  Score=112.01  Aligned_cols=64  Identities=17%  Similarity=0.102  Sum_probs=59.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ...+|||+||++.+||++|+++|+.||+|.+|+|.+  +.+|||||+|.+.++|+.|+ .|+|..|.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~   69 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIV   69 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeC
Confidence            457999999999999999999999999999999987  45789999999999999999 69999986

>PF13893 RRM_5: RNA recognition motif

Probab=99.32  E-value=9.2e-12  Score=87.23  Aligned_cols=56  Identities=32%  Similarity=0.641  Sum_probs=50.2

Q ss_pred             HHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          245 LKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       245 L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      |+++|++||.|.++......+++|||+|.+.++|++|++.|||..++|++|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999654444699999999999999999999999999999999986

(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 ....

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

Probab=99.31  E-value=4.4e-12  Score=100.71  Aligned_cols=79  Identities=22%  Similarity=0.448  Sum_probs=73.0

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ....|||.++...+++++|.+.|..||+|+.+     +.++..+|||+|+|++.++|++|+.+|||..|.|+.|.|.|+-
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEE
Confidence            35789999999999999999999999999999     5688899999999999999999999999999999999999986


Q ss_pred             CCCC
Q 046223          302 PGGH  305 (408)
Q Consensus       302 ~~~~  305 (408)
                      .++.
T Consensus       151 v~gp  154 (170)
T KOG0130|consen  151 VKGP  154 (170)
T ss_pred             ecCC
Confidence            5443

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

Probab=99.30  E-value=8.8e-12  Score=111.89  Aligned_cols=82  Identities=20%  Similarity=0.354  Sum_probs=71.6

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccc
Q 046223           74 LPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQ  148 (408)
Q Consensus        74 ~p~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~g  148 (408)
                      .+.....+-+||||+-|+++++|.+|+..|+.||+|+.|.|++     +++|||||+|+++.+...|.+..+|..|.  +
T Consensus        93 dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Id--g  170 (335)
T KOG0113|consen   93 DPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKID--G  170 (335)
T ss_pred             CCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceec--C
Confidence            4445667899999999999999999999999999999999987     68999999999999999999999998876  6


Q ss_pred             cccceeccccC
Q 046223          149 QSYGLKNPYSS  159 (408)
Q Consensus       149 r~l~~~~~~s~  159 (408)
                      +  .|.|+|..
T Consensus       171 r--ri~VDvER  179 (335)
T KOG0113|consen  171 R--RILVDVER  179 (335)
T ss_pred             c--EEEEEecc
Confidence            6  45555543

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

Probab=99.30  E-value=5.3e-12  Score=105.68  Aligned_cols=78  Identities=29%  Similarity=0.505  Sum_probs=69.9

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec--cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~--~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ..++|||+|||.++.+.||+++|.+||.|..|.  .......||||+|++..+|+.||..-+|..++|..|+|+|+....
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr   84 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGR   84 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCC
Confidence            358999999999999999999999999999994  223346799999999999999999999999999999999997654

>PLN03213 repressor of silencing 3; Provisional

Probab=99.30  E-value=7.2e-12  Score=119.18  Aligned_cols=72  Identities=14%  Similarity=0.101  Sum_probs=63.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-cCccEEEEEECCH--HHHHHHHHHhcCccccccccccce
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-LMEGIVTVHFYDL--RHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-~~kG~afV~F~~~--~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....+||||||++++|+++|+.+|..||.|..|.|++ ..||||||+|.+.  .++.+||+.|||..+.  ||.|++
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWK--GR~LKV   82 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWK--GGRLRL   82 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeec--CceeEE
Confidence            3457899999999999999999999999999999997 4499999999987  7899999999999987  664333

>smart00362 RRM_2 RNA recognition motif

Probab=99.29  E-value=1.8e-11  Score=89.46  Aligned_cols=69  Identities=35%  Similarity=0.586  Sum_probs=62.1

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCceeeccC---CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q 046223          230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRET---PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE  298 (408)
Q Consensus       230 ~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~---~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  298 (408)
                      +|+|+|||..+++++|+++|..||.|..+...   +..+++|||+|.+.++|++|++.++|..+.|+.|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999888322   4457999999999999999999999999999999873

>smart00362 RRM_2 RNA recognition motif

Probab=99.28  E-value=1.9e-11  Score=89.33  Aligned_cols=62  Identities=24%  Similarity=0.401  Sum_probs=56.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec---CccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL---MEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~---~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      +|||+|||.++++++|+++|++||.|..+.+...   ++|+|||+|.+.++|++|++.++|..+.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~   65 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLG   65 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEEC
Confidence            5899999999999999999999999999988764   3799999999999999999999987764

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

Probab=99.28  E-value=5.3e-12  Score=109.99  Aligned_cols=59  Identities=22%  Similarity=0.241  Sum_probs=53.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIR  140 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~ln  140 (408)
                      -..||||+|+|+++.++|++.|++||+|.+..++.     ++||||||+|.|.++|.+|++.-|
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~   75 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN   75 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC
Confidence            45799999999999999999999999999966654     789999999999999999997543

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.26  E-value=2.3e-11  Score=107.86  Aligned_cols=74  Identities=18%  Similarity=0.240  Sum_probs=66.4

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec--cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~--~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..+|||+||++.+|+++|+++|+.||.|.+|+  ..+..+++|||+|++.++|+.|+. |+|..|.++.|.|.....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            47999999999999999999999999999993  345567899999999999999995 999999999999987643

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

Probab=99.25  E-value=3.7e-10  Score=106.26  Aligned_cols=72  Identities=22%  Similarity=0.363  Sum_probs=65.3

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeecc--CCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRE--TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~--~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ..++|||.|||+++|++.|++-|..||.|..+..  .++++|  .|.|.+.++|++|+..|+|..+.||.|+|.|.
T Consensus       535 Ka~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  535 KACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cccEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            4688999999999999999999999999998864  555555  99999999999999999999999999999873

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

Probab=99.25  E-value=1.3e-11  Score=105.22  Aligned_cols=79  Identities=25%  Similarity=0.352  Sum_probs=68.4

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           76 PPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        76 ~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      +++...-.+|-|-||-+.++.++|+.+|++||.|-+|.|.+     .++|||||.|.+..+|+.|+++|+|..|+  |+ 
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ld--gR-   83 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLD--GR-   83 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeec--cc-
Confidence            34555667899999999999999999999999999999986     67999999999999999999999998876  77 


Q ss_pred             cceecccc
Q 046223          151 YGLKNPYS  158 (408)
Q Consensus       151 l~~~~~~s  158 (408)
                       .|+|.++
T Consensus        84 -elrVq~a   90 (256)
T KOG4207|consen   84 -ELRVQMA   90 (256)
T ss_pred             -eeeehhh
Confidence             4555443

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

Probab=99.21  E-value=2.1e-11  Score=102.02  Aligned_cols=76  Identities=36%  Similarity=0.464  Sum_probs=70.8

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      +...+|||+||+..++++.|+++|-+.|.|..+     +.+...+|||||+|.++|+|+-|++.||..++.|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            345899999999999999999999999999998     456678999999999999999999999999999999999998


Q ss_pred             c
Q 046223          301 R  301 (408)
Q Consensus       301 ~  301 (408)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            7

>smart00360 RRM RNA recognition motif

Probab=99.20  E-value=6.1e-11  Score=86.24  Aligned_cols=66  Identities=36%  Similarity=0.611  Sum_probs=59.3

Q ss_pred             EcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q 046223          233 VFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE  298 (408)
Q Consensus       233 V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  298 (408)
                      |+||+..+++++|+++|+.||.|..+.     ..+..+++|||+|.+.++|.+|++.|++..+.|+.|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            579999999999999999999998883     235568999999999999999999999999999999873

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

Probab=99.19  E-value=2e-12  Score=108.02  Aligned_cols=75  Identities=19%  Similarity=0.383  Sum_probs=70.4

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ++.-|||||||+.+||.||..+|++||+|..|     ..+|+++||||+.|++..+..-|+..|||..|.||.|+|.-..
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            45789999999999999999999999999999     4799999999999999999999999999999999999998653

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.19  E-value=1.2e-10  Score=85.42  Aligned_cols=70  Identities=40%  Similarity=0.632  Sum_probs=62.7

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCceeeccC----CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRET----PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       230 ~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~----~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      +|+|+|||..+++++|+++|..||.|..+...    ...+++|||+|.+.++|..|++.+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            48999999999999999999999999888322    23489999999999999999999999999999999874

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).

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

Probab=99.18  E-value=1.2e-10  Score=109.94  Aligned_cols=77  Identities=26%  Similarity=0.340  Sum_probs=70.3

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeC-CeEEEEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY-GKHVVIEF  299 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~l~v~~  299 (408)
                      ...+-||||.||.++.|+||.-+|++.|+|-+++     ..+.++|||||+|.+.++|++|++.||+.+|. |+.|.|+.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            3468999999999999999999999999999983     78899999999999999999999999999885 89998887


Q ss_pred             ecC
Q 046223          300 SRP  302 (408)
Q Consensus       300 a~~  302 (408)
                      +..
T Consensus       161 Sva  163 (506)
T KOG0117|consen  161 SVA  163 (506)
T ss_pred             eee
Confidence            753

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

Probab=99.17  E-value=4.3e-11  Score=116.61  Aligned_cols=77  Identities=30%  Similarity=0.468  Sum_probs=72.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      +.|||||||+++++++|.++|+..|.|.++     +.+|+.+||||++|.+.++|..|++.|||.++.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            889999999999999999999999999988     478999999999999999999999999999999999999999765


Q ss_pred             CC
Q 046223          304 GH  305 (408)
Q Consensus       304 ~~  305 (408)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

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

Probab=99.17  E-value=1.9e-11  Score=105.03  Aligned_cols=78  Identities=18%  Similarity=0.317  Sum_probs=70.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ...||||||+|..+|||.-|...|-.||+|..|.+.-     +++|||||+|.-.|||..||..||+.+|.  ||  .|+
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~--Gr--tir   83 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELF--GR--TIR   83 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhc--ce--eEE
Confidence            3578999999999999999999999999999998764     77999999999999999999999999988  77  577


Q ss_pred             ccccCcc
Q 046223          155 NPYSSGL  161 (408)
Q Consensus       155 ~~~s~~~  161 (408)
                      |+|+.+.
T Consensus        84 VN~AkP~   90 (298)
T KOG0111|consen   84 VNLAKPE   90 (298)
T ss_pred             EeecCCc
Confidence            7777644

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

Probab=99.17  E-value=1.2e-10  Score=114.21  Aligned_cols=187  Identities=18%  Similarity=0.241  Sum_probs=135.3

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhcc-----------C-CeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcc
Q 046223           76 PPSTGPTRTLVLSYVPGDVSETIVRRDLEVF-----------G-EVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQH  143 (408)
Q Consensus        76 ~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~-----------G-~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~  143 (408)
                      .......+.+||++++..++|+.+-.+|..-           | .|..|.+. ..++|||++|.+.++|..|+. +++..
T Consensus       169 ~~~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n-~~~nfa~ie~~s~~~at~~~~-~~~~~  246 (500)
T KOG0120|consen  169 SQATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLN-LEKNFAFIEFRSISEATEAMA-LDGII  246 (500)
T ss_pred             cchhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeec-ccccceeEEecCCCchhhhhc-ccchh
Confidence            3456678899999999999999999998874           3 35666655 469999999999999999985 66644


Q ss_pred             ccccccccceeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCC
Q 046223          144 MQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVP  223 (408)
Q Consensus       144 i~~~gr~l~~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~  223 (408)
                        ++|+.++++........             ..+-                        ...+.   .......+....
T Consensus       247 --f~g~~~~~~r~~d~~~~-------------p~~~------------------------~~~~~---~~~~~~~~~~t~  284 (500)
T KOG0120|consen  247 --FEGRPLKIRRPHDYQPV-------------PGIT------------------------LSPSQ---LGKVGLLPASTD  284 (500)
T ss_pred             --hCCCCceecccccccCC-------------ccch------------------------hhhcc---ccccCCcccccC
Confidence              34666556553321000             0000                        00000   000011111122


Q ss_pred             CCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q 046223          224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE  298 (408)
Q Consensus       224 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  298 (408)
                      .......+||++|+..+++.+++++...||.+...     ..++.++||||.+|.+......|+..|||..+++++|.|.
T Consensus       285 ~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq  364 (500)
T KOG0120|consen  285 VPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQ  364 (500)
T ss_pred             cccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEee
Confidence            23445889999999999999999999999988766     3457899999999999999999999999999999999999


Q ss_pred             EecCCCCC
Q 046223          299 FSRPGGHS  306 (408)
Q Consensus       299 ~a~~~~~~  306 (408)
                      .|-.....
T Consensus       365 ~A~~g~~~  372 (500)
T KOG0120|consen  365 RAIVGASN  372 (500)
T ss_pred             hhhccchh
Confidence            99776543

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

Probab=99.16  E-value=3.3e-12  Score=106.65  Aligned_cols=75  Identities=12%  Similarity=0.232  Sum_probs=67.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      -..+.-|||||||++.||.||..+|++||+|..|.+++     +++||||+.|+|..+...|+..|||..|.  ||.|++
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~--gRtirV  109 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKIL--GRTIRV  109 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceec--ceeEEe
Confidence            35678899999999999999999999999999999998     77999999999999999999999997766  885554


Q ss_pred             ec
Q 046223          154 KN  155 (408)
Q Consensus       154 ~~  155 (408)
                      -.
T Consensus       110 DH  111 (219)
T KOG0126|consen  110 DH  111 (219)
T ss_pred             ee
Confidence            43

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

Probab=99.15  E-value=1e-10  Score=101.83  Aligned_cols=78  Identities=28%  Similarity=0.587  Sum_probs=71.9

Q ss_pred             CceEEEcCCCCCCcHHHHHH----HHhcCCCceee--ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          228 QGTIVVFNLDSGVSSSTLKE----IFQAFGPVKEL--RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~----~F~~~G~v~~v--~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      +.||||.||+..+..++|+.    +|++||.|.+|  ..+.+.+|.|||.|++.+.|..|++.|+|..+.|+.++|.||+
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~   88 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAK   88 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheeccc
Confidence            45999999999999999887    99999999999  3577889999999999999999999999999999999999998


Q ss_pred             CCCC
Q 046223          302 PGGH  305 (408)
Q Consensus       302 ~~~~  305 (408)
                      .+..
T Consensus        89 s~sd   92 (221)
T KOG4206|consen   89 SDSD   92 (221)
T ss_pred             Cccc
Confidence            7653

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

Probab=99.13  E-value=1.9e-10  Score=107.23  Aligned_cols=75  Identities=37%  Similarity=0.636  Sum_probs=70.0

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..+|||+||+..+++++|+++|..||.|..+     +.++..+|||||+|.+.++|..|++.++|..|.|+.|.|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            5999999999999999999999999999777     24688999999999999999999999999999999999999754

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.13  E-value=3e-10  Score=83.29  Aligned_cols=62  Identities=31%  Similarity=0.460  Sum_probs=57.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecC----ccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLM----EGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~----kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      +|+|+|||.++++++|+++|+.||.|..+.+....    +|+|||+|.+.++|..|++.+++..+.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~   66 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELG   66 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeEC
Confidence            48999999999999999999999999999888633    899999999999999999999997754

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).

>smart00360 RRM RNA recognition motif

Probab=99.12  E-value=2.1e-10  Score=83.31  Aligned_cols=59  Identities=25%  Similarity=0.439  Sum_probs=53.5

Q ss_pred             EcCCCCCCCHHHHHHHhhccCCeEEEEEeec-----CccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           87 LSYVPGDVSETIVRRDLEVFGEVRGVQMERL-----MEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        87 V~nLp~~vte~~L~~~F~~~G~V~~v~~~~~-----~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      |+|||.++++++|+++|+.||.|..+.+...     ++|+|||+|.+.++|.+|++.|++..+.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~   64 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELD   64 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeC
Confidence            6899999999999999999999999988762     3799999999999999999999987764

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

Probab=99.12  E-value=1.8e-11  Score=105.23  Aligned_cols=142  Identities=22%  Similarity=0.290  Sum_probs=112.1

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           76 PPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        76 ~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ++.....|||||+|+...|+|+-|.++|-+.|.|..|.|..   ...-||||.|.++-+...|++.+||..+.  ++.+ 
T Consensus         3 aaaae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~--~~e~-   79 (267)
T KOG4454|consen    3 AAAAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLE--EDEE-   79 (267)
T ss_pred             CCCcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhc--cchh-
Confidence            34455679999999999999999999999999999998875   12339999999999999999999996655  2210 


Q ss_pred             eeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEE
Q 046223          153 LKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIV  232 (408)
Q Consensus       153 ~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~  232 (408)
                                                                                                 ..+++
T Consensus        80 ---------------------------------------------------------------------------q~~~r   84 (267)
T KOG4454|consen   80 ---------------------------------------------------------------------------QRTLR   84 (267)
T ss_pred             ---------------------------------------------------------------------------hcccc
Confidence                                                                                       13444


Q ss_pred             EcC----CCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEE
Q 046223          233 VFN----LDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHV  295 (408)
Q Consensus       233 V~n----Lp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l  295 (408)
                      .|+    |...++++.+.+.|+.-|.+..++    ..+.++.++|+.+....+.-.++....+....-+++
T Consensus        85 ~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~~  155 (267)
T KOG4454|consen   85 CGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLELFQKKV  155 (267)
T ss_pred             cCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccCcCCCCc
Confidence            555    677889999999999999998883    346678899999988888888888777665444433

>PF13893 RRM_5: RNA recognition motif

Probab=99.12  E-value=1.8e-10  Score=80.62  Aligned_cols=55  Identities=22%  Similarity=0.436  Sum_probs=46.6

Q ss_pred             HHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           99 VRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        99 L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      |+++|++||+|..|.+.++.+++|||+|.+.++|++|++.|||..+.  |+.  +++.|
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~--g~~--l~V~~   55 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFN--GRP--LKVSY   55 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEET--TEE--EEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEC--CcE--EEEEE
Confidence            78999999999999998755699999999999999999999999875  663  55443

(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 ....

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

Probab=99.08  E-value=1.1e-09  Score=105.69  Aligned_cols=161  Identities=18%  Similarity=0.201  Sum_probs=104.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEE---EEEee----cCcc---EEEEEECCHHHHHHHHHHhcCccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRG---VQMER----LMEG---IVTVHFYDLRHAEMAFKEIREQHMQLQQ  148 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~---v~~~~----~~kG---~afV~F~~~~~A~~Ai~~lng~~i~~~g  148 (408)
                      ..-++.||||+||++++|++|...|..||.+.-   .+...    ..+|   |+|+.|+++.+.+.-+.++.-    ..+
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~----~~~  331 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE----GEG  331 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh----ccc
Confidence            345788999999999999999999999997654   11111    2366   999999999998887766532    111


Q ss_pred             cccceeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCC
Q 046223          149 QSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQ  228 (408)
Q Consensus       149 r~l~~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~  228 (408)
                      + +-+.+.-..               .+....++.            |+-..          ...+..   +....-+..
T Consensus       332 ~-~yf~vss~~---------------~k~k~VQIr------------PW~la----------Ds~fv~---d~sq~lDpr  370 (520)
T KOG0129|consen  332 N-YYFKVSSPT---------------IKDKEVQIR------------PWVLA----------DSDFVL---DHNQPIDPR  370 (520)
T ss_pred             c-eEEEEecCc---------------ccccceeEE------------eeEec----------cchhhh---ccCcccCcc
Confidence            1 111110000               000000000            00000          000000   011123446


Q ss_pred             ceEEEcCCCCCCcHHHHHHHHh-cCCCceee----c-cCCCCccEEEEEECCHHHHHHHHHH
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQ-AFGPVKEL----R-ETPLKKHQRFIEFYDVRDAAKALKE  284 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~-~~G~v~~v----~-~~~~~~g~afV~F~~~~~A~~A~~~  284 (408)
                      +|||||+||.-++-++|-.+|. -||.|..+    + ..+..+|-|=|+|.+..+-.+||.+
T Consensus       371 rTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  371 RTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            9999999999999999999999 79999888    1 4556789999999999999999874

>smart00361 RRM_1 RNA recognition motif

Probab=99.08  E-value=3.9e-10  Score=82.76  Aligned_cols=56  Identities=27%  Similarity=0.445  Sum_probs=49.5

Q ss_pred             HHHHHHHHh----cCCCceeec------cC--CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q 046223          242 SSTLKEIFQ----AFGPVKELR------ET--PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVI  297 (408)
Q Consensus       242 ~~~L~~~F~----~~G~v~~v~------~~--~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  297 (408)
                      +++|+++|+    +||.|.++.      .+  +.++|||||+|.+.++|.+|++.|||+.+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578888888    999998762      22  678999999999999999999999999999999986

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

Probab=99.05  E-value=2.2e-10  Score=102.61  Aligned_cols=73  Identities=22%  Similarity=0.408  Sum_probs=68.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      .+|||||||..+++.+|+.+|++||+|.+++   .-|.||||..++...|+.|+..|||.+|.|..|.|+-++.+.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECD---IvKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECD---IVKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeee---eecccceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            5799999999999999999999999999997   348899999999999999999999999999999999998773

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

Probab=99.04  E-value=1.8e-09  Score=100.11  Aligned_cols=184  Identities=15%  Similarity=0.108  Sum_probs=115.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcc----CCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVF----GEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~----G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      -.|-+++||+++|+.|+.++|..-    |.++.|-+++    +..|-|||.|..+++|+.|+..-.+ .|   |+  +..
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq-~i---Gq--RYI  235 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQ-NI---GQ--RYI  235 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHHHHH-HH---hH--HHH
Confidence            346688999999999999999632    2445555554    4589999999999999999975332 11   22  011


Q ss_pred             ccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEc
Q 046223          155 NPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVF  234 (408)
Q Consensus       155 ~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~  234 (408)
                      ..|...                   ...+.+.+..   +...      .++.+.........|. ...+......+|.++
T Consensus       236 ElFRST-------------------aaEvqqvlnr---~~s~------pLi~~~~sp~~p~~p~-~~~p~~~~kdcvRLR  286 (508)
T KOG1365|consen  236 ELFRST-------------------AAEVQQVLNR---EVSE------PLIPGLTSPLLPGGPA-RLVPPTRSKDCVRLR  286 (508)
T ss_pred             HHHHHh-------------------HHHHHHHHHh---hccc------cccCCCCCCCCCCCcc-ccCCCCCCCCeeEec
Confidence            111110                   0111111111   1100      1111110000000010 112223346899999


Q ss_pred             CCCCCCcHHHHHHHHhcCCCceee-------ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          235 NLDSGVSSSTLKEIFQAFGPVKEL-------RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       235 nLp~~~t~~~L~~~F~~~G~v~~v-------~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      +||+..+.|||.++|..|..-+..       ...|...|-|||+|.+.|+|..|....|++...+|-|+|--+.
T Consensus       287 GLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  287 GLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             CCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence            999999999999999887532221       4567778999999999999999999999888888888887654

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

Probab=99.03  E-value=4.2e-10  Score=114.51  Aligned_cols=164  Identities=18%  Similarity=0.250  Sum_probs=132.9

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec----CccEEEEEECCHHHHHHHHHHhcCcccccccc
Q 046223           74 LPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL----MEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQ  149 (408)
Q Consensus        74 ~p~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~----~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr  149 (408)
                      ++--+...++|||+|||+..+++.+|+..|..+|.|.+|.|...    ..-||||.|.+...+-.|...+.+..|.-.. 
T Consensus       364 ~~~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~-  442 (975)
T KOG0112|consen  364 LKLDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGT-  442 (975)
T ss_pred             ccccchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCc-
Confidence            34446678999999999999999999999999999999998762    3668999999999999999888876654111 


Q ss_pred             ccceeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCc
Q 046223          150 SYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQG  229 (408)
Q Consensus       150 ~l~~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~  229 (408)
                         ++.-|.                                                 .              .......
T Consensus       443 ---~r~glG-------------------------------------------------~--------------~kst~tt  456 (975)
T KOG0112|consen  443 ---HRIGLG-------------------------------------------------Q--------------PKSTPTT  456 (975)
T ss_pred             ---cccccc-------------------------------------------------c--------------cccccce
Confidence               111000                                                 0              0112248


Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEEecCCCC
Q 046223          230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG--KHVVIEFSRPGGH  305 (408)
Q Consensus       230 ~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~a~~~~~  305 (408)
                      .+++++|...+....|...|..||.|..|. ..+..-||+|.|++...|+.|+..|.|..|+|  +.++|.|+.+...
T Consensus       457 r~~sgglg~w~p~~~l~r~fd~fGpir~Id-y~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  457 RLQSGGLGPWSPVSRLNREFDRFGPIRIID-YRHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPGA  533 (975)
T ss_pred             eeccCCCCCCChHHHHHHHhhccCcceeee-cccCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCCC
Confidence            899999999999999999999999999885 33567799999999999999999999999986  7899999987553

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

Probab=99.03  E-value=2.3e-09  Score=94.52  Aligned_cols=160  Identities=16%  Similarity=0.195  Sum_probs=113.1

Q ss_pred             EEEEcCCCCCCCHHH-H--HHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           84 TLVLSYVPGDVSETI-V--RRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        84 tlfV~nLp~~vte~~-L--~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ..+++++-.++..+- |  ...|+.|-.+...++++    .-++++|+.|.....-.++-..-+++++.  .+  .++  
T Consensus        98 ~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~--~~--~VR--  171 (290)
T KOG0226|consen   98 RPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIG--KP--PVR--  171 (290)
T ss_pred             cccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhcccccccccc--Cc--cee--
Confidence            346677666665554 3  67777777666655544    34899999998877777766655554432  00  011  


Q ss_pred             ccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCC
Q 046223          157 YSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNL  236 (408)
Q Consensus       157 ~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nL  236 (408)
                                                                      ..+...|...++..|.     .+..+||+|.|
T Consensus       172 ------------------------------------------------~a~gtswedPsl~ew~-----~~DfRIfcgdl  198 (290)
T KOG0226|consen  172 ------------------------------------------------LAAGTSWEDPSLAEWD-----EDDFRIFCGDL  198 (290)
T ss_pred             ------------------------------------------------eccccccCCcccccCc-----cccceeecccc
Confidence                                                            1122334444444433     33489999999


Q ss_pred             CCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          237 DSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       237 p~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..+++++.|-..|.+|-.....     ..+++++||+||.|.+..++..|+++|+|+.++.+.|++..+.-
T Consensus       199 gNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~w  269 (290)
T KOG0226|consen  199 GNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEW  269 (290)
T ss_pred             cccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhH
Confidence            9999999999999998543222     45889999999999999999999999999999999998876543

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

Probab=99.01  E-value=5.5e-10  Score=108.98  Aligned_cols=73  Identities=19%  Similarity=0.246  Sum_probs=66.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ++|||||||++++|++|.++|+..|.|.+++++.     +.+||||++|.+.++|+.|++.|||.++.  ||  +|++.|
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~--gr--~l~v~~   94 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFN--GR--KLRVNY   94 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccC--Cc--eEEeec
Confidence            8999999999999999999999999999999875     56999999999999999999999998876  67  677777


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus        95 ~~   96 (435)
T KOG0108|consen   95 AS   96 (435)
T ss_pred             cc
Confidence            65

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

Probab=99.00  E-value=5.5e-10  Score=88.93  Aligned_cols=70  Identities=16%  Similarity=0.321  Sum_probs=61.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEe--ec---CccEEEEEECCHHHHHHHHHHhcCcccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQME--RL---MEGIVTVHFYDLRHAEMAFKEIREQHMQLQ  147 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~--~~---~kG~afV~F~~~~~A~~Ai~~lng~~i~~~  147 (408)
                      ..-..=-|||.++...+||++|.+.|..||+|+.+.+.  ++   .||||+|+|++.++|++|+..|||..|.++
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q  142 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQ  142 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCC
Confidence            34455679999999999999999999999999997764  32   399999999999999999999999988744

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

Probab=98.89  E-value=2.5e-09  Score=107.31  Aligned_cols=67  Identities=21%  Similarity=0.343  Sum_probs=61.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      .+||||||+|+..++|.||.++|+.||+|.+|.++ .++|+|||.+....+|.+|+..|++..+.  ++.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li-~~R~cAfI~M~~RqdA~kalqkl~n~kv~--~k~  486 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI-PPRGCAFIKMVRRQDAEKALQKLSNVKVA--DKT  486 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeec-cCCceeEEEEeehhHHHHHHHHHhccccc--cee
Confidence            47999999999999999999999999999999888 48999999999999999999999987654  553

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

Probab=98.89  E-value=1.9e-09  Score=104.95  Aligned_cols=75  Identities=53%  Similarity=0.822  Sum_probs=70.6

Q ss_pred             CCCCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          222 VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       222 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      .+.+.+..+|+|-|||..|++++|.++|+.||+|+.|+.+...+|..||+|.|+.+|++|+++|++.++.|+.|+
T Consensus        69 ~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   69 SEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            344567899999999999999999999999999999998889999999999999999999999999999999988

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

Probab=98.88  E-value=3.9e-09  Score=105.96  Aligned_cols=79  Identities=22%  Similarity=0.359  Sum_probs=73.6

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSK  307 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  307 (408)
                      ++|||||.|+..+++.||.++|+.||+|.+|... ..+++|||+.....+|.+|+.+|+...+.++.|+|.|+..++.+.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li-~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI-PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKS  499 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeec-cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcch
Confidence            6899999999999999999999999999999644 689999999999999999999999999999999999998777554

>smart00361 RRM_1 RNA recognition motif

Probab=98.86  E-value=6.6e-09  Score=76.23  Aligned_cols=52  Identities=19%  Similarity=0.308  Sum_probs=44.5

Q ss_pred             HHHHHHHhh----ccCCeEEEE-Ee--e-----cCccEEEEEECCHHHHHHHHHHhcCcccccccc
Q 046223           96 ETIVRRDLE----VFGEVRGVQ-ME--R-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQ  149 (408)
Q Consensus        96 e~~L~~~F~----~~G~V~~v~-~~--~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr  149 (408)
                      +++|+++|+    +||.|.+|. +.  +     .++|||||+|.+.++|.+|++.|||..+.  ||
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~--gr   65 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFD--GR   65 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEEC--CE
Confidence            678999998    999999984 32  2     35999999999999999999999998876  55

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

Probab=98.83  E-value=1e-08  Score=94.29  Aligned_cols=79  Identities=24%  Similarity=0.415  Sum_probs=68.8

Q ss_pred             CCCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHh-CCceeCCeEEEEEEec
Q 046223          223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEM-NGQEIYGKHVVIEFSR  301 (408)
Q Consensus       223 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l-~g~~~~g~~l~v~~a~  301 (408)
                      +.+....+|||++|...+++.||++.|.+||+|+.++.. ..+++|||+|.+.++|+.|.+.+ +...|+|++|+|.|.+
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~-~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRIL-PRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEee-cccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            345567899999999999999999999999999999644 45779999999999999988766 4557899999999998


Q ss_pred             C
Q 046223          302 P  302 (408)
Q Consensus       302 ~  302 (408)
                      +
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            8

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

Probab=98.83  E-value=4.7e-10  Score=113.79  Aligned_cols=142  Identities=15%  Similarity=0.142  Sum_probs=120.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ...++||+||+..+.+.+|...|..+|.+..|++..     +-+|+|||+|.+.++|.+||....+..+   |       
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~---g-------  735 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF---G-------  735 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh---h-------
Confidence            345789999999999999999999999888766552     4499999999999999999974433221   0       


Q ss_pred             cccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcC
Q 046223          156 PYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFN  235 (408)
Q Consensus       156 ~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~n  235 (408)
                                                                                              ...++|.|
T Consensus       736 ------------------------------------------------------------------------K~~v~i~g  743 (881)
T KOG0128|consen  736 ------------------------------------------------------------------------KISVAISG  743 (881)
T ss_pred             ------------------------------------------------------------------------hhhhheeC
Confidence                                                                                    26789999


Q ss_pred             CCCCCcHHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          236 LDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       236 Lp~~~t~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      +|+..|+++|+.+|.++|.+.++    ...++.+|.|+|.|.+..+|.+++...++..+..+.+.|..+.+..
T Consensus       744 ~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~~  816 (881)
T KOG0128|consen  744 PPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPER  816 (881)
T ss_pred             CCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCcc
Confidence            99999999999999999999888    3567889999999999999999999999888888888888876643

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

Probab=98.82  E-value=5e-08  Score=84.48  Aligned_cols=84  Identities=21%  Similarity=0.285  Sum_probs=69.1

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceee--ccCCCC----ccEEEEEECCHHHHHHHHHHhCCceeC---CeEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL--RETPLK----KHQRFIEFYDVRDAAKALKEMNGQEIY---GKHVV  296 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v--~~~~~~----~g~afV~F~~~~~A~~A~~~l~g~~~~---g~~l~  296 (408)
                      ...+||||.+||.++...||..+|..|-..+..  +.+.+.    +-+|||+|.+..+|.+|+++|||..|+   +..|+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            446999999999999999999999988544443  333333    479999999999999999999999987   78999


Q ss_pred             EEEecCCCCCCCc
Q 046223          297 IEFSRPGGHSKKF  309 (408)
Q Consensus       297 v~~a~~~~~~~~~  309 (408)
                      |++|+...+..+.
T Consensus       112 iElAKSNtK~kr~  124 (284)
T KOG1457|consen  112 IELAKSNTKRKRR  124 (284)
T ss_pred             eeehhcCcccccC
Confidence            9999987655443

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

Probab=98.80  E-value=1.6e-08  Score=93.07  Aligned_cols=84  Identities=23%  Similarity=0.315  Sum_probs=69.1

Q ss_pred             CCCCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           74 LPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        74 ~p~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      +-++.....++|||++|-..++|.+|++.|.+||+|++|.+.. .+++|||+|.+.++|+.|.+.+-+ .+..+|+  ++
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~-~~~CAFv~ftTR~aAE~Aae~~~n-~lvI~G~--Rl  295 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILP-RKGCAFVTFTTREAAEKAAEKSFN-KLVINGF--RL  295 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeec-ccccceeeehhhHHHHHHHHhhcc-eeeecce--EE
Confidence            5556777889999999999999999999999999999998874 688999999999999999987766 3444565  35


Q ss_pred             eccccCcc
Q 046223          154 KNPYSSGL  161 (408)
Q Consensus       154 ~~~~s~~~  161 (408)
                      .+.|...+
T Consensus       296 ~i~Wg~~~  303 (377)
T KOG0153|consen  296 KIKWGRPK  303 (377)
T ss_pred             EEEeCCCc
Confidence            55566643

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

Probab=98.73  E-value=1.8e-08  Score=92.75  Aligned_cols=78  Identities=23%  Similarity=0.359  Sum_probs=71.9

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      +.+.|||--|.+-++++||+-+|+.||.|..+     +.++.+-.||||+|++.+++++|.=.|++..|+.++|.|.|+.
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            45899999999999999999999999999988     4678888999999999999999999999999999999999987


Q ss_pred             CCC
Q 046223          302 PGG  304 (408)
Q Consensus       302 ~~~  304 (408)
                      +-.
T Consensus       318 SVs  320 (479)
T KOG0415|consen  318 SVS  320 (479)
T ss_pred             hhh
Confidence            543

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.70  E-value=2.4e-08  Score=93.25  Aligned_cols=171  Identities=18%  Similarity=0.211  Sum_probs=123.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ....++|++++..++.+.++..++..+|.+....+..     .++|++.|.|...+.+..|+.......+.  ++.  +.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~--~~~--~~  161 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLD--GNK--GE  161 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccc--ccc--cc
Confidence            3577899999999999999999999999777755543     46999999999999999999754322222  110  11


Q ss_pred             ccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEE-E
Q 046223          155 NPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIV-V  233 (408)
Q Consensus       155 ~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~-V  233 (408)
                      ..+..              ..+ +                          ......          ..-......++| |
T Consensus       162 ~dl~~--------------~~~-~--------------------------~~~n~~----------~~~~~~~s~~~~~~  190 (285)
T KOG4210|consen  162 KDLNT--------------RRG-L--------------------------RPKNKL----------SRLSSGPSDTIFFV  190 (285)
T ss_pred             Ccccc--------------ccc-c--------------------------cccchh----------cccccCccccceee
Confidence            11000              000 0                          000000          000111234555 9


Q ss_pred             cCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCCC
Q 046223          234 FNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHS  306 (408)
Q Consensus       234 ~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~  306 (408)
                      +||++.+++++|+..|..+|.|..+     ..++..+|||+|.|.+...+..++.. ....++++.+.+.+.++....
T Consensus       191 ~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  191 GELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPKS  267 (285)
T ss_pred             cccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCccc
Confidence            9999999999999999999999988     35777899999999999999999987 888999999999998776543

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

Probab=98.70  E-value=2.7e-08  Score=88.24  Aligned_cols=68  Identities=13%  Similarity=0.194  Sum_probs=61.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEE--Eee---cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQ--MER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~--~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ...+..+|||-.||.+..+.||..+|-.||.|.+.+  +.|   .+|-|+||.|.+..+|+.||.+|||..|.
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIG  353 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIG  353 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhh
Confidence            566789999999999999999999999999999955  444   67999999999999999999999998875

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

Probab=98.66  E-value=7e-08  Score=82.93  Aligned_cols=79  Identities=22%  Similarity=0.292  Sum_probs=71.0

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcC-CCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAF-GPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE  298 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~-G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  298 (408)
                      ......++|..++..+.+.++..+|.+| |.|..+     +.+|.++|||||+|++.+.|.-|-+.||+..+.|+.|.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3445789999999999999999999999 666666     4689999999999999999999999999999999999999


Q ss_pred             EecCC
Q 046223          299 FSRPG  303 (408)
Q Consensus       299 ~a~~~  303 (408)
                      +-.+.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            98776

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

Probab=98.61  E-value=9e-08  Score=82.26  Aligned_cols=72  Identities=17%  Similarity=0.208  Sum_probs=61.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcc-CCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVF-GEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~-G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ....+||..+|.-+.|.++..+|.+| |.|..+++.|     .++|||||+|++.+.|+-|-+.||+..|.  ++-|.+.
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~--e~lL~c~  125 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLM--EHLLECH  125 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhh--hheeeeE
Confidence            34568999999999999999999998 6777788865     67999999999999999999999998876  5543333

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

Probab=98.60  E-value=4.1e-08  Score=86.48  Aligned_cols=72  Identities=25%  Similarity=0.517  Sum_probs=66.7

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ..+||++|++.+.+.+|+++|..||.|.++.   ...||+||+|.+..+|..|+..||++.|+|.++.|++++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~---mk~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDAD---MKNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccce---eecccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            4689999999999999999999999998875   45789999999999999999999999999999999999854

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

Probab=98.56  E-value=1.4e-07  Score=91.87  Aligned_cols=76  Identities=20%  Similarity=0.373  Sum_probs=67.7

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      -.++|||.+|...+.-.||+++|++||.|+..+     .+...+.|+||++.+.++|.+||+.||.++|.|+-|.|+.++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            357899999999999999999999999987662     233457899999999999999999999999999999999987


Q ss_pred             C
Q 046223          302 P  302 (408)
Q Consensus       302 ~  302 (408)
                      .
T Consensus       484 N  484 (940)
T KOG4661|consen  484 N  484 (940)
T ss_pred             c
Confidence            4

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

Probab=98.55  E-value=3e-07  Score=82.91  Aligned_cols=79  Identities=29%  Similarity=0.404  Sum_probs=71.4

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ..+|+|.||++.|+++||+++|..||.++.+    ...+.+.|.|-|.|...++|.+|++.+||..++|+.+++....+.
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSP  162 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCc
Confidence            4789999999999999999999999988877    467788899999999999999999999999999999999988765


Q ss_pred             CCC
Q 046223          304 GHS  306 (408)
Q Consensus       304 ~~~  306 (408)
                      ...
T Consensus       163 ~~~  165 (243)
T KOG0533|consen  163 SQS  165 (243)
T ss_pred             ccc
Confidence            433

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

Probab=98.52  E-value=1.3e-07  Score=87.25  Aligned_cols=78  Identities=12%  Similarity=0.182  Sum_probs=68.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ..+...|||..|.+-+|+++|.-+|+.||.|.++.+++     .+.-||||+|++.+++++|.=.|++..|.  .|  .|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLID--Dr--RI  311 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLID--DR--RI  311 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeec--cc--eE
Confidence            34567899999999999999999999999999999987     45779999999999999999999997766  55  47


Q ss_pred             eccccCc
Q 046223          154 KNPYSSG  160 (408)
Q Consensus       154 ~~~~s~~  160 (408)
                      .|.|+..
T Consensus       312 HVDFSQS  318 (479)
T KOG0415|consen  312 HVDFSQS  318 (479)
T ss_pred             Eeehhhh
Confidence            8888763

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

Probab=98.51  E-value=2.1e-05  Score=76.06  Aligned_cols=71  Identities=15%  Similarity=0.203  Sum_probs=56.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCc---eeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPV---KELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v---~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ..++..+||+..++.++.++|+..-.+   ..+..+++..|-|+|+|.+.++|..|+. -++..+..+-|.+-.-
T Consensus       282 ~fv~MRGlpy~a~~~di~nfFspl~p~~v~i~ig~dGr~TGEAdveF~t~edav~Ams-kd~anm~hrYVElFln  355 (510)
T KOG4211|consen  282 HFVHMRGLPYDATENDIANFFSPLNPYRVHIEIGPDGRATGEADVEFATGEDAVGAMG-KDGANMGHRYVELFLN  355 (510)
T ss_pred             ceeeecCCCccCCCcchhhhcCCCCceeEEEEeCCCCccCCcceeecccchhhHhhhc-cCCcccCcceeeeccc
Confidence            678889999999999999999865332   3335678889999999999999999976 5667777776665443

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.44  E-value=5.2e-08  Score=90.83  Aligned_cols=191  Identities=16%  Similarity=0.194  Sum_probs=115.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--------cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ..|-|.||.+.+|.++++.||...|+|..+.++.        .....|||.|.|...+..|.. |.+..+.  ++-| +.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfv--dral-iv   83 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFV--DRAL-IV   83 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceee--eeeE-EE
Confidence            4899999999999999999999999999988875        226789999999999999986 4454443  2322 22


Q ss_pred             ccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCC-CCCCcCCCCCCCCc-------cccccCCcCCC----C
Q 046223          155 NPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPV-LPPPARGLVAGRPV-------WAQFIVPTCNA----V  222 (408)
Q Consensus       155 ~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~g~~~-------~~~~~~p~~~~----~  222 (408)
                      +.|...                -+.++..-..+.  ...+.+ ..++..-+....++       ......|.-..    .
T Consensus        84 ~p~~~~----------------~~p~r~af~~l~--~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~  145 (479)
T KOG4676|consen   84 RPYGDE----------------VIPDRFAFVELA--DQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAK  145 (479)
T ss_pred             EecCCC----------------CCccHHHHHhcC--cccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhh
Confidence            222210                011110000000  011111 11111111111111       00000111100    0


Q ss_pred             CCCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       223 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      .-.....+++|++|...+...++.+.|..+|+|...+ ..+...-++.|+|....+...|+. ++|..+.-+...
T Consensus       146 kleeirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gre~k~qhsr  219 (479)
T KOG4676|consen  146 KLEEIRRTREVQSLISAAILPESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGRERKRQHSR  219 (479)
T ss_pred             hhHHHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcchhhhhhhhh
Confidence            0112247899999999999999999999999998773 344456678899999888888887 677665533333

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

Probab=98.39  E-value=2.4e-07  Score=86.91  Aligned_cols=78  Identities=18%  Similarity=0.283  Sum_probs=67.9

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ..++|||++|+++++++.|++.|++||+|.++     ..+++++||+||+|++.+...+++. ..-..|+|+.|.+..|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            45899999999999999999999999999988     3568899999999999999888876 44567899999999887


Q ss_pred             CCCC
Q 046223          302 PGGH  305 (408)
Q Consensus       302 ~~~~  305 (408)
                      ++..
T Consensus        84 ~r~~   87 (311)
T KOG4205|consen   84 SRED   87 (311)
T ss_pred             Cccc
Confidence            7653

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

Probab=98.38  E-value=4.8e-07  Score=88.17  Aligned_cols=69  Identities=13%  Similarity=0.149  Sum_probs=61.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--c---CccEEEEEECCHHHHHHHHHHhcCcccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--L---MEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQ  149 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--~---~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr  149 (408)
                      ...+|+|||.+|...+--.+|+++|++||+|+..+++.  +   .+-|+||++.+.++|.+||+.|+...|+  ||
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELH--Gr  475 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELH--GR  475 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhc--ce
Confidence            45678999999999999999999999999999988775  2   2779999999999999999999998877  66

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

Probab=98.34  E-value=1.3e-06  Score=78.75  Aligned_cols=75  Identities=20%  Similarity=0.252  Sum_probs=62.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      +.-...|+|.||++.|+++||+++|+.||.++.+-+..    .+.|.|-|.|...+||..|++.+||  +.++|+.+.+.
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~g--v~ldG~~mk~~  157 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNG--VALDGRPMKIE  157 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcC--cccCCceeeeE
Confidence            33446799999999999999999999999888876654    5689999999999999999999999  55568865544


Q ss_pred             c
Q 046223          155 N  155 (408)
Q Consensus       155 ~  155 (408)
                      +
T Consensus       158 ~  158 (243)
T KOG0533|consen  158 I  158 (243)
T ss_pred             E
Confidence            4

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

Probab=98.34  E-value=1.2e-06  Score=85.36  Aligned_cols=77  Identities=30%  Similarity=0.421  Sum_probs=65.1

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec----c-CCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----E-TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~-~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..+|||+|||.+++.++|+++|..||.|+...    . .++..+||||+|.+.++++.|+.+- -..++|++|.|+-.++
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCCeeEEEEeccc
Confidence            45699999999999999999999999998872    1 2334489999999999999999854 7789999999998776


Q ss_pred             CCC
Q 046223          303 GGH  305 (408)
Q Consensus       303 ~~~  305 (408)
                      ...
T Consensus       367 ~~~  369 (419)
T KOG0116|consen  367 GFR  369 (419)
T ss_pred             ccc
Confidence            543

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

Probab=98.34  E-value=6.4e-07  Score=87.19  Aligned_cols=71  Identities=10%  Similarity=0.167  Sum_probs=57.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ...+|||+|||.++++++|+++|+.||.|+...|..     +...||||+|.+.++++.||++-   .+.++++.+.+.
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As---p~~ig~~kl~Ve  362 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS---PLEIGGRKLNVE  362 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC---ccccCCeeEEEE
Confidence            345699999999999999999999999999976654     22389999999999999999864   555566644443

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

Probab=98.30  E-value=3e-06  Score=78.31  Aligned_cols=75  Identities=15%  Similarity=0.214  Sum_probs=67.6

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee------------ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeE
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL------------RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH  294 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v------------~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~  294 (408)
                      .+..|||.|||.++|.+++.++|+++|.|..-            ...|.-+|=|.|.|.-.++..-|++.|++..+.|++
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            35779999999999999999999999987654            245677899999999999999999999999999999


Q ss_pred             EEEEEec
Q 046223          295 VVIEFSR  301 (408)
Q Consensus       295 l~v~~a~  301 (408)
                      |+|+.|+
T Consensus       213 ~rVerAk  219 (382)
T KOG1548|consen  213 LRVERAK  219 (382)
T ss_pred             EEEehhh
Confidence            9999986

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

Probab=98.30  E-value=1.2e-06  Score=87.67  Aligned_cols=79  Identities=20%  Similarity=0.245  Sum_probs=66.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--------cCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      ...+++|||+||++.++|+.|-..|..||.|.+|+++.        ..+.+|||-|-+..+|++|++.|+|..+.  +. 
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~--~~-  247 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVM--EY-  247 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeee--ee-
Confidence            44578899999999999999999999999999999885        34789999999999999999999998776  22 


Q ss_pred             cceeccccCcc
Q 046223          151 YGLKNPYSSGL  161 (408)
Q Consensus       151 l~~~~~~s~~~  161 (408)
                       .++..|++..
T Consensus       248 -e~K~gWgk~V  257 (877)
T KOG0151|consen  248 -EMKLGWGKAV  257 (877)
T ss_pred             -eeeecccccc
Confidence             4555565433

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

Probab=98.28  E-value=1e-07  Score=89.65  Aligned_cols=149  Identities=13%  Similarity=0.178  Sum_probs=113.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccC--CeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccCcc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFG--EVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGL  161 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G--~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~~~  161 (408)
                      .+|++||.+.++..+|..+|...-  --..+ ++  ..||+||.+.|...|.+|++.++|+. .++|+  .+.+.++..+
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~f-l~--k~gyafvd~pdq~wa~kaie~~sgk~-elqGk--r~e~~~sv~k   76 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQF-LV--KSGYAFVDCPDQQWANKAIETLSGKV-ELQGK--RQEVEHSVPK   76 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcce-ee--ecceeeccCCchhhhhhhHHhhchhh-hhcCc--eeeccchhhH
Confidence            589999999999999999998652  11112 22  37999999999999999999998863 44555  2333222100


Q ss_pred             ccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCCCCCc
Q 046223          162 MLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVS  241 (408)
Q Consensus       162 s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp~~~t  241 (408)
                                                                                     ...++.+-|.|++....
T Consensus        77 ---------------------------------------------------------------kqrsrk~Qirnippql~   93 (584)
T KOG2193|consen   77 ---------------------------------------------------------------KQRSRKIQIRNIPPQLQ   93 (584)
T ss_pred             ---------------------------------------------------------------HHHhhhhhHhcCCHHHH
Confidence                                                                           01125688999999999


Q ss_pred             HHHHHHHHhcCCCceeeccCCCC--ccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          242 SSTLKEIFQAFGPVKELRETPLK--KHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       242 ~~~L~~~F~~~G~v~~v~~~~~~--~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ++.|..+...||.++.+......  .-..-|+|.+.+.++.|+..|+|..+....++|.|--
T Consensus        94 wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen   94 WEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             HHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            99999999999999988432222  2334588999999999999999999999999998863

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

Probab=98.28  E-value=1.4e-06  Score=87.25  Aligned_cols=78  Identities=24%  Similarity=0.445  Sum_probs=69.4

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec--------cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--------ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~--------~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      +....+|||+||+..++++.|...|..||.|..|+        .....+.+|||-|-+..+|++|++.|+|..+.+..++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            34568999999999999999999999999999882        2334577999999999999999999999999999999


Q ss_pred             EEEecC
Q 046223          297 IEFSRP  302 (408)
Q Consensus       297 v~~a~~  302 (408)
                      +.|++.
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999864

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

Probab=98.23  E-value=4.7e-07  Score=78.37  Aligned_cols=74  Identities=24%  Similarity=0.290  Sum_probs=65.6

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+|+-..++|+-|.++|-.-|.|.+|.    ..++.+ ||||.|.++.+..-|++.|||..+.++.++|.+-..
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            48999999999999999999999999999882    233444 999999999999999999999999999999887543

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

Probab=98.22  E-value=2.5e-06  Score=77.10  Aligned_cols=78  Identities=21%  Similarity=0.290  Sum_probs=69.8

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      .+...+||+|+.+.+|.++++..|+.+|.|..+     +..+..+||+||+|.+.+.+++|+. |+|..|.|+.++|.+.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLK  177 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeee
Confidence            446899999999999999999999999999644     4566789999999999999999999 9999999999999998


Q ss_pred             cCCC
Q 046223          301 RPGG  304 (408)
Q Consensus       301 ~~~~  304 (408)
                      +.+.
T Consensus       178 r~~~  181 (231)
T KOG4209|consen  178 RTNV  181 (231)
T ss_pred             eeec
Confidence            7653

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

Probab=98.18  E-value=1.9e-06  Score=76.39  Aligned_cols=71  Identities=15%  Similarity=0.238  Sum_probs=62.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      -.||.|.|..+++++.|...|.+|-.....++++     +++||+||.|.+..++..|+++|+|+.+.  .|.+++|.
T Consensus       191 fRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVg--srpiklRk  266 (290)
T KOG0226|consen  191 FRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVG--SRPIKLRK  266 (290)
T ss_pred             ceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccc--cchhHhhh
Confidence            4699999999999999999999998766655554     67999999999999999999999999876  67777765

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.17  E-value=6.3e-06  Score=60.74  Aligned_cols=69  Identities=23%  Similarity=0.424  Sum_probs=48.2

Q ss_pred             ceEEEcCCCCCCcHHH----HHHHHhcCC-CceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          229 GTIVVFNLDSGVSSST----LKEIFQAFG-PVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~----L~~~F~~~G-~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..|+|.|||.+.+...    |+.++..+| .|..|     ..+.|+|.|.+.+.|.+|.+.|+|..+.|++|.|.|...
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCC
Confidence            5699999999887654    566777775 56554     358899999999999999999999999999999999743

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

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

Probab=98.17  E-value=1.1e-05  Score=62.29  Aligned_cols=76  Identities=20%  Similarity=0.284  Sum_probs=62.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcC--CCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeC----CeEEEE
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAF--GPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY----GKHVVI  297 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~--G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~----g~~l~v  297 (408)
                      .||-|+|||...|.++|.+++...  |....+     ..++-+.|||||.|.+.+.|.+-.+.++|+.+.    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            689999999999999999988653  433333     245567899999999999999999999999886    467788


Q ss_pred             EEecCCC
Q 046223          298 EFSRPGG  304 (408)
Q Consensus       298 ~~a~~~~  304 (408)
                      .||+-++
T Consensus        82 ~yAriQG   88 (97)
T PF04059_consen   82 SYARIQG   88 (97)
T ss_pred             ehhHhhC
Confidence            8987665

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

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.10  E-value=0.0002  Score=72.03  Aligned_cols=188  Identities=15%  Similarity=0.094  Sum_probs=111.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      .+-+.+.+.+..+.|++++|...- |..+.+..     ...|-++|+|....++++|+..-+-..+   .|.+.+.-.-.
T Consensus       313 y~~~~gm~fn~~~nd~rkfF~g~~-~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~---~R~~q~~P~g~  388 (944)
T KOG4307|consen  313 YNNYKGMEFNNDFNDGRKFFPGRN-AQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDV---NRPFQTGPPGN  388 (944)
T ss_pred             eeeecccccccccchhhhhcCccc-ccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhh---hcceeecCCCc
Confidence            344678999999999999997532 33333222     3389999999999999999864222111   23222211100


Q ss_pred             CccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccc--cCCcCCCCCCCCCCceEEEcCC
Q 046223          159 SGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQF--IVPTCNAVPDGNNQGTIVVFNL  236 (408)
Q Consensus       159 ~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~--~~p~~~~~~~~~~~~~l~V~nL  236 (408)
                      ..|..+          -....             .   ..+...+...|++...-.  ..+.....-......+|||..|
T Consensus       389 ~~~~~a----------~~~~~-------------~---~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~l  442 (944)
T KOG4307|consen  389 LGRNGA----------PPFQA-------------G---VPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQL  442 (944)
T ss_pred             cccccC----------ccccc-------------c---CCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccC
Confidence            000000          00000             0   000000001111110000  0000001112334689999999


Q ss_pred             CCCCcHHHHHHHHhcCCCcee-e----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          237 DSGVSSSTLKEIFQAFGPVKE-L----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       237 p~~~t~~~L~~~F~~~G~v~~-v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      |..+++.++.++|...-.|++ |    -.+++.++.|||.|.+++++.+|...-+...++.+.|+|.-..
T Consensus       443 P~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~  512 (944)
T KOG4307|consen  443 PVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIA  512 (944)
T ss_pred             CccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeechh
Confidence            999999999999998777776 4    2455677899999999999999988777778888999988654

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

Probab=98.07  E-value=2e-05  Score=60.96  Aligned_cols=63  Identities=14%  Similarity=0.190  Sum_probs=52.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcc--CCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVF--GEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~--G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      +||.|+|||...|.++|.+++...  |...-+.+.-     .+.|||||.|.+.++|.+-.+.++|..+.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~   71 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWP   71 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccc
Confidence            589999999999999999988763  4444444432     45999999999999999999999998764

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

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.04  E-value=2.4e-05  Score=57.67  Aligned_cols=67  Identities=21%  Similarity=0.277  Sum_probs=45.7

Q ss_pred             CEEEEcCCCCCCCHHH----HHHHhhccC-CeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           83 RTLVLSYVPGDVSETI----VRRDLEVFG-EVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        83 rtlfV~nLp~~vte~~----L~~~F~~~G-~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ..|||.|||.+.+-..    |+.++..|| .|.+|     ..+.|+|.|.+.+.|++|.+.|+|..+.  |+  +|.+.|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-----~~~tAilrF~~~~~A~RA~KRmegEdVf--G~--kI~v~~   73 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-----SGGTAILRFPNQEFAERAQKRMEGEDVF--GN--KISVSF   73 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SS--SS----EEES
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-----eCCEEEEEeCCHHHHHHHHHhhcccccc--cc--eEEEEE
Confidence            3689999999998776    566777887 45555     4799999999999999999999998887  44  355555


Q ss_pred             c
Q 046223          158 S  158 (408)
Q Consensus       158 s  158 (408)
                      .
T Consensus        74 ~   74 (90)
T PF11608_consen   74 S   74 (90)
T ss_dssp             S
T ss_pred             c
Confidence            4

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

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

Probab=97.94  E-value=0.00016  Score=67.90  Aligned_cols=155  Identities=19%  Similarity=0.149  Sum_probs=95.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCe-----EEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEV-----RGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V-----~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ..+..|-.++||+..++.+|..+|+-.--.     ......++..|.|.|.|.|.|.-+.|++.-.   .+.++|-  +.
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhk---hh~g~ry--ie  132 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHK---HHMGTRY--IE  132 (508)
T ss_pred             CcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhh---hhccCCc--ee
Confidence            344455678999999999999999864322     2222233568899999999999988987432   2223441  11


Q ss_pred             ccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEc
Q 046223          155 NPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVF  234 (408)
Q Consensus       155 ~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~  234 (408)
                       .|...-                      .+.++    ++           .|.......       .....+.-.|.++
T Consensus       133 -vYka~g----------------------e~f~~----ia-----------gg~s~e~~~-------flsk~~qvivRmR  167 (508)
T KOG1365|consen  133 -VYKATG----------------------EEFLK----IA-----------GGTSNEAAP-------FLSKENQVIVRMR  167 (508)
T ss_pred             -eeccCc----------------------hhheE----ec-----------CCccccCCC-------CCCcccceEEEec
Confidence             121100                      00000    00           000000000       0111234678889


Q ss_pred             CCCCCCcHHHHHHHHhcC----CC---ceee-ccCCCCccEEEEEECCHHHHHHHHHH
Q 046223          235 NLDSGVSSSTLKEIFQAF----GP---VKEL-RETPLKKHQRFIEFYDVRDAAKALKE  284 (408)
Q Consensus       235 nLp~~~t~~~L~~~F~~~----G~---v~~v-~~~~~~~g~afV~F~~~~~A~~A~~~  284 (408)
                      +||+++++.|+.++|..-    |.   |..| +.+++..|-|||.|..+++|+.|+..
T Consensus       168 GLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  168 GLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK  225 (508)
T ss_pred             CCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH
Confidence            999999999999999632    12   3333 45788899999999999999999863

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

Probab=97.94  E-value=1.1e-05  Score=72.88  Aligned_cols=67  Identities=18%  Similarity=0.209  Sum_probs=59.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ...+.+.+||+|+.+.+|.+++...|+.||.|..|.+..     ..+|||||+|.+.+.+++|+. |+|..|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~  168 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIP  168 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccc
Confidence            455678999999999999999999999999998766654     459999999999999999998 9998887

>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=97.87  E-value=2.3e-05  Score=62.05  Aligned_cols=70  Identities=26%  Similarity=0.377  Sum_probs=44.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCc-----eeCCeEEEEEE
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ-----EIYGKHVVIEF  299 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~-----~~~g~~l~v~~  299 (408)
                      ..|+|.++...++.++|++.|+.||.|..|... .....|+|.|.+.++|++|+..+...     .+.+..+.++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~-~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFS-RGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE---TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEec-CCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            568899999999999999999999999999644 45678999999999999999887543     55565555554

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

>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=97.80  E-value=6.8e-05  Score=59.31  Aligned_cols=59  Identities=24%  Similarity=0.258  Sum_probs=40.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQ  142 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~  142 (408)
                      ..|.|.++...++-++|+++|+.||.|..|.+.+ ....|||.|.+.++|++|++.+...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~-G~~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR-GDTEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--T-T-SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecC-CCCEEEEEECCcchHHHHHHHHHhc
Confidence            3588999999999999999999999999998874 5668999999999999999987654

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

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

Probab=97.58  E-value=8.2e-05  Score=69.55  Aligned_cols=80  Identities=19%  Similarity=0.312  Sum_probs=71.0

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-------------ccCCCCccEEEEEECCHHHHHHHHHHhCCceeC
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-------------RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY  291 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-------------~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~  291 (408)
                      .....+|||.+|+..+++++|.++|.++|.|..=             +.+...|+-|.|.|++...|+.|+..++++.+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            4557899999999999999999999999987543             356778999999999999999999999999999


Q ss_pred             CeEEEEEEecCCC
Q 046223          292 GKHVVIEFSRPGG  304 (408)
Q Consensus       292 g~~l~v~~a~~~~  304 (408)
                      |..|+|.+|..+.
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999999987554

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

Probab=97.56  E-value=0.0002  Score=49.06  Aligned_cols=53  Identities=21%  Similarity=0.319  Sum_probs=44.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHH
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAF  136 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai  136 (408)
                      ++.|-|.+.+.+..+. +...|..||+|..+.+. ......+|+|.+..+|++|+
T Consensus         1 ~~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    1 STWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             CcEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            3578899998777654 55589999999998886 46889999999999999985

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.54  E-value=0.00015  Score=66.92  Aligned_cols=74  Identities=18%  Similarity=0.392  Sum_probs=59.7

Q ss_pred             CceEEEcCCCCCCcHHHH------HHHHhcCCCceeeccCCC------Ccc-E-EEEEECCHHHHHHHHHHhCCceeCCe
Q 046223          228 QGTIVVFNLDSGVSSSTL------KEIFQAFGPVKELRETPL------KKH-Q-RFIEFYDVRDAAKALKEMNGQEIYGK  293 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L------~~~F~~~G~v~~v~~~~~------~~g-~-afV~F~~~~~A~~A~~~l~g~~~~g~  293 (408)
                      ..-+||-+|+..+..|++      .++|.+||.|..|....+      ..+ + .+|+|.+.|+|.+||.+.+|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            467899999998876662      589999999999821111      112 2 48999999999999999999999999


Q ss_pred             EEEEEEec
Q 046223          294 HVVIEFSR  301 (408)
Q Consensus       294 ~l~v~~a~  301 (408)
                      .|+..|..
T Consensus       194 ~lkatYGT  201 (480)
T COG5175         194 VLKATYGT  201 (480)
T ss_pred             eEeeecCc
Confidence            99999865

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

Probab=97.43  E-value=0.00015  Score=69.04  Aligned_cols=64  Identities=17%  Similarity=0.264  Sum_probs=56.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec------------------CccEEEEEECCHHHHHHHHHHhc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL------------------MEGIVTVHFYDLRHAEMAFKEIR  140 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~------------------~kG~afV~F~~~~~A~~Ai~~ln  140 (408)
                      +-++|+|.+.|||.+-.-+.|.++|..+|.|..|+|..-                  .+-+|+|+|+..+.|.+|.+.|+
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            348999999999999999999999999999999998751                  25579999999999999999885


Q ss_pred             Cc
Q 046223          141 EQ  142 (408)
Q Consensus       141 g~  142 (408)
                      ..
T Consensus       308 ~e  309 (484)
T KOG1855|consen  308 PE  309 (484)
T ss_pred             hh
Confidence            53

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.24  E-value=0.00077  Score=67.95  Aligned_cols=71  Identities=17%  Similarity=0.338  Sum_probs=61.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCcee-e----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKE-L----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~-v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      +.|-+.|+|++++-+||.++|..|-.+-. |    ...+...|-|.|-|++.++|.+|...|+++.|..++|.+.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            37889999999999999999999954321 1    35677889999999999999999999999999999998865

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.15  E-value=0.0017  Score=50.65  Aligned_cols=72  Identities=22%  Similarity=0.294  Sum_probs=52.4

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec------------cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeE-
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR------------ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH-  294 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~------------~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~-  294 (408)
                      ..-|.|-+.|.. ....|.+.|++||.|.+..            .......+..|+|++..+|.+||. .||..++|.. 
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            356888888877 4567889999999998773            233457789999999999999998 8999999864 


Q ss_pred             EEEEEec
Q 046223          295 VVIEFSR  301 (408)
Q Consensus       295 l~v~~a~  301 (408)
                      +-|.+.+
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            4577664

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.

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

Probab=97.13  E-value=0.00025  Score=63.39  Aligned_cols=60  Identities=20%  Similarity=0.312  Sum_probs=48.3

Q ss_pred             HHHHHHHh-cCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          243 STLKEIFQ-AFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       243 ~~L~~~F~-~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      +||...|+ +||+|+++.    ....-.|-++|.|..+++|++|+..||+.++.|++|..++.--
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            44555555 999999882    1122367899999999999999999999999999999998753

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

Probab=97.13  E-value=0.0011  Score=45.31  Aligned_cols=52  Identities=21%  Similarity=0.346  Sum_probs=42.1

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHH
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKAL  282 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~  282 (408)
                      +.|-|.+.+.+.. +++...|..||+|..+... ....+.+|+|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            5678888887665 4566688899999998644 56789999999999999985

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.12  E-value=0.0009  Score=61.89  Aligned_cols=75  Identities=12%  Similarity=0.249  Sum_probs=59.2

Q ss_pred             CEEEEcCCCCCCCHHH----H--HHHhhccCCeEEEEEeecC------ccE--EEEEECCHHHHHHHHHHhcCccccccc
Q 046223           83 RTLVLSYVPGDVSETI----V--RRDLEVFGEVRGVQMERLM------EGI--VTVHFYDLRHAEMAFKEIREQHMQLQQ  148 (408)
Q Consensus        83 rtlfV~nLp~~vte~~----L--~~~F~~~G~V~~v~~~~~~------kG~--afV~F~~~~~A~~Ai~~lng~~i~~~g  148 (408)
                      .-+||-+|++.+-.++    |  .++|.+||.|..|.+.++.      .+.  .||+|.+.|||.+||.+.+|..++  |
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D--G  192 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD--G  192 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccccc--C
Confidence            4589999999988877    2  4799999999998887622      333  399999999999999999998876  7


Q ss_pred             cccceeccccCcc
Q 046223          149 QSYGLKNPYSSGL  161 (408)
Q Consensus       149 r~l~~~~~~s~~~  161 (408)
                      |  .++..|...+
T Consensus       193 r--~lkatYGTTK  203 (480)
T COG5175         193 R--VLKATYGTTK  203 (480)
T ss_pred             c--eEeeecCchH
Confidence            7  4566665543

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

Probab=97.07  E-value=0.00072  Score=64.57  Aligned_cols=64  Identities=30%  Similarity=0.334  Sum_probs=53.5

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCC------------------CccEEEEEECCHHHHHHHHHHhC
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPL------------------KKHQRFIEFYDVRDAAKALKEMN  286 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~------------------~~g~afV~F~~~~~A~~A~~~l~  286 (408)
                      .-..++|.+.|||.+-.-+.|.++|+.+|.|+.|+....                  .+-+|+|+|+..+.|.+|.+.|+
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            346799999999999989999999999999999942211                  14579999999999999999886


Q ss_pred             Cc
Q 046223          287 GQ  288 (408)
Q Consensus       287 g~  288 (408)
                      ..
T Consensus       308 ~e  309 (484)
T KOG1855|consen  308 PE  309 (484)
T ss_pred             hh
Confidence            44

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

Probab=96.99  E-value=0.002  Score=63.56  Aligned_cols=73  Identities=14%  Similarity=0.205  Sum_probs=57.3

Q ss_pred             CCCCCCCEEEEcCCCCCCC--HH----HHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVS--ET----IVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQL  146 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vt--e~----~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~  146 (408)
                      ..+.-...|+|.|+|.--.  .+    -|..+|+++|+|..+.+..    ..+||.|++|.+..+|+.|++.|||+.|..
T Consensus        53 ~~eg~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldk  132 (698)
T KOG2314|consen   53 TAEGFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDK  132 (698)
T ss_pred             ccCCcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecc
Confidence            3445567899999985322  11    2668999999999988763    569999999999999999999999999875


Q ss_pred             ccc
Q 046223          147 QQQ  149 (408)
Q Consensus       147 ~gr  149 (408)
                      +..
T Consensus       133 nHt  135 (698)
T KOG2314|consen  133 NHT  135 (698)
T ss_pred             cce
Confidence            443

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.97  E-value=0.0016  Score=59.16  Aligned_cols=62  Identities=26%  Similarity=0.316  Sum_probs=49.3

Q ss_pred             HHHHHHHHhcCCCceeec---cCC---CCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          242 SSTLKEIFQAFGPVKELR---ETP---LKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       242 ~~~L~~~F~~~G~v~~v~---~~~---~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ++++++.+.+||.|..|.   ..+   ...---||+|...++|.+|+-.|||+.|+||.+...|....
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~e  367 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLE  367 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccHH
Confidence            457889999999998772   111   11223799999999999999999999999999999887543

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

Probab=96.92  E-value=0.00058  Score=60.96  Aligned_cols=65  Identities=22%  Similarity=0.185  Sum_probs=56.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec-------------Cc----cEEEEEECCHHHHHHHHHHhcCcc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL-------------ME----GIVTVHFYDLRHAEMAFKEIREQH  143 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~-------------~k----G~afV~F~~~~~A~~Ai~~lng~~  143 (408)
                      -.-.||+++||+.+.-.-|+++|+.||+|-.|.+...             ++    .-|+|+|.+...|..+.+.|||..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4567999999999999999999999999999998651             11    127899999999999999999998


Q ss_pred             cc
Q 046223          144 MQ  145 (408)
Q Consensus       144 i~  145 (408)
                      |.
T Consensus       153 Ig  154 (278)
T KOG3152|consen  153 IG  154 (278)
T ss_pred             cC
Confidence            86

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

Probab=96.89  E-value=0.0022  Score=62.85  Aligned_cols=61  Identities=21%  Similarity=0.263  Sum_probs=54.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhh-ccCCeEEEEEeec-----CccEEEEEECCHHHHHHHHHH
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLE-VFGEVRGVQMERL-----MEGIVTVHFYDLRHAEMAFKE  138 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~-~~G~V~~v~~~~~-----~kG~afV~F~~~~~A~~Ai~~  138 (408)
                      .-.+.||||||+||.-++-++|..+|+ -||.|..|-|..+     .+|-|-|+|.+-.+-.+||++
T Consensus       366 ~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  366 PIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            345789999999999999999999999 6999999887753     499999999999999999984

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

Probab=96.86  E-value=0.0033  Score=62.12  Aligned_cols=74  Identities=23%  Similarity=0.334  Sum_probs=58.9

Q ss_pred             CCceEEEcCCCCCCc------HHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeC-CeEE
Q 046223          227 NQGTIVVFNLDSGVS------SSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY-GKHV  295 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t------~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~l  295 (408)
                      -...|+|-|+|---.      ..-|..+|+++|+|..+    ...+..+||.|++|.+..+|+.|++.|||+.|+ .++.
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            347899999985321      23567889999998877    355678999999999999999999999999887 4566


Q ss_pred             EEEEe
Q 046223          296 VIEFS  300 (408)
Q Consensus       296 ~v~~a  300 (408)
                      .|..-
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            66543

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

Probab=96.85  E-value=0.00073  Score=60.37  Aligned_cols=68  Identities=22%  Similarity=0.365  Sum_probs=56.7

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----c--------CCCCcc----EEEEEECCHHHHHHHHHHhCCce
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----E--------TPLKKH----QRFIEFYDVRDAAKALKEMNGQE  289 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~--------~~~~~g----~afV~F~~~~~A~~A~~~l~g~~  289 (408)
                      ....||+++||+.+...-|+++|+.||.|-.|.     .        .+.+.+    -|.|+|.+...|..+...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            347899999999999999999999999998881     0        111121    28899999999999999999999


Q ss_pred             eCCeE
Q 046223          290 IYGKH  294 (408)
Q Consensus       290 ~~g~~  294 (408)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99864

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

Probab=96.84  E-value=0.0016  Score=61.02  Aligned_cols=70  Identities=16%  Similarity=0.127  Sum_probs=59.8

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEE--------EEEee-----cCccEEEEEECCHHHHHHHHHHhcCcc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRG--------VQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQH  143 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~--------v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~  143 (408)
                      .......+|||-+|+..+++.+|.++|.++|.|..        |.+.+     +.||-|.|.|.|...|+.||..++++.
T Consensus        61 ~~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkd  140 (351)
T KOG1995|consen   61 ADKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKD  140 (351)
T ss_pred             ccccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccc
Confidence            34556778999999999999999999999998765        33322     569999999999999999999999999


Q ss_pred             ccc
Q 046223          144 MQL  146 (408)
Q Consensus       144 i~~  146 (408)
                      +..
T Consensus       141 f~g  143 (351)
T KOG1995|consen  141 FCG  143 (351)
T ss_pred             ccC
Confidence            873

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

Probab=96.68  E-value=0.00041  Score=71.56  Aligned_cols=161  Identities=16%  Similarity=0.085  Sum_probs=103.7

Q ss_pred             CCCEEEEcCCCCCCCHH-HHHHHhhccCCeEEEEEee----cC-ccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           81 PTRTLVLSYVPGDVSET-IVRRDLEVFGEVRGVQMER----LM-EGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~-~L~~~F~~~G~V~~v~~~~----~~-kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ..+...+.++-+...+. .++..|+.+|.|+.|++..    .+ ..++++.+....+++.|... .+..+.  ++  ...
T Consensus       570 ~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~p-a~~~~a--~~--~~a  644 (881)
T KOG0128|consen  570 ERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVP-AGGALA--NR--SAA  644 (881)
T ss_pred             hhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcccc-cccccC--Cc--ccc
Confidence            34567778887776666 5788999999999999875    11 22677888877777777642 222221  11  000


Q ss_pred             ccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEc
Q 046223          155 NPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVF  234 (408)
Q Consensus       155 ~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~  234 (408)
                      +..+.                                               .+.....   .+ ..........++||+
T Consensus       645 v~~ad-----------------------------------------------~~~~~~~---~k-vs~n~~R~~~~~fvs  673 (881)
T KOG0128|consen  645 VGLAD-----------------------------------------------AEEKEEN---FK-VSPNEIRDLIKIFVS  673 (881)
T ss_pred             CCCCC-----------------------------------------------chhhhhc---cC-cCchHHHHHHHHHHh
Confidence            00000                                               0000000   00 000011234689999


Q ss_pred             CCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q 046223          235 NLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVI  297 (408)
Q Consensus       235 nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  297 (408)
                      ||+..+.++||.+.|..+|.+..++     ..+.-+|+|+|.|...++|.+|+...++..++...+.|
T Consensus       674 nl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~~v~i  741 (881)
T KOG0128|consen  674 NLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKISVAI  741 (881)
T ss_pred             hcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhhhhhe
Confidence            9999999999999999999887772     45667899999999999999999977766655333333

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

Probab=96.67  E-value=0.006  Score=50.50  Aligned_cols=56  Identities=25%  Similarity=0.456  Sum_probs=45.2

Q ss_pred             HHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          244 TLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       244 ~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      +|.+.|..||++.-+|..+   +.-+|+|.+-++|.+|+. |+|.+++|+.|+|+...+.
T Consensus        52 ~ll~~~~~~GevvLvRfv~---~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVG---DTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEET---TCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEeC---CeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            6788899999988877553   467999999999999988 9999999999999987654

; PDB: 1UFW_A 2DNR_A.

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

Probab=96.57  E-value=0.0017  Score=60.45  Aligned_cols=69  Identities=6%  Similarity=0.035  Sum_probs=57.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccC--CeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFG--EVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQ  149 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G--~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr  149 (408)
                      ..-++|||||-|.+|++||.+.....|  .+.++++..     .+||||+|...+..+.++.++.|-.+.|+++.-
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P  154 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSP  154 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCC
Confidence            345789999999999999999999888  344444432     679999999999999999999999988886654

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=96.50  E-value=0.0015  Score=61.31  Aligned_cols=64  Identities=14%  Similarity=0.281  Sum_probs=54.9

Q ss_pred             CCCEEE-EcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           81 PTRTLV-LSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        81 ~~rtlf-V~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ...++| |++|+.++++++|+..|..+|.|..|++..     ..+|||||.|.+...+..|+.. +...+.
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~  252 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIG  252 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCccc
Confidence            445566 999999999999999999999999998864     4599999999999999999976 555544

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.47  E-value=0.0023  Score=63.62  Aligned_cols=80  Identities=11%  Similarity=0.123  Sum_probs=65.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhc-cCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEV-FGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~-~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ....+..|+|.||=.-.|.-+|++++.+ .|.|.+.+|. +-|..|||.|.+.++|.+.+.+|||..+... .+-+|.+.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmD-kIKShCyV~yss~eEA~atr~AlhnV~WP~s-NPK~L~ad  517 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMD-KIKSHCYVSYSSVEEAAATREALHNVQWPPS-NPKHLIAD  517 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHH-HhhcceeEecccHHHHHHHHHHHhccccCCC-CCceeEee
Confidence            6778899999999999999999999995 6777777665 3477899999999999999999999887643 23356666


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |..
T Consensus       518 f~~  520 (718)
T KOG2416|consen  518 FVR  520 (718)
T ss_pred             ecc
Confidence            654

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.40  E-value=0.0058  Score=60.85  Aligned_cols=79  Identities=20%  Similarity=0.300  Sum_probs=66.6

Q ss_pred             CCCCCceEEEcCCCCCCcHHHHHHHHhc-CCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCcee---CCeEEEEEE
Q 046223          224 DGNNQGTIVVFNLDSGVSSSTLKEIFQA-FGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI---YGKHVVIEF  299 (408)
Q Consensus       224 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~-~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~---~g~~l~v~~  299 (408)
                      ....++.|+|.||-.-.|.-+|++++.+ .|.|++.+ ..+-+..|||.|.+.++|.+...+|||..|   +++.|.+.|
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~W-mDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf  518 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFW-MDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADF  518 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHH-HHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeee
Confidence            3456789999999999999999999994 56677764 345678899999999999999999999876   478999999


Q ss_pred             ecCC
Q 046223          300 SRPG  303 (408)
Q Consensus       300 a~~~  303 (408)
                      ....
T Consensus       519 ~~~d  522 (718)
T KOG2416|consen  519 VRAD  522 (718)
T ss_pred             cchh
Confidence            8654

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

Probab=96.28  E-value=0.005  Score=57.36  Aligned_cols=70  Identities=16%  Similarity=0.115  Sum_probs=58.1

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCC-----ceee--ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGP-----VKEL--RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVI  297 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~-----v~~v--~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  297 (408)
                      .-++|||||-+.+|++||.+.....|-     ++..  +..+.+||||+|...+..+.++-++.|-.++|.|+.-.|
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            468999999999999999998876652     2222  578899999999999999999999999999999874333

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

Probab=96.12  E-value=0.01  Score=53.23  Aligned_cols=59  Identities=25%  Similarity=0.442  Sum_probs=51.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHHhCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNG  287 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g  287 (408)
                      ..|+|.||..-++.+.|.+.|+.||.|...    ...++..+-++|.|...-.|.+|+..++-
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhcc
Confidence            679999999999999999999999987644    45667778899999999999999998853

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

Probab=96.06  E-value=0.0031  Score=56.61  Aligned_cols=54  Identities=22%  Similarity=0.329  Sum_probs=42.7

Q ss_pred             HHHHHHhh-ccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           97 TIVRRDLE-VFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        97 ~~L~~~F~-~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ++|...|+ +||+|+.+++..    .-.|-+||.|..+++|++|++.|||..+.  |++|.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~--G~pi~  141 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYN--GRPIH  141 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCcccc--CCcce
Confidence            34555555 899999987654    23889999999999999999999998876  66433

>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=96.04  E-value=0.016  Score=45.17  Aligned_cols=63  Identities=11%  Similarity=0.073  Sum_probs=46.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEE------------EeecCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQ------------MERLMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~------------~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ....|.|=+.|.. ....|.+.|++||+|.+..            -.........|+|.+..+|.+|+. .||..|.
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~   79 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFS   79 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEET
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEc
Confidence            3456888888887 5567888999999998875            122457889999999999999996 7887765

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.

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

Probab=96.00  E-value=0.0043  Score=59.25  Aligned_cols=77  Identities=25%  Similarity=0.350  Sum_probs=61.2

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCc-eeCCeEEEEEEecCCCCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ-EIYGKHVVIEFSRPGGHS  306 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~-~~~g~~l~v~~a~~~~~~  306 (408)
                      ..+|++||...++..||+.+|... .+-.-...-...||+||.+.+...|.+|++.++|+ ++.|+++.|..+-++..+
T Consensus         2 nklyignL~p~~~psdl~svfg~a-k~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqr   79 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDA-KIPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQR   79 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccc-cCCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHH
Confidence            468999999999999999999754 11111111135789999999999999999999997 788999999998776543

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

Probab=95.90  E-value=0.026  Score=46.82  Aligned_cols=69  Identities=19%  Similarity=0.232  Sum_probs=48.9

Q ss_pred             CCCEEEEcCCC-----CCCCHH----HHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           81 PTRTLVLSYVP-----GDVSET----IVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        81 ~~rtlfV~nLp-----~~vte~----~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      +..||.|.=+.     ...-.+    +|.+.|..||+|.-|++.   .+.-+|+|.+-++|.+|+. ++|.++.  |+.+
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv---~~~mwVTF~dg~sALaals-~dg~~v~--g~~l   99 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFV---GDTMWVTFRDGQSALAALS-LDGIQVN--GRTL   99 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEE---TTCEEEEESSCHHHHHHHH-GCCSEET--TEEE
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEe---CCeEEEEECccHHHHHHHc-cCCcEEC--CEEE
Confidence            34567766555     112233    577889999999888876   4689999999999999996 9998876  6655


Q ss_pred             ceec
Q 046223          152 GLKN  155 (408)
Q Consensus       152 ~~~~  155 (408)
                      +++.
T Consensus       100 ~i~L  103 (146)
T PF08952_consen  100 KIRL  103 (146)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            5554

; PDB: 1UFW_A 2DNR_A.

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

Probab=95.87  E-value=0.012  Score=61.39  Aligned_cols=79  Identities=15%  Similarity=0.178  Sum_probs=68.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ....++.+||++|...+....|...|..||.|..|.+. ...-||+|.|++...|+.|++.|.|..|..-.+  .+++.|
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~-hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~--r~rvdl  527 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR-HGQPYAYIQYESPPAAQAATHDMRGAPLGGPPR--RLRVDL  527 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecc-cCCcceeeecccCccchhhHHHHhcCcCCCCCc--cccccc
Confidence            44567889999999999999999999999999998775 467899999999999999999999988875555  577777


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus       528 a~  529 (975)
T KOG0112|consen  528 AS  529 (975)
T ss_pred             cc
Confidence            65

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=95.62  E-value=0.022  Score=57.70  Aligned_cols=61  Identities=16%  Similarity=0.119  Sum_probs=53.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      +.-+|||+|+...+..+-++.+...+|-|.++....    |||++|....-+.+|+..++...+.
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~----fgf~~f~~~~~~~ra~r~~t~~~~~   99 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK----FGFCEFLKHIGDLRASRLLTELNID   99 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh----hcccchhhHHHHHHHHHHhcccCCC
Confidence            456899999999999999999999999988876653    9999999999999999988776554

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

Probab=95.57  E-value=0.05  Score=40.43  Aligned_cols=55  Identities=11%  Similarity=0.250  Sum_probs=42.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNG  287 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g  287 (408)
                      ...+|+ .|..+...||.++|+.||.|.--.   ....-|||...+.+.|..|+..+..
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsW---i~dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSW---INDTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEE---ECTTEEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEE---EcCCcEEEEeecHHHHHHHHHHhcc
Confidence            566666 999999999999999999875444   3456799999999999999998863

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=95.54  E-value=0.031  Score=53.05  Aligned_cols=71  Identities=18%  Similarity=0.404  Sum_probs=56.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccC--------CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRET--------PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~--------~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ..|-|.||...+|.++++.+|...|.|.+++..        ......|||.|.|...+..|.. |.++.|-++.|.|-.+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            579999999999999999999999999998422        2234579999999999998866 6666666666555543

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

Probab=95.39  E-value=0.11  Score=38.59  Aligned_cols=54  Identities=11%  Similarity=0.214  Sum_probs=41.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcC
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIRE  141 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng  141 (408)
                      ..+|+ .|..+...||.++|+.||.|.--.|   +..-|||...+.+.|..|+..+.-
T Consensus        11 VFhlt-FPkeWK~~DI~qlFspfG~I~VsWi---~dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   11 VFHLT-FPKEWKTSDIYQLFSPFGQIYVSWI---NDTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             EEEEE---TT--HHHHHHHCCCCCCEEEEEE---CTTEEEEEECCCHHHHHHHHHHTT
T ss_pred             EEEEe-CchHhhhhhHHHHhccCCcEEEEEE---cCCcEEEEeecHHHHHHHHHHhcc
Confidence            34555 9999999999999999998765544   467899999999999999988753

; 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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.36  E-value=0.085  Score=43.25  Aligned_cols=75  Identities=19%  Similarity=0.325  Sum_probs=55.3

Q ss_pred             CCCCCceEEEcCCCCCC-cHHH---HHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          224 DGNNQGTIVVFNLDSGV-SSST---LKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       224 ~~~~~~~l~V~nLp~~~-t~~~---L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      .+..-.+|.|.=|..++ ..+|   +...++.||.|.+|...  ++..|.|.|+|..+|-+|+.+++. ..-|..+.+.|
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c--GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsW  158 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC--GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSW  158 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec--CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeec
Confidence            34456888887665554 2344   44556789999998544  467899999999999999999987 34577778777


Q ss_pred             ec
Q 046223          300 SR  301 (408)
Q Consensus       300 a~  301 (408)
                      -.
T Consensus       159 qq  160 (166)
T PF15023_consen  159 QQ  160 (166)
T ss_pred             cc
Confidence            53

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.25  E-value=0.038  Score=50.53  Aligned_cols=52  Identities=17%  Similarity=0.174  Sum_probs=42.6

Q ss_pred             HHHHHHHhhccCCeEEEEEee------cCccEEEEEECCHHHHHHHHHHhcCcccccccc
Q 046223           96 ETIVRRDLEVFGEVRGVQMER------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQ  149 (408)
Q Consensus        96 e~~L~~~F~~~G~V~~v~~~~------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr  149 (408)
                      |+++++.+++||.|..|.|.-      ...--.||+|...++|.+|+-.|||..|.  ||
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFG--Gr  357 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFG--GR  357 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceec--ce
Confidence            446888999999999987654      11334899999999999999999999876  66

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.00  E-value=0.084  Score=43.28  Aligned_cols=61  Identities=23%  Similarity=0.336  Sum_probs=48.4

Q ss_pred             CCCCCEEEEcCCCCCCCH-HH---HHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcC
Q 046223           79 TGPTRTLVLSYVPGDVSE-TI---VRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIRE  141 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte-~~---L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng  141 (408)
                      +.+-.||.|+=|..++.. +|   |...++.||+|.+|.+.  .+--|.|.|.|..+|-+|+.+++.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c--GrqsavVvF~d~~SAC~Av~Af~s  147 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC--GRQSAVVVFKDITSACKAVSAFQS  147 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec--CCceEEEEehhhHHHHHHHHhhcC
Confidence            445668999877776643 23   55567789999999887  577899999999999999999875

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

Probab=94.92  E-value=0.11  Score=36.51  Aligned_cols=53  Identities=23%  Similarity=0.400  Sum_probs=40.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcC----CCceeeccCCCCccEEEEEECCHHHHHHHHHHh
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAF----GPVKELRETPLKKHQRFIEFYDVRDAAKALKEM  285 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~----G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l  285 (408)
                      ..|+|.|+. +++.+||+.+|..|    +. ..|..  ....-|-|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~-~~IEW--IdDtScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGP-FRIEW--IDDTSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCC-ceEEE--ecCCcEEEEECCHHHHHHHHHcC
Confidence            679999996 58889999999999    42 23321  12334789999999999999865

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=94.46  E-value=0.15  Score=53.16  Aligned_cols=74  Identities=20%  Similarity=0.293  Sum_probs=60.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCcee--CCeEEEEEEecCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI--YGKHVVIEFSRPG  303 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~~  303 (408)
                      .+..+.|..-..+..-|..+|+.||.|.+.+.. +.-..|.|+|.+.+.|..|+++|+|+++  .|-..+|.+|+.-
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtl-r~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTL-RDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheec-ccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            344455666677788899999999999998632 4566799999999999999999999975  4788999999864

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.42  E-value=0.079  Score=52.66  Aligned_cols=70  Identities=16%  Similarity=0.254  Sum_probs=52.0

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhc--CCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCC--ceeCCeEEEEEE
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQA--FGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNG--QEIYGKHVVIEF  299 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~--~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g--~~~~g~~l~v~~  299 (408)
                      .+.|.|+-|+..+..|+++.+|+.  +-.+.++.+. . ..--||+|++..||+.|.+.|..  ++|.|+.|..++
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa-~-N~nWyITfesd~DAQqAykylreevk~fqgKpImARI  248 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFA-H-NDNWYITFESDTDAQQAYKYLREEVKTFQGKPIMARI  248 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeee-e-cCceEEEeecchhHHHHHHHHHHHHHhhcCcchhhhh
Confidence            477888999999999999999975  4456665322 1 22259999999999999998863  466677665443

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

Probab=94.41  E-value=0.22  Score=35.05  Aligned_cols=53  Identities=15%  Similarity=0.167  Sum_probs=41.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcc----CCeEEEEEeecCccEEEEEECCHHHHHHHHHHh
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVF----GEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEI  139 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~----G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~l  139 (408)
                      ..|+|.++. +++.++|+.+|..|    + ...|.-+  .-.-|=|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~-~~~IEWI--dDtScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEG-PFRIEWI--DDTSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCC-CceEEEe--cCCcEEEEECCHHHHHHHHHcC
Confidence            469999985 69999999999999    4 2333333  3445889999999999999764

>PF07145 PAM2: Ataxin-2 C-terminal region; InterPro: IPR009818 This entry represents a conserved region approximately 250 residues long located towards the C terminus of eukaryotic ataxin-2

Probab=94.34  E-value=0.028  Score=28.88  Aligned_cols=14  Identities=43%  Similarity=0.873  Sum_probs=10.8

Q ss_pred             CCCCCCCCCCCCCC
Q 046223           11 GNLDPRAQEFRPTT   24 (408)
Q Consensus        11 ~~~~~~a~~~~p~~   24 (408)
                      -.|||.|+||+|..
T Consensus         4 s~LNp~A~eFvP~~   17 (18)
T PF07145_consen    4 SKLNPNAPEFVPSS   17 (18)
T ss_dssp             SSSSTTSSSS-TTT
T ss_pred             cccCCCCccccCCC
Confidence            46999999999963

Ataxin-2 is a protein of unknown function, within which expansion of a polyglutamine tract (due to expansion of unstable CAG repeats in the coding region of the SCA2 gene) causes spinocerebellar ataxia type 2 (SCA2), a late-onset neurodegenerative disorder []. The expanded polyglutamine repeat in ataxin-2 causes disruption of the normal morphology of the Golgi complex and increased incidence of cell death []. Ataxin-2 is predicted to consist of mostly non-globular domains [].; PDB: 3NTW_B 1JH4_B 3KTR_B 3KUJ_B 3KUT_D 3KUS_D 1JGN_B 2RQG_A 2RQH_A.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=93.98  E-value=0.15  Score=44.47  Aligned_cols=62  Identities=19%  Similarity=0.360  Sum_probs=45.1

Q ss_pred             cHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhC--CceeCCeEEEEEEecCC
Q 046223          241 SSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMN--GQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       241 t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~--g~~~~g~~l~v~~a~~~  303 (408)
                      ..+.|+++|..|+.+..+... ++-+-..|.|.+.++|.+|...|+  +..+.|..++|.|+...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L-~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPL-KSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEE-TTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEc-CCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            458899999999988877433 334457999999999999999999  99999999999998543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=93.75  E-value=0.67  Score=36.84  Aligned_cols=67  Identities=13%  Similarity=0.132  Sum_probs=50.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccC-CeEEEEEeecC---ccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFG-EVRGVQMERLM---EGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G-~V~~v~~~~~~---kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ...+..+.+...|..++-++|..+.+.+- .|..+++++..   +=.++++|.+.++|.+-.+.+||+.+.
T Consensus        10 ~~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   10 ERRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             CCCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            33455566666777777777877766654 46668888744   446999999999999999999998875

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

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

Probab=93.71  E-value=0.066  Score=48.20  Aligned_cols=62  Identities=16%  Similarity=0.170  Sum_probs=52.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEE--e--ecCccEEEEEECCHHHHHHHHHHhcCccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQM--E--RLMEGIVTVHFYDLRHAEMAFKEIREQHM  144 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~--~--~~~kG~afV~F~~~~~A~~Ai~~lng~~i  144 (408)
                      ..|||.||..-++.+.|...|+.||+|..-.+  .  .+..+-++|.|...-.|.+|...++..-+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~   97 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGF   97 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCcc
Confidence            68999999999999999999999999888222  2  26678899999999999999998754333

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=93.62  E-value=0.11  Score=45.17  Aligned_cols=80  Identities=8%  Similarity=0.022  Sum_probs=49.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhc-cCCe---EEEEEee-------cCccEEEEEECCHHHHHHHHHHhcCcccccc-
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEV-FGEV---RGVQMER-------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQ-  147 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~-~G~V---~~v~~~~-------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~-  147 (408)
                      .....|.|++||+++||+++.+.+.. +++-   ..+.-..       ..-.-|||.|.+.+++..-...++|..|... 
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34568999999999999999998887 7766   2333111       1145699999999999999999999776421 


Q ss_pred             ccccceeccccC
Q 046223          148 QQSYGLKNPYSS  159 (408)
Q Consensus       148 gr~l~~~~~~s~  159 (408)
                      |......+.|+-
T Consensus        85 g~~~~~~VE~Ap   96 (176)
T PF03467_consen   85 GNEYPAVVEFAP   96 (176)
T ss_dssp             S-EEEEEEEE-S
T ss_pred             CCCcceeEEEcc
Confidence            222334445544

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=93.40  E-value=0.17  Score=50.42  Aligned_cols=71  Identities=15%  Similarity=0.177  Sum_probs=57.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhc--cCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEV--FGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~--~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      +.|.++-||.++-+|+++.||+.  |-++.++.+-.  ..-=||+|++..||+.|.+.|....-.++||.|..|+
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~--N~nWyITfesd~DAQqAykylreevk~fqgKpImARI  248 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAH--NDNWYITFESDTDAQQAYKYLREEVKTFQGKPIMARI  248 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeee--cCceEEEeecchhHHHHHHHHHHHHHhhcCcchhhhh
Confidence            34678999999999999999986  77888887763  2235899999999999999887766666777666554

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=92.84  E-value=0.083  Score=51.54  Aligned_cols=76  Identities=13%  Similarity=0.317  Sum_probs=61.0

Q ss_pred             CCceEEEcCCCCCC-cHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          227 NQGTIVVFNLDSGV-SSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp~~~-t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      +.+.|-+.-.+... +-++|...|.+||+|..|. .+.+---|.|+|.+..+|-+|.. .++..|++|.|+|.|-.+..
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~q-v~~~~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQ-VDYSSLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCcccccc-ccCchhhheeeeeccccccchhc-cccceecCceeEEEEecCCc
Confidence            34556666666654 5689999999999999984 23445679999999999988865 89999999999999998755

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=92.72  E-value=0.23  Score=45.77  Aligned_cols=64  Identities=28%  Similarity=0.354  Sum_probs=50.1

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEE
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHV  295 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l  295 (408)
                      .=|-|-+.+..- -.-|..+|++||+|.+.. ......+-+|.|.+..+|++||. .||+.|+|..+
T Consensus       198 ~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv-~~~ngNwMhirYssr~~A~KALs-kng~ii~g~vm  261 (350)
T KOG4285|consen  198 TWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHV-TPSNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVM  261 (350)
T ss_pred             ceEEEeccCccc-hhHHHHHHHhhCeeeeee-cCCCCceEEEEecchhHHHHhhh-hcCeeeccceE
Confidence            445555777654 346788999999999874 44667789999999999999998 79999988653

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=92.59  E-value=0.03  Score=52.38  Aligned_cols=75  Identities=13%  Similarity=0.314  Sum_probs=57.2

Q ss_pred             ceEEEcCCCCCCcHHHH---HHHHhcCCCceeeccCCC------C--ccEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q 046223          229 GTIVVFNLDSGVSSSTL---KEIFQAFGPVKELRETPL------K--KHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVI  297 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L---~~~F~~~G~v~~v~~~~~------~--~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  297 (408)
                      .-+||-+|+..+.++++   .+.|.+||.|..|.....      .  ..-++|+|...++|..||...+|..++|+.++.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            56778888877655544   367899999998832211      1  123899999999999999999999999999888


Q ss_pred             EEecCC
Q 046223          298 EFSRPG  303 (408)
Q Consensus       298 ~~a~~~  303 (408)
                      .+...+
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            877644

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=92.41  E-value=0.21  Score=50.92  Aligned_cols=71  Identities=20%  Similarity=0.200  Sum_probs=61.6

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ....++||+|+...+..+-++.+...+|.|.....    --|||..|.....+..|+..++-..++|..+.+...
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr----~~fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKR----DKFGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhh----hhhcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            34589999999999999999999999999887632    229999999999999999999999999988877663

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

Probab=91.01  E-value=1.2  Score=31.77  Aligned_cols=55  Identities=16%  Similarity=0.392  Sum_probs=43.6

Q ss_pred             CCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q 046223          239 GVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVI  297 (408)
Q Consensus       239 ~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  297 (408)
                      .++-++++..+.+|+- ..|..  ...| -||.|.+.++|+++....+|+.+.+.+|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~I~~--d~tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DRIRD--DRTG-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ceEEe--cCCE-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            5778999999999974 44431  2233 379999999999999999999998877654

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

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=90.99  E-value=0.12  Score=54.02  Aligned_cols=76  Identities=12%  Similarity=0.147  Sum_probs=62.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccCccc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLM  162 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~~~s  162 (408)
                      +.++.|.+-..+..-|..+|.+||.|.+.+..+ .-..|.|+|...+.|..|+++|+|+++..-|-  +.+|.|++...
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr-~~N~alvs~~s~~sai~a~dAl~gkevs~~g~--Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLR-DLNMALVSFSSVESAILALDALQGKEVSVTGA--PSRVSFAKTLP  375 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecc-cccchhhhhHHHHHHHHhhhhhcCCcccccCC--ceeEEeccccc
Confidence            456677778888999999999999999998874 56789999999999999999999998875554  46666666443

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=90.91  E-value=0.25  Score=43.01  Aligned_cols=74  Identities=15%  Similarity=0.228  Sum_probs=48.4

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhc-CCCc---eeec-------cCCCCccEEEEEECCHHHHHHHHHHhCCceeCC----
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQA-FGPV---KELR-------ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG----  292 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~-~G~v---~~v~-------~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g----  292 (408)
                      ..+|.|++||+.+|++++.+.++. ++..   ..+.       .....-.-|+|.|.+.+++..-...++|..|-+    
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            478999999999999999986665 5543   2221       111122359999999999999999999976642    


Q ss_pred             -eEEEEEEec
Q 046223          293 -KHVVIEFSR  301 (408)
Q Consensus       293 -~~l~v~~a~  301 (408)
                       ....|++|-
T Consensus        87 ~~~~~VE~Ap   96 (176)
T PF03467_consen   87 EYPAVVEFAP   96 (176)
T ss_dssp             EEEEEEEE-S
T ss_pred             CcceeEEEcc
Confidence             355677764

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=90.83  E-value=1  Score=46.94  Aligned_cols=16  Identities=0%  Similarity=-0.060  Sum_probs=8.0

Q ss_pred             CEEEEcCCCCCCCHHH
Q 046223           83 RTLVLSYVPGDVSETI   98 (408)
Q Consensus        83 rtlfV~nLp~~vte~~   98 (408)
                      .+.||+-=....+.++
T Consensus       642 ~cFWvkv~Edk~en~d  657 (1102)
T KOG1924|consen  642 NCFWVKVNEDKLENDD  657 (1102)
T ss_pred             cceeeecchhhccchH
Confidence            4556664444444444

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

Probab=90.82  E-value=0.94  Score=32.37  Aligned_cols=49  Identities=16%  Similarity=0.239  Sum_probs=39.2

Q ss_pred             CCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           93 DVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        93 ~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      .++-++++..+..|+ -..|...  ..| -||.|.+.++|+++....+|..+.
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~I~~d--~tG-fYIvF~~~~Ea~rC~~~~~~~~~f   59 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDRIRDD--RTG-FYIVFNDSKEAERCFRAEDGTLFF   59 (66)
T ss_pred             CccHHHHHHHHhcCC-cceEEec--CCE-EEEEECChHHHHHHHHhcCCCEEE
Confidence            577889999999998 4444443  355 479999999999999999997764

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

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

Probab=90.09  E-value=0.58  Score=34.29  Aligned_cols=61  Identities=21%  Similarity=0.276  Sum_probs=35.8

Q ss_pred             CCcHHHHHHHHhcCCCceee--ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          239 GVSSSTLKEIFQAFGPVKEL--RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       239 ~~t~~~L~~~F~~~G~v~~v--~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      .++..+|..++...+.|..-  -.......|+||+-. .+.|..+++.|++..+.|++|+|+.|
T Consensus        12 g~~~~~iv~~i~~~~gi~~~~IG~I~I~~~~S~vev~-~~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   12 GLTPRDIVGAICNEAGIPGRDIGRIDIFDNFSFVEVP-EEVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             T--HHHHHHHHHTCTTB-GGGEEEEEE-SS-EEEEE--TT-HHHHHHHHTT--SSS----EEE-
T ss_pred             CCCHHHHHHHHHhccCCCHHhEEEEEEeeeEEEEEEC-HHHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            57888999999887666433  122234678899875 45789999999999999999999865

; PDB: 2G0C_A 3MOJ_B.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=89.49  E-value=2.8  Score=33.36  Aligned_cols=64  Identities=17%  Similarity=0.163  Sum_probs=44.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCC-ceee---ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGP-VKEL---RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG  292 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~-v~~v---~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g  292 (408)
                      ..+.+...+..++-++|..+.+.+-. |..+   +....++-.+.++|.+.++|..-.+.+||+.+..
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            44555556666777777766666543 3333   3333345569999999999999999999998763

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=89.07  E-value=7.4  Score=36.16  Aligned_cols=57  Identities=12%  Similarity=0.155  Sum_probs=48.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecC------------ccEEEEEECCHHHHHH
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLM------------EGIVTVHFYDLRHAEM  134 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~------------kG~afV~F~~~~~A~~  134 (408)
                      ++--+|.|...|+..+++--.+...|.+||.|++|+++...            .--..+.|-+.+.+-.
T Consensus        11 D~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLd   79 (309)
T PF10567_consen   11 DEYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLD   79 (309)
T ss_pred             ccceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHH
Confidence            45568899999999999999999999999999999998632            3568899999887654

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=88.39  E-value=0.93  Score=39.63  Aligned_cols=60  Identities=8%  Similarity=0.000  Sum_probs=42.3

Q ss_pred             CHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhc--CccccccccccceeccccC
Q 046223           95 SETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIR--EQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        95 te~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~ln--g~~i~~~gr~l~~~~~~s~  159 (408)
                      ..+.|+++|..|+.+..+... ++-+-..|.|.+.++|.+|...|+  +..+.  |.  .+++.|+.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L-~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~--g~--~l~~yf~~   69 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPL-KSFRRIRVVFESPESAQRARQLLHWDGTSFN--GK--RLRVYFGQ   69 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEE-TTTTEEEEE-SSTTHHHHHHHTST--TSEET--TE--E-EEE---
T ss_pred             hHHHHHHHHHhcCCceEEEEc-CCCCEEEEEeCCHHHHHHHHHHhcccccccC--CC--ceEEEEcc
Confidence            357899999999999987766 466779999999999999999998  76665  43  36666654

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=87.78  E-value=0.83  Score=42.27  Aligned_cols=58  Identities=16%  Similarity=0.119  Sum_probs=44.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           85 LVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        85 lfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      |=|-++++.-. .-|..+|++||+|.+.... .+..+-+|.|.+.-+|++||. -||+.|.
T Consensus       200 VTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~-~ngNwMhirYssr~~A~KALs-kng~ii~  257 (350)
T KOG4285|consen  200 VTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP-SNGNWMHIRYSSRTHAQKALS-KNGTIID  257 (350)
T ss_pred             EEEeccCccch-hHHHHHHHhhCeeeeeecC-CCCceEEEEecchhHHHHhhh-hcCeeec
Confidence            44445555433 3467789999999997666 567899999999999999996 6777665

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.36  E-value=2.4  Score=42.82  Aligned_cols=79  Identities=14%  Similarity=0.105  Sum_probs=62.3

Q ss_pred             CCCCCCCEEEEcCCCCC-CCHHHHHHHhhcc----CCeEEEEEee---------------c-------------C-----
Q 046223           77 PSTGPTRTLVLSYVPGD-VSETIVRRDLEVF----GEVRGVQMER---------------L-------------M-----  118 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~-vte~~L~~~F~~~----G~V~~v~~~~---------------~-------------~-----  118 (408)
                      .....++.|-|.|+.|+ +.-.+|.-+|..|    |.|.+|.|..               .             +     
T Consensus       169 ~~~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~e  248 (650)
T KOG2318|consen  169 VLGEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDE  248 (650)
T ss_pred             ccccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchh
Confidence            34667899999999997 7888899988886    5888888763               0             0     


Q ss_pred             -----------------c--cEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223          119 -----------------E--GIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus       119 -----------------k--G~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                                       .  =||.|+|.+++.|.+..+.++|..+.-.+..+.||.
T Consensus       249 e~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  249 EEEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             hhhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                             1  169999999999999999999998876665555553

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=87.19  E-value=0.78  Score=34.80  Aligned_cols=23  Identities=13%  Similarity=0.317  Sum_probs=20.2

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHh
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQ  250 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~  250 (408)
                      .++|.|.|||...++++|++..+
T Consensus        52 ~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen   52 KRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             CCEEEEeCCCCCCChhhheeeEE
Confidence            58999999999999999987654

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=85.28  E-value=0.62  Score=43.84  Aligned_cols=63  Identities=10%  Similarity=0.146  Sum_probs=49.5

Q ss_pred             CEEEEcCCCCCCCHHHHH---HHhhccCCeEEEEEeecC------c--cEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           83 RTLVLSYVPGDVSETIVR---RDLEVFGEVRGVQMERLM------E--GIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~---~~F~~~G~V~~v~~~~~~------k--G~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      .-+||-+|+..+..+++-   +.|.+||.|..|.+.+..      .  --++|+|...++|..||...+|..+.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~d  151 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDD  151 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhh
Confidence            457899998887665543   589999999998876521      1  12899999999999999999997665

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=81.97  E-value=3.9  Score=40.16  Aligned_cols=64  Identities=17%  Similarity=0.254  Sum_probs=55.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccC-CeEEEEEeecC---ccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFG-EVRGVQMERLM---EGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G-~V~~v~~~~~~---kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ++.|+|-.+|..+|--||..|...+- .|..++++|+.   +=.++|.|.+.++|..-.+.+||+.|.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            88999999999999999999888754 57778888843   445899999999999999999999875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	408
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		5e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		6e-05
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		1e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		5e-04
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		5e-04
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		6e-04
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		6e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		6e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		7e-04
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		7e-04
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		8e-04

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 24/78 (30%), Positives = 46/78 (58%), Gaps = 3/78 (3%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           + V NL + V+   L++ F  FG ++ +++    K   FI F +   A KA++EMNG+++
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDL 70
Query: 291 YGKHVVIEFSRPGGHSKK 308
            G+++ I F++P    +K
Sbjct: 71  EGENIEIVFAKPPDQKRK 88

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 5/86 (5%)
Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRD 277
           PD     ++ V NL    S  TL+ +F+ +G V ++     R T   +   F+ F+D RD
Sbjct: 42  PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101
Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPG 303
           A  A+  M+G  + G+ + ++ +R G
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMARYG 127

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/92 (28%), Positives = 49/92 (53%), Gaps = 7/92 (7%)
Query: 218 TCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR------FIE 271
           + ++ PD +   T+ V NL    S  +L+ +F+ +G V ++   P + H +      F+ 
Sbjct: 3   SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDV-YIPREPHTKAPRGFAFVR 61
Query: 272 FYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG 303
           F+D RDA  A   M+G E+ G+ + ++ +R G
Sbjct: 62  FHDRRDAQDAEAAMDGAELDGRELRVQVARYG 93

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 5/83 (6%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEM 285
           ++V  L   ++   L  +F+A GP+   R     +T       F++F    D+ +A+K +
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 286 NGQEIYGKHVVIEFSRPGGHSKK 308
           NG  +  K + + ++RPGG S K
Sbjct: 66  NGITVRNKRLKVSYARPGGESIK 88

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 36/70 (51%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           + V NL +G     L+  F  +GP++ +          F+EF D RDA  A++ ++G+ I
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 291 YGKHVVIEFS 300
            G  V +E S
Sbjct: 63  CGSRVRVELS 72

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 4/74 (5%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR----FIEFYDVRDAAKALKEMN 286
           + V NLD  ++   LK+ FQ  GP+  ++    K ++     F+E++   DA  AL+ +N
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 287 GQEIYGKHVVIEFS 300
           G++I    V I ++
Sbjct: 63  GKQIENNIVKINWA 76

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 5/79 (6%)
Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
           ++ V NL    S  TL+ +F+ +G V ++     R T   +   F+ F+D RDA  A+  
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 285 MNGQEIYGKHVVIEFSRPG 303
           M+G  + G+ + ++ +R G
Sbjct: 132 MDGAVLDGRELRVQMARYG 150

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKEMNG 287
           VF L    +   L+E+F  +GP+ ++     ++ +R     F+ F +V DA +A +  NG
Sbjct: 51  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 288 QEIYGKHVVIEFS 300
            E+ G+ + ++FS
Sbjct: 111 MELDGRRIRVDFS 123

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 45/85 (52%), Gaps = 7/85 (8%)
Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDV 275
           A PD N    + VF L    +   L+E+F  +GP+ ++     ++ +R     F+ F +V
Sbjct: 7   ANPDPN--CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 64
Query: 276 RDAAKALKEMNGQEIYGKHVVIEFS 300
            DA +A +  NG E+ G+ + ++FS
Sbjct: 65  DDAKEAKERANGMELDGRRIRVDFS 89

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKEMNG 287
           VF L    +   L+E+F  +GP+ ++     ++ +R     F+ F +V DA +A +  NG
Sbjct: 20  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 288 QEIYGKHVVIEFS 300
            E+ G+ + ++FS
Sbjct: 80  MELDGRRIRVDFS 92

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 5/83 (6%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEM 285
           ++V  L   ++   L  +F+A GP+   R     +T       F++F    D+ +A+K +
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 286 NGQEIYGKHVVIEFSRPGGHSKK 308
           NG  +  K + + ++RPGG S K
Sbjct: 66  NGITVRNKRLKVSYARPGGESIK 88

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	408
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-18
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-16
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-15
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-15
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-15
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-15
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	5e-15
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-15
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-11
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-11
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-10
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-08
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-14
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-14
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-14
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-14
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-14
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	6e-14
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	7e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-13
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	8e-14
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-13
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-13
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-13
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-13
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	7e-13
1x5p_A	97	Negative elongation factor E; structure genomics,	8e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-09
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	9e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-12
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-12
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-12
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-09
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-12
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	9e-09
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-12
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-12
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-12
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-12
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-05
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-12
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	5e-12
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	8e-12
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-05
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-11
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-11
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-05
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-11
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-11
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-11
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-11
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-11
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	6e-11
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	6e-11
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-11
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	6e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-11
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	8e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	8e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	8e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-10
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-10
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-10
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-10
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-10
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-10
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-10
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-10
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-10
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-10
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-10
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-10
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-10
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-10
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-10
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-10
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-10
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-09
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	7e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	7e-10
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	7e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	9e-10
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-09
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-09
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-09
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-09
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-09
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-09
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-09
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-09
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-09
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-09
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-09
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-09
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-09
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-09
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-09
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-09
1x4e_A	85	RNA binding motif, single-stranded interacting pro	6e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-08
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-08
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	5e-08
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	9e-08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-07
2div_A	99	TRNA selenocysteine associated protein; structural	2e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-07
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-07
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	9e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-06
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	2e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-06
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-06
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-06
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-06
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	9e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-05
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-05
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	6e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-04
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	3e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	4e-04
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	4e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	5e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	5e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	5e-04
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	6e-04

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 78.8 bits (194), Expect = 4e-18
 Identities = 14/89 (15%), Positives = 32/89 (35%), Gaps = 6/89 (6%)

Query: 220 NAVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKELR--ETPLKKHQRFIEFY 273
           +  P       +++ N++  V    L+     +  + G + ++    +     + +I F 
Sbjct: 21  STPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFA 80

Query: 274 DVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
               A   ++   G    G  +VI FS  
Sbjct: 81  TQESAQAFVEAFQGYPFQGNPLVITFSET 109

>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 = 75.4 bits (186), Expect = 3e-17
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            + V NL    S   +++ F    P    R     +   F+ F +  DA +A+K +NG+ 
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVER-VKKIRDYAFVHFSNREDAVEAMKALNGKV 75

Query: 290 IYGKHVVIEFSRP 302
           + G  + +  ++P
Sbjct: 76  LDGSPIEVTLAKP 88

>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 = 71.9 bits (177), Expect = 6e-16
 Identities = 21/73 (28%), Positives = 37/73 (50%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           T++  NL   ++   LKE+F+    ++ + +    K   +IEF    DA K L+E  G E
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77

Query: 290 IYGKHVVIEFSRP 302
           I G+ V + ++  
Sbjct: 78  IDGRSVSLYYTGE 90

>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 = 71.1 bits (175), Expect = 1e-15
 Identities = 25/88 (28%), Positives = 43/88 (48%), Gaps = 6/88 (6%)

Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKE--LRETPLKKHQRFIEFYD 274
           AVP+     TI + NL+  +    LK+    IF  FG + +  +  +   + Q F+ F +
Sbjct: 1   AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 60

Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSRP 302
           V  A  AL+ M G   Y K + I++++ 
Sbjct: 61  VSSATNALRSMQGFPFYDKPMRIQYAKT 88

>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 = 71.2 bits (175), Expect = 2e-15
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            + + NL   V+   L  +F  F   K         T   + Q FI F +   A +AL  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NG ++YGK +VIEF + 
Sbjct: 87  VNGYKLYGKILVIEFGKN 104

>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 = 70.0 bits (172), Expect = 4e-15
 Identities = 24/79 (30%), Positives = 45/79 (56%), Gaps = 3/79 (3%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            + V NL + V+   L++ F  FG ++ ++     K   FI F +   A KA++EMNG++
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVK---KLKDYAFIHFDERDGAVKAMEEMNGKD 69

Query: 290 IYGKHVVIEFSRPGGHSKK 308
           + G+++ I F++P    +K
Sbjct: 70  LEGENIEIVFAKPPDQKRK 88

>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 = 70.0 bits (172), Expect = 4e-15
 Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 8/86 (9%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRD 277
           P GNN   I V NL   + +  ++++F  +G ++++    LK  +      F+EF D RD
Sbjct: 17  PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDID---LKNRRGGPPFAFVEFEDPRD 73

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPG 303
           A  A+   +G +  G  + +EF R G
Sbjct: 74  AEDAVYGRDGYDYDGYRLRVEFPRSG 99

>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 = 69.2 bits (170), Expect = 5e-15
 Identities = 16/74 (21%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ- 288
            + + NL   V++  L+++F          +  LK    F+++ D   A +A++ ++G+ 
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRKLPLA-GQVLLKSGYAFVDYPDQNWAIRAIETLSGKV 68

Query: 289 EIYGKHVVIEFSRP 302
           E++GK + +++S  
Sbjct: 69  ELHGKIMEVDYSVS 82

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 69.7 bits (171), Expect = 5e-15
 Identities = 15/86 (17%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            +    L+  V  + LK++ + +G V+E+       T        + F   R A + +K 
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 285 MNGQEIYGKHVVIEFSRPGGHSKKFF 310
           ++   + G  +  +    G    K++
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRMKYY 93

>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 = 72.3 bits (177), Expect = 9e-15
 Identities = 44/256 (17%), Positives = 86/256 (33%), Gaps = 41/256 (16%)

Query: 58  GVGYAQY-------PTHPQLGVPLPPPSTG-PTRTLVLSYV-PGDVSETIVRRDLEVFGE 108
           G  +  +       P    +G    P   G     L++S + P  V+   +     V+G+
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGD 61

Query: 109 VRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGLMLMNNDN 168
           V+ V++    +    V   D   A++A   +     +L  +   +       + L     
Sbjct: 62  VQRVKILFNKKENALVQMADGNQAQLAMSHL--NGHKLHGKPIRITLSKHQNVQLPREGQ 119

Query: 169 NNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQ 228
            +  L    Y N                  P  R    G   +     P+          
Sbjct: 120 EDQGLTKD-YGN-----------------SPLHRFKKPGSKNFQNIFPPSA--------- 152

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGP-VKELRETPLKKHQRFIEFYDVRDAAKALKEMNG 287
            T+ + N+   VS   LK +F + G  VK  +     +    I+   V +A +AL +++ 
Sbjct: 153 -TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 211

Query: 288 QEIY-GKHVVIEFSRP 302
            ++    H+ + FS+ 
Sbjct: 212 HDLGENHHLRVSFSKS 227

>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 = 61.9 bits (150), Expect = 3e-11
 Identities = 29/150 (19%), Positives = 56/150 (37%), Gaps = 8/150 (5%)

Query: 198 PPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLD-SGVSSSTLKEIFQAFGPVK 256
              + GLV       +  +P       G     ++V NL+   V+  +L  +F  +G V+
Sbjct: 8   HHHSSGLVPRGSHMGRIAIPG----LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQ 63

Query: 257 ELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSS 316
            ++    KK    ++  D   A  A+  +NG +++GK + I  S+    + +        
Sbjct: 64  RVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK--HQNVQLPREGQED 121

Query: 317 CASSLNYSTIYQTR-NSDCPPPPLSADPPS 345
              + +Y      R          +  PPS
Sbjct: 122 QGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 151

>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 = 68.9 bits (169), Expect = 1e-14
 Identities = 16/81 (19%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNG 287
            + + NL   +++  + +IF  +GP++++R   TP  +   ++ + D+ DA  A+  ++G
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSG 69

Query: 288 QEIYGKHVVIEFSRPGGHSKK 308
             +  +++V+ +       +K
Sbjct: 70  FNVSNRYLVVLYYNANRAFQK 90

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 71.7 bits (175), Expect = 1e-14
 Identities = 28/226 (12%), Positives = 60/226 (26%), Gaps = 34/226 (15%)

Query: 80  GPTRTLVLSYV-PGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKE 138
             +  L++  +    ++   V     ++G V  V+  +   G   V   D    + A   
Sbjct: 2   ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITH 61

Query: 139 IREQHMQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLP 198
           +   +  +  Q   +    S    +M   +      +  Y +   + +            
Sbjct: 62  L--NNNFMFGQK--MNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAA-- 115

Query: 199 PPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGP---- 254
                           I    N          +  FN    V+     EI    G     
Sbjct: 116 -------------KNRIQHPSN---------VLHFFNAPLEVTEENFFEICDELGVKRPT 153

Query: 255 -VKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF 299
            VK       +     +E+    DA + L  +N  ++   +    +
Sbjct: 154 SVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 199

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 60.9 bits (147), Expect = 5e-11
 Identities = 15/78 (19%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 225 GNNQGTIVVFNLD-SGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK 283
           G +   ++V+ LD S ++   +  +F  +G V++++    K     +E  D     +A+ 
Sbjct: 1   GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAIT 60

Query: 284 EMNGQEIYGKHVVIEFSR 301
            +N   ++G+ + +  S+
Sbjct: 61  HLNNNFMFGQKMNVCVSK 78

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 68.9 bits (169), Expect = 1e-14
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 3/79 (3%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            + V      V  S L EIF  FGP+KE++   +     F+EF +   AAKA++E++G+ 
Sbjct: 33  RLFVRPFPLDVQESELNEIFGPFGPMKEVK---ILNGFAFVEFEEAESAAKAIEEVHGKS 89

Query: 290 IYGKHVVIEFSRPGGHSKK 308
              + + + +S+      +
Sbjct: 90  FANQPLEVVYSKLPAKRYR 108

>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 = 72.3 bits (178), Expect = 2e-14
 Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKE---LRETPLKKHQR--FIEFYDVRDAAKALKE 284
           T+ + N     +   ++++ Q    V     L        +R  +I+     DA   +++
Sbjct: 119 TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 178

Query: 285 MNGQEIYGKHVVIEFSRPGGHSKK 308
           +NG +I G  +V + S P   SK+
Sbjct: 179 LNGLKIEGYTLVTKVSNPLEKSKR 202

>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 = 60.8 bits (148), Expect = 1e-10
 Identities = 16/73 (21%), Positives = 33/73 (45%), Gaps = 4/73 (5%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-ETPLKKHQR--FIEFYDVRDAAKALKEM 285
            T++V NL    + + + + F+  GP+  +     LKK+ R   IEF     A  A+ + 
Sbjct: 42  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 101

Query: 286 NGQEIYGKHVVIE 298
           +   +    +++ 
Sbjct: 102 HK-VVGQNEIIVS 113

>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 = 53.5 bits (129), Expect = 4e-08
 Identities = 16/80 (20%), Positives = 37/80 (46%), Gaps = 8/80 (10%)

Query: 230 TIVVFNLDSGVSS-STLKEIFQAFGPVKELRETPLKKHQR------FIEFYDVRDAAKAL 282
            I++ NL + +   + L+E F+ FG ++++     +K         F+ F +   A +AL
Sbjct: 212 EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 271

Query: 283 KEMNGQEIYGKHVVIEFSRP 302
            +MN   +  + + +  +  
Sbjct: 272 -QMNRSLLGNREISVSLADK 290

>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 = 68.3 bits (167), Expect = 3e-14
 Identities = 28/83 (33%), Positives = 38/83 (45%), Gaps = 10/83 (12%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKE----------LRETPLKKHQRFIEFYDVRDAA 279
            I V NL   V    LK IF  +               L +    K Q FI   + + AA
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 280 KALKEMNGQEIYGKHVVIEFSRP 302
           KALKE NG  ++GK +V++F+R 
Sbjct: 107 KALKEANGYVLFGKPMVVQFARS 129

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 67.8 bits (165), Expect = 3e-14
 Identities = 24/103 (23%), Positives = 41/103 (39%), Gaps = 5/103 (4%)

Query: 217 PTCNAVPDGNNQGTIV-VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDV 275
           P     P G N+  ++ + N    ++   L  +    G V+ +        Q  +EF  V
Sbjct: 13  PGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESV 72

Query: 276 RDAAKALKEMNGQEIYGK--HVVIEFSRPGGHSKKFFYANSSS 316
             A KA   +NG +IY     + IE++RP          ++ S
Sbjct: 73  LCAQKAKAALNGADIYAGCCTLKIEYARP--TRLNVIRNDNDS 113

>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 = 66.8 bits (164), Expect = 3e-14
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR------ETPLKKHQRFIEFYDVRDAAKALK 283
            + +  L   V+   + EIF  +G +K +          L K   ++EF +  +A KALK
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 284 EMNGQEIYGKHVVIEFSRP 302
            M+G +I G+ +       
Sbjct: 66  HMDGGQIDGQEITATAVLA 84

>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 = 66.9 bits (164), Expect = 5e-14
 Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 9/89 (10%)

Query: 222 VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-------FIEFYD 274
           VP       I+V N+    +   ++E+F  FG +K +R  P K           F++F  
Sbjct: 9   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVR-LPKKMTGTGAHRGFGFVDFIT 67

Query: 275 VRDAAKALKEM-NGQEIYGKHVVIEFSRP 302
            +DA KA   + +   +YG+ +V+E++  
Sbjct: 68  KQDAKKAFNALCHSTHLYGRRLVLEWADS 96

>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 = 68.0 bits (166), Expect = 6e-14
 Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 6/77 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR---FIEFYDVRDAAKALKEMN 286
            + V NL +  + + L+  F  +GP++ +    + ++     F+EF D RDAA A++E++
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVW---VARNPPGFAFVEFEDPRDAADAVRELD 131

Query: 287 GQEIYGKHVVIEFSRPG 303
           G+ + G  V +E S   
Sbjct: 132 GRTLCGCRVRVELSNGE 148

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 66.5 bits (163), Expect = 6e-14
 Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 5/86 (5%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRD 277
           PD +   T+ V NL    S  +L+ +F+ +G V ++       T   +   F+ F+D RD
Sbjct: 8   PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPG 303
           A  A   M+G E+ G+ + ++ +R G
Sbjct: 68  AQDAEAAMDGAELDGRELRVQVARYG 93

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 66.1 bits (162), Expect = 7e-14
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-RETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
           T+V+ NL    +  TL+E+F+    +K    +    K   FIEF    DA +AL   N +
Sbjct: 17  TLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKR 76

Query: 289 EIYGKHVVIEFSRP 302
           EI G+ + +E   P
Sbjct: 77  EIEGRAIRLELQGP 90

>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 = 68.4 bits (168), Expect = 7e-14
 Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 2/100 (2%)

Query: 205 VAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLK 264
           V G  +  +      +         T++  NL   ++   LKE+F+    ++ + +    
Sbjct: 78  VFGNEIKLEKPKGRDSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKS 135

Query: 265 KHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG 304
           K   +IEF    DA K L+E  G EI G+ V + ++   G
Sbjct: 136 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 175

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 65.7 bits (161), Expect = 5e-13
 Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 7/84 (8%)

Query: 224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDA 278
           +      + + NL+   S + LK          +L      +        +++F    D 
Sbjct: 9   ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESAEDL 67

Query: 279 AKALKEMNGQEIYGKHVVIEFSRP 302
            KAL E+ G +++G  + +E  + 
Sbjct: 68  EKAL-ELTGLKVFGNEIKLEKPKG 90

>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 = 66.1 bits (162), Expect = 8e-14
 Identities = 28/96 (29%), Positives = 44/96 (45%), Gaps = 5/96 (5%)

Query: 217 PTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR----FIEF 272
            +   + D     T+ V NL   V+   + ++F   GP K  +    +        F+EF
Sbjct: 4   GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCK-MITEHTSNDPYCFVEF 62

Query: 273 YDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKK 308
           Y+ RDAA AL  MNG++I GK V + ++      K 
Sbjct: 63  YEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKS 98

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 68.0 bits (166), Expect = 1e-13
 Identities = 35/214 (16%), Positives = 70/214 (32%), Gaps = 32/214 (14%)

Query: 91  PGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS 150
           P  V+   +     V+G+V+ V++    +    V   D   A++A       H+      
Sbjct: 13  PERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAM-----SHLN----- 62

Query: 151 YGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPV 210
                    G   ++       L+                 +      P  R    G   
Sbjct: 63  ---------G-HKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKN 112

Query: 211 WAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFG-PVKELRETPLKKHQRF 269
           +     P+           T+ + N+   VS   LK +F + G  VK  +     +    
Sbjct: 113 FQNIFPPSA----------TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMAL 162

Query: 270 IEFYDVRDAAKALKEMNGQEIY-GKHVVIEFSRP 302
           I+   V +A +AL +++  ++    H+ + FS+ 
Sbjct: 163 IQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 196

>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 = 61.1 bits (148), Expect = 4e-11
 Identities = 24/121 (19%), Positives = 48/121 (39%), Gaps = 4/121 (3%)

Query: 227 NQGTIVVFNLD-SGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEM 285
               ++V NL+   V+  +L  +F  +G V+ ++    KK    ++  D   A  A+  +
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHL 61

Query: 286 NGQEIYGKHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTIYQTR-NSDCPPPPLSADPP 344
           NG +++GK + I  S+    + +           + +Y      R          +  PP
Sbjct: 62  NGHKLHGKPIRITLSK--HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP 119

Query: 345 S 345
           S
Sbjct: 120 S 120

>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 = 64.9 bits (159), Expect = 1e-13
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG 292
           V N+ +  +S  L+ +F+  G V E     + K   F+      DA  A+ ++NG+E+ G
Sbjct: 14  VGNVSAACTSQELRSLFERRGRVIECD---VVKDYAFVHMEKEADAKAAIAQLNGKEVKG 70

Query: 293 KHVVIEFSRPG 303
           K + +E S  G
Sbjct: 71  KRINVELSTKG 81

>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 = 65.0 bits (159), Expect = 2e-13
 Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 3/76 (3%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            + V  L    S + L   F  FG ++ +          +I++  +  A  A  +M G  
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTID-HVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 290 IYGKHVVI--EFSRPG 303
           + G    +  +F++ G
Sbjct: 78  LGGPDRRLRVDFAKSG 93

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

 Score = 64.6 bits (158), Expect = 2e-13
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 3/80 (3%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKAL 282
             G     + V N+    ++  L+  F+ +GPV E     + K   F+      DA +A+
Sbjct: 5   SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECD---IVKDYAFVHMERAEDAVEAI 61

Query: 283 KEMNGQEIYGKHVVIEFSRP 302
           + ++  E  GK + ++ S  
Sbjct: 62  RGLDNTEFQGKRMHVQLSTS 81

>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 = 64.6 bits (158), Expect = 3e-13
 Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 9/90 (10%)

Query: 220 NAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQ--RFIEF 272
             + + N   T+ V  LD  VS   L E+F   GPV        R T   +HQ   F+EF
Sbjct: 7   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVT--GQHQGYGFVEF 64

Query: 273 YDVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
               DA  A+K M+  ++YGK + +  +  
Sbjct: 65  LSEEDADYAIKIMDMIKLYGKPIRVNKASA 94

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

 Score = 63.9 bits (156), Expect = 5e-13
 Identities = 22/93 (23%), Positives = 43/93 (46%), Gaps = 6/93 (6%)

Query: 235 NLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR---FIEFYDVRDAAKALKEMNGQEIY 291
           NL +G     L+  F  +GP++ +    + ++     F+EF D RDA  A++ ++G+ I 
Sbjct: 7   NLGTGAGKGELERAFSYYGPLRTVW---IARNPPGFAFVEFEDPRDAEDAVRGLDGKVIC 63

Query: 292 GKHVVIEFSRPGGHSKKFFYANSSSCASSLNYS 324
           G  V +E S       +F    +      + ++
Sbjct: 64  GSRVRVELSTGMPRRSRFDRPPARRKLLEVLFN 96

>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 = 63.8 bits (156), Expect = 5e-13
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 5/82 (6%)

Query: 226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAK 280
             +  + V  L   V    L   F  FG + ++      ET   +   F+EF    DAA 
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69

Query: 281 ALKEMNGQEIYGKHVVIEFSRP 302
           A+  MN  E++G+ + +  ++P
Sbjct: 70  AIDNMNESELFGRTIRVNLAKP 91

>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 = 63.4 bits (155), Expect = 5e-13
 Identities = 14/69 (20%), Positives = 34/69 (49%), Gaps = 3/69 (4%)

Query: 235 NLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH 294
           NL    +   ++ +F+ +G V E     + K+  F+   D   A  A++ ++  +++G +
Sbjct: 15  NLPREATEQEIRSLFEQYGKVLECD---IIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVN 71

Query: 295 VVIEFSRPG 303
           + +E S+  
Sbjct: 72  INVEASKNK 80

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 64.8 bits (158), Expect = 7e-13
 Identities = 24/110 (21%), Positives = 40/110 (36%), Gaps = 22/110 (20%)

Query: 204 LVAGRPVWAQFIVPTCNAV-------------PDGNNQGTIVVFNLDSGVSSSTLKEIFQ 250
           +++  P    +    C                     +  + V  L   V    L   F 
Sbjct: 26  ILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFI 85

Query: 251 AFGPVKEL-----RETPLKKHQ--RFIEFYDVRDAAKALKEMNGQEIYGK 293
            FG + ++      ET  +KH+   F+EF    DAA A+  MN  E++G+
Sbjct: 86  PFGDITDIQIPLDYET--EKHRGFAFVEFELAEDAAAAIDNMNESELFGR 133

>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 = 63.1 bits (154), Expect = 8e-13
 Identities = 15/80 (18%), Positives = 36/80 (45%), Gaps = 3/80 (3%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKAL 282
                  T+ V+  D  ++ + L+  F  FG + +L      ++  F+ +  +  A +A+
Sbjct: 10  RAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLS-MDPPRNCAFVTYEKMESADQAV 66

Query: 283 KEMNGQEIYGKHVVIEFSRP 302
            E+NG ++    + +  +R 
Sbjct: 67  AELNGTQVESVQLKVNIARK 86

>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 = 64.9 bits (159), Expect = 9e-13
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 6/84 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
            + V NLD  ++   LK+ FQ  GP+  ++   + K+ +     F+E++   DA  AL+ 
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIK-IMIDKNNKNVNYAFVEYHQSHDANIALQT 60

Query: 285 MNGQEIYGKHVVIEFSRPGGHSKK 308
           +NG++I    V I ++     S  
Sbjct: 61  LNGKQIENNIVKINWAFQSQQSSS 84

>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 = 53.7 bits (130), Expect = 8e-09
 Identities = 21/102 (20%), Positives = 39/102 (38%), Gaps = 13/102 (12%)

Query: 207 GRPV---WAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---- 259
              V   WA       +     ++   + V +L+  V   TL+  F+ F           
Sbjct: 68  NNIVKINWAFQ-----SQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD 122

Query: 260 -ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS 300
            +T   +   F+ F    DA  A+  M GQ++ G+ + I ++
Sbjct: 123 MQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164

>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 = 63.0 bits (154), Expect = 9e-13
 Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 5/85 (5%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRD 277
              ++  TI V NL      + L+E+F+ FG +  +     + T   K   FI F+   D
Sbjct: 10  RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRP 302
           AA+A+  ++G       + +E+++P
Sbjct: 70  AARAIAGVSGFGYDHLILNVEWAKP 94

>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 = 62.6 bits (153), Expect = 1e-12
 Identities = 20/91 (21%), Positives = 42/91 (46%), Gaps = 15/91 (16%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR-----FIEF 272
            + +    + VF L    +   L+E+F  +GP+ ++     +++     +R     F+ F
Sbjct: 10  ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQS-----RRSRGFAFVYF 64

Query: 273 YDVRDAAKALKEMNGQEIYGKHVVIEFSRPG 303
            +V DA +A +  NG E+ G+ + +     G
Sbjct: 65  ENVDDAKEAKERANGMELDGRRIRVSGPSSG 95

>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 = 63.1 bits (154), Expect = 1e-12
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           T+    + SG++   +++ F  FG + E+R    +K   F+ F     AA A+  +NG  
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIR-VFPEKGYSFVRFSTHESAAHAIVSVNGTT 85

Query: 290 IYGKHVVIEFSRP 302
           I G  V   + + 
Sbjct: 86  IEGHVVKCYWGKE 98

>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 = 62.7 bits (153), Expect = 1e-12
 Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 8/83 (9%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR---FIEFYDVRDAAK 280
             + + NL+   +  TLK +F   G +K       +            F+E+     A K
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 281 ALKEMNGQEIYGKHVVIEFSRPG 303
           ALK++ G  + G  + +  S   
Sbjct: 66  ALKQLQGHTVDGHKLEVRISERA 88

>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 = 62.3 bits (152), Expect = 1e-12
 Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR--FIEFYDVRDAAKALKE 284
            +  + V NL   ++   ++++F+ +G   E+    + K +   FI       A  A  E
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF---IHKDKGFGFIRLETRTLAEIAKVE 70

Query: 285 MNGQEIYGKHVVIEFSRPG 303
           ++   + GK + + F+   
Sbjct: 71  LDNMPLRGKQLRVRFACHS 89

>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 = 61.9 bits (151), Expect = 2e-12
 Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 5/86 (5%)

Query: 220 NAVPDGNNQGT-IVVFNLDS-GVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRD 277
             VP G++  + + + NL    VS   L  IF  +G + ++    +K    FI+F + + 
Sbjct: 13  GLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQS 69

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPG 303
              A++  + +  +GK +++E S   
Sbjct: 70  VRDAIEXESQEMNFGKKLILEVSSSN 95

>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 = 65.0 bits (159), Expect = 2e-12
 Identities = 24/95 (25%), Positives = 40/95 (42%), Gaps = 5/95 (5%)

Query: 224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL---RETPLKKHQR--FIEFYDVRDA 278
                 ++ V +L   V+ + L E F   GP+  +   R+   ++     ++ F    DA
Sbjct: 11  PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADA 70

Query: 279 AKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYAN 313
            +AL  MN   I GK V I +S+     +K    N
Sbjct: 71  ERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 105

>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 = 56.5 bits (137), Expect = 2e-09
 Identities = 26/102 (25%), Positives = 45/102 (44%), Gaps = 11/102 (10%)

Query: 207 GRPV---WAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKE---LRE 260
           G+PV   W+Q   P+      GN    I + NLD  + +  L + F AFG +     + +
Sbjct: 84  GKPVRIMWSQR-DPSLRKSGVGN----IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD 138

Query: 261 TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
               K   F+ F     A +A+++MNG  +  + V +   + 
Sbjct: 139 ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 180

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 65.0 bits (159), Expect = 2e-12
 Identities = 20/110 (18%), Positives = 45/110 (40%), Gaps = 8/110 (7%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKE---LRETPLKKHQR--FIEFYDVRD 277
                   + V ++   +   T+++ F  FGP+K      ++   KH+   F+E+     
Sbjct: 23  GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA 82

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTIY 327
           A  AL++MN   + G+++ +      G ++            +  ++ IY
Sbjct: 83  AQLALEQMNSVMLGGRNIKVGRPSNIGQAQP---IIDQLAEEARAFNRIY 129

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 54.2 bits (131), Expect = 9e-09
 Identities = 20/104 (19%), Positives = 41/104 (39%), Gaps = 12/104 (11%)

Query: 204 LVAGRPVWAQFIVPTCNAVPDGNNQG-------TIVVFNLDSGVSSSTLKEIFQAFGPVK 256
           ++ GR +          A P  +           I V ++   +S   +K +F+AFG +K
Sbjct: 94  MLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIK 153

Query: 257 ELRETPLKKHQR-----FIEFYDVRDAAKALKEMNGQEIYGKHV 295
                      +     FIE+   + +  A+  MN  ++ G+++
Sbjct: 154 SATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 197

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           T  + N+    + + L  +FQ FG + + +    +K   FI++     AA  +  +    
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFK-HYPEKGCCFIKYDTHEQAAVCIVALANFP 87

Query: 290 IYGKHVVIEFSRP 302
             G+++   + + 
Sbjct: 88  FQGRNLRTGWGKE 100

>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 = 63.4 bits (155), Expect = 3e-12
 Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 5/87 (5%)

Query: 227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKE---LRETPLKKHQR--FIEFYDVRDAAKA 281
           +   ++V  L   ++   L  +F+A GP+     +R+          F++F    D+ +A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 282 LKEMNGQEIYGKHVVIEFSRPGGHSKK 308
           +K +NG  +  K + + ++RPGG S K
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESIK 88

>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 = 48.7 bits (117), Expect = 3e-07
 Identities = 18/96 (18%), Positives = 37/96 (38%), Gaps = 15/96 (15%)

Query: 205 VAGRPV---WAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-- 259
           V  + +   +A+   P   ++ D N    + V NL   ++   L  IF  +G + +    
Sbjct: 70  VRNKRLKVSYAR---PGGESIKDTN----LYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 122

Query: 260 ---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG 292
               T   +   F+ +    +A +A+  +N     G
Sbjct: 123 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG 158

>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 = 60.6 bits (148), Expect = 4e-12
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 9/75 (12%)

Query: 226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQ--RFIEFYDVRDA 278
             +  + V  L   V    L   F  FG + ++      ET  +KH+   F+EF    DA
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYET--EKHRGFAFVEFELAEDA 62

Query: 279 AKALKEMNGQEIYGK 293
           A A+  MN  E++G+
Sbjct: 63  AAAIDNMNESELFGR 77

>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 = 63.0 bits (154), Expect = 4e-12
 Identities = 17/87 (19%), Positives = 42/87 (48%), Gaps = 5/87 (5%)

Query: 227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKE---LRETPLKKHQR--FIEFYDVRDAAKA 281
           ++  ++V  L   ++    + +F + G ++    +R+    +     F+ + D +DA KA
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 282 LKEMNGQEIYGKHVVIEFSRPGGHSKK 308
           +  +NG  +  K + + ++RP   S +
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSASIR 87

>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 = 43.7 bits (104), Expect = 2e-05
 Identities = 21/90 (23%), Positives = 42/90 (46%), Gaps = 12/90 (13%)

Query: 208 RPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETP 262
           +  +A+   P+  ++ D N    + V  L   ++   L+++F  +G +   R      T 
Sbjct: 75  KVSYAR---PSSASIRDAN----LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTG 127

Query: 263 LKKHQRFIEFYDVRDAAKALKEMNGQEIYG 292
           + +   FI F    +A +A+K +NGQ+  G
Sbjct: 128 VSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157

>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 = 62.5 bits (152), Expect = 5e-12
 Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 5/85 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
           T+ V NL    +   + E+F   G +K++     +         F+E+Y   DA  A++ 
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100

Query: 285 MNGQEIYGKHVVIEFSRPGGHSKKF 309
           +NG  +  + +  ++       +++
Sbjct: 101 INGTRLDDRIIRTDWDAGFKEGRQY 125

>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 = 61.7 bits (150), Expect = 5e-12
 Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 17/90 (18%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR-----FIEF 272
           PD N    + VF L    +   L+E+F  +GP+ ++     +++     +R     F+ F
Sbjct: 43  PDPNC--CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQS-----RRSRGFAFVYF 95

Query: 273 YDVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
            +V DA +A +  NG E+ G+ + ++FS  
Sbjct: 96  ENVDDAKEAKERANGMELDGRRIRVDFSIT 125

>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 = 63.9 bits (156), Expect = 8e-12
 Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 1/83 (1%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKAL 282
                +  + V NL + ++    K +F+ +G   E+      +   FI       A  A 
Sbjct: 17  KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVF-INRDRGFGFIRLESRTLAEIAK 75

Query: 283 KEMNGQEIYGKHVVIEFSRPGGH 305
            E++G  +  + + I F+  G  
Sbjct: 76  AELDGTILKSRPLRIRFATHGAA 98

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 43.1 bits (102), Expect = 6e-05
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 4/67 (5%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMN 286
           + V NL   VS+  L++ F  FGPV++      +      + F+EF     A KAL+   
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCG 158

Query: 287 GQEIYGK 293
                  
Sbjct: 159 DGAFLLT 165

>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 = 62.7 bits (153), Expect = 1e-11
 Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 7/90 (7%)

Query: 220 NAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYD 274
             VPD  +   + +  L + ++   +KE+  +FGP+K         T L K   F E+ D
Sbjct: 108 TVVPDSAH--KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 165

Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSRPGG 304
           +    +A+  +NG ++  K ++++ +  G 
Sbjct: 166 INVTDQAIAGLNGMQLGDKKLLVQRASVGA 195

>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 = 54.7 bits (132), Expect = 5e-09
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 11/83 (13%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR----------FIEFYDVRDAA 279
            + V N+  G++   + + F A   +  L + P                F+EF  V +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 280 KALKEMNGQEIYGKHVVIEFSRP 302
           +A+   +G    G+ + I     
Sbjct: 66  QAM-AFDGIIFQGQSLKIRRPHD 87

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 61.8 bits (150), Expect = 1e-11
 Identities = 27/112 (24%), Positives = 46/112 (41%), Gaps = 7/112 (6%)

Query: 197 LPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGT-IVVFNLDSGVSSSTLKEIFQAFGPV 255
            P P          W   +  +     +G   G  ++V NLD GVS + ++E+F  FG +
Sbjct: 56  RPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTL 115

Query: 256 KELRETPLKKHQR-----FIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
           K+       +  R      + F    DA KA+K+  G  + G+ + I+    
Sbjct: 116 KKA-AVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS 166

>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 = 61.0 bits (148), Expect = 2e-11
 Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 15/91 (16%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR-----FIEF 272
            D     ++ V NL    S  TL+ +F+ +G V ++     R T     +      F+ F
Sbjct: 65  MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT-----KESRGFAFVRF 119

Query: 273 YDVRDAAKALKEMNGQEIYGKHVVIEFSRPG 303
           +D RDA  A+  M+G  + G+ + ++ +R G
Sbjct: 120 HDKRDAEDAMDAMDGAVLDGRELRVQMARYG 150

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 59.4 bits (144), Expect = 2e-11
 Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            + +  L  GV  + L E  Q FGP+  +   P KK Q  +EF DV  A  A+      +
Sbjct: 23  VVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-KKRQALVEFEDVLGACNAVNYAADNQ 81

Query: 290 IY--GKHVVIEFSR 301
           IY  G    + +S 
Sbjct: 82  IYIAGHPAFVNYST 95

>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 = 61.5 bits (150), Expect = 2e-11
 Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 7/84 (8%)

Query: 226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR--FIEFYDVRDA 278
           ++   + V  +    S   L+E+F+ +G V E+     R     + +   F+ FY  + A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 279 AKALKEMNGQEIYGKHVVIEFSRP 302
            +A   ++  ++          +P
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMKP 84

>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 = 43.4 bits (103), Expect = 3e-05
 Identities = 13/89 (14%), Positives = 31/89 (34%), Gaps = 9/89 (10%)

Query: 207 GRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKH 266
             P+  +      N   +      + +  +    + + ++ +F +FG ++E R       
Sbjct: 77  HHPIQMKPADSEKNNAVEDRK---LFIGMISKKCTENDIRVMFSSFGQIEECR-ILRGPD 132

Query: 267 QR-----FIEFYDVRDAAKALKEMNGQEI 290
                  F+ F     A  A+K M+  + 
Sbjct: 133 GLSRGCAFVTFTTRAMAQTAIKAMHQAQT 161

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

 Score = 59.1 bits (144), Expect = 2e-11
 Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 4/77 (5%)

Query: 233 VFNLDS-GVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY 291
           + NL    VS   L  IF  +G + ++    +K    FI+F + +    A++  + +  +
Sbjct: 15  IGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIECESQEMNF 71

Query: 292 GKHVVIEFSRPGGHSKK 308
           GK +++E S      + 
Sbjct: 72  GKKLILEVSSSNARPQF 88

>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 = 59.6 bits (145), Expect = 2e-11
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 6/84 (7%)

Query: 224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDA 278
           + ++ G + +  L+   +   LK +F   GP+ E+      +  +     FI F +  DA
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVL-LIKDRTSKSRGFAFITFENPADA 61

Query: 279 AKALKEMNGQEIYGKHVVIEFSRP 302
             A K+MNG+ ++GK + +E ++ 
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKK 85

>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 = 59.2 bits (144), Expect = 2e-11
 Identities = 21/87 (24%), Positives = 44/87 (50%), Gaps = 15/87 (17%)

Query: 226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR-----FIEFYDV 275
           +++G + V  L    +  +L+++F  +G + E+     RET     QR     F+ F ++
Sbjct: 10  SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRET-----QRSRGFGFVTFENI 64

Query: 276 RDAAKALKEMNGQEIYGKHVVIEFSRP 302
            DA  A+  MNG+ + G+ + ++ +  
Sbjct: 65  DDAKDAMMAMNGKSVDGRQIRVDQAGK 91

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 58.4 bits (142), Expect = 3e-11
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 10/75 (13%)

Query: 226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR--FIEFYDVRDA 278
               T+ V NL++ V    L E+F   GP+ ++     RE    K +   F+ F      
Sbjct: 14  EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG---KPKSFGFVCFKHPESV 70

Query: 279 AKALKEMNGQEIYGK 293
           + A+  +NG  +YG+
Sbjct: 71  SYAIALLNGIRLYGR 85

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 58.6 bits (142), Expect = 3e-11
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 2/83 (2%)

Query: 222 VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAA 279
           VP       + + N+   +    L  +   +G V+      T  +     + +     A 
Sbjct: 9   VPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQAR 68

Query: 280 KALKEMNGQEIYGKHVVIEFSRP 302
           +AL ++NG ++    + + +   
Sbjct: 69  QALDKLNGFQLENFTLKVAYIPD 91

>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 = 58.2 bits (141), Expect = 3e-11
 Identities = 10/76 (13%), Positives = 28/76 (36%), Gaps = 2/76 (2%)

Query: 226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEM 285
           +    I+V NL    +   + ++ + +    +       K   F+   +   A  A++  
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYDL--KYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 286 NGQEIYGKHVVIEFSR 301
           +     GK ++++   
Sbjct: 61  HQYSFRGKDLIVQLQP 76

>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 = 58.5 bits (142), Expect = 4e-11
 Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 4/80 (5%)

Query: 230 TIVVFNLD-SGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
            + + NL+ + V  S ++ IF  +G V       + K   F+++ + R A  A+   NG+
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCS---VHKGYAFVQYSNERHARAAVLGENGR 85

Query: 289 EIYGKHVVIEFSRPGGHSKK 308
            + G+ + I  +      + 
Sbjct: 86  VLAGQTLDINMAGEPKPDRS 105

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 57.9 bits (140), Expect = 5e-11
 Identities = 14/74 (18%), Positives = 27/74 (36%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            + V NL      S LK   +  G V         + + F+ + D   A +A+  + G  
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLR 80

Query: 290 IYGKHVVIEFSRPG 303
           +    + +  +R  
Sbjct: 81  LGTDTLRVALARQQ 94

>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 = 57.9 bits (140), Expect = 6e-11
 Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 3/74 (4%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            + V  L   V  + L E  + FG +  +   P  K Q  +EF ++  A + +       
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMP-FKRQALVEFENIDSAKECVTFAADVP 75

Query: 290 IY--GKHVVIEFSR 301
           +Y  G+     +S 
Sbjct: 76  VYIAGQQAFFNYST 89

>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 = 58.5 bits (142), Expect = 6e-11
 Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 8/91 (8%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRD 277
           P+G N   + +++L        L ++F  FG V        ++T L K   F+ + +   
Sbjct: 23  PEGAN---LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVS 79

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPGGHSKK 308
           A  A++ MNG +I  K + ++  R    SK 
Sbjct: 80  AQAAIQSMNGFQIGMKRLKVQLKRSKNDSKS 110

>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 = 59.5 bits (144), Expect = 6e-11
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            + V ++        ++E F  +G +K +     R T   K    +E+   + A  A + 
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NG EI G+ + +++   
Sbjct: 134 LNGAEIMGQTIQVDWCFV 151

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 59.0 bits (143), Expect = 6e-11
 Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 5/86 (5%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRD 277
           PD     ++ V NL    S  TL+ +F+ +G V ++     R T   +   F+ F+D RD
Sbjct: 42  PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPG 303
           A  A+  M+G  + G+ + ++ +R G
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMARYG 127

>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 = 61.5 bits (150), Expect = 7e-11
 Identities = 15/95 (15%), Positives = 38/95 (40%), Gaps = 11/95 (11%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKE---LRETPLKKHQR--FIEFYDVRDAAKALKE 284
            + V NL   ++    +E+ + FG ++    +      + +   F E+     AA+A  +
Sbjct: 97  LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156

Query: 285 MNGQEIYGKHVVIEFSRPGG------HSKKFFYAN 313
           + G+ +  + + + ++  G       HS+      
Sbjct: 157 LLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDR 191

>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 = 61.1 bits (149), Expect = 9e-11
 Identities = 8/85 (9%), Positives = 29/85 (34%), Gaps = 6/85 (7%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR--FIEFYDVRDAAK 280
               N+  I++  L   V++  + ++   +          + K++   F+   +   A  
Sbjct: 17  RQFRNRRKILIRGLPGDVTNQEVHDLLSDYELK----YCFVDKYKGTAFVTLLNGEQAEA 72

Query: 281 ALKEMNGQEIYGKHVVIEFSRPGGH 305
           A+   +   +  + + ++       
Sbjct: 73  AINAFHQSRLRERELSVQLQPTDAL 97

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 58.5 bits (142), Expect = 8e-10
 Identities = 22/124 (17%), Positives = 42/124 (33%), Gaps = 12/124 (9%)

Query: 207 GRPV---WAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSS-TLKEIFQAFGPVKELRETP 262
            R +   W           P   +   + V  L  G +    L     A       +   
Sbjct: 164 PRTLYVHWTD----AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLAC 219

Query: 263 LKKHQR----FIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSSCA 318
            +  Q      +E+     A +A ++ +G  + G H+ + F  PG   +    A  ++ A
Sbjct: 220 GQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQA 279

Query: 319 SSLN 322
           ++LN
Sbjct: 280 TALN 283

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 57.9 bits (140), Expect = 8e-11
 Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            I+  NL +G  ++ ++E F  FG +  +           +EF +  +A KA + +   +
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-GGITAIVEFLEPLEARKAFRHLAYSK 70

Query: 290 IYGKHVVIEF 299
            +   + +E+
Sbjct: 71  FHHVPLYLEW 80

>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 = 58.0 bits (141), Expect = 8e-11
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR---FIEFYDVRDAAKALKEM 285
           G I + NLD  + +  L + F AFG +   +    +   +   F+ F     A +A+++M
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65

Query: 286 NGQEIYGKHVVIEFSRP 302
           NG  +  + V +   + 
Sbjct: 66  NGMLLNDRKVFVGRFKS 82

>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 = 56.9 bits (138), Expect = 8e-11
 Identities = 15/73 (20%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEM-NGQ 288
           T+ V  L   ++ + L+  F  FG ++ +     ++   FI+F   + A  A ++  N  
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTIT-VVQRQQCAFIQFATRQAAEVAAEKSFNKL 72

Query: 289 EIYGKHVVIEFSR 301
            + G+ + +++ R
Sbjct: 73  IVNGRRLNVKWGR 85

>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 = 61.4 bits (148), Expect = 8e-11
 Identities = 30/151 (19%), Positives = 53/151 (35%), Gaps = 8/151 (5%)

Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKELR--ETPLKKHQRFIEFYD 274
           AVP+     TI + NL+  +    LK+    IF  FG + ++    +   + Q F+ F +
Sbjct: 2   AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKE 61

Query: 275 VRDAAKALKEMNGQEIYGKHVVIEF--SRPGGHSKKFFYANSSSCASSLNYSTIYQTRNS 332
           V  A  AL+ M G   Y K + I++  +     +K                    +T  +
Sbjct: 62  VSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPAT 121

Query: 333 DCPPPPLSADPPSYSPRSFASQAPHFRKKSP 363
                   A P   + +      P   +   
Sbjct: 122 KKAVQGGGATPVVGAVQGPVPGMPPMTQAPR 152

>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 = 60.7 bits (146), Expect = 1e-10
 Identities = 38/281 (13%), Positives = 74/281 (26%), Gaps = 53/281 (18%)

Query: 74  LPPPSTGPTRTLVLSYVPGDVSETIVRRDLEV----FGEVRGVQMER--LMEGIVTVHFY 127
           +  P T P  T+ ++ +   + +  +++ L      FG++  + + R   M G   V F 
Sbjct: 1   MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 60

Query: 128 DLRHAEMAFKE----------------------------------------------IRE 141
           ++  A  A +                                                  
Sbjct: 61  EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA 120

Query: 142 QHMQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPA 201
               +Q            G +                  Q        M     + P   
Sbjct: 121 TKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQI 180

Query: 202 RGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRET 261
                         +P    + +      + + NL    +   L  +F  F   KE+R  
Sbjct: 181 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 240

Query: 262 PLKKHQRFIEFYDVRDAAKALKEMNGQEIY-GKHVVIEFSR 301
           P +    F+EF +   A  A   + G +I     + I F++
Sbjct: 241 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 281

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 57.4 bits (139), Expect = 1e-10
 Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 9/75 (12%)

Query: 230 TIVVFNL------DSGVSSSTLKEIFQAFGPVKEL---RETPLKKHQRFIEFYDVRDAAK 280
            IVV N+            + + +IF  FG +       E    K   F+E+     A  
Sbjct: 17  VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 76

Query: 281 ALKEMNGQEIYGKHV 295
           A+K  +G ++  +H 
Sbjct: 77  AVKNADGYKLDKQHT 91

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 15/85 (17%), Positives = 35/85 (41%), Gaps = 11/85 (12%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFG--PVKELRETPLKKHQR-----FIEFYDVRDAAKAL 282
           TI++ N+       ++      +    V  +R    K+ Q+     F++     DA++ L
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 283 KEMNGQE----IYGKHVVIEFSRPG 303
           + +        I GK + ++F++  
Sbjct: 71  QILQSLHPPLKIDGKTIGVDFAKSA 95

>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 = 57.8 bits (140), Expect = 1e-10
 Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 7/86 (8%)

Query: 223 PDGNNQGT-IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVR 276
            +G   G  ++V NLD GVS + ++E+F  FG +K+       +  R      + F    
Sbjct: 29  GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA-VDYDRSGRSLGTADVHFERRA 87

Query: 277 DAAKALKEMNGQEIYGKHVVIEFSRP 302
           DA KA+K+  G  + G+ + I+    
Sbjct: 88  DALKAMKQYKGVPLDGRPMDIQLVAS 113

>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 = 56.8 bits (138), Expect = 1e-10
 Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALK 283
           G + V NL    S   L+++F A+GP+ EL       T   K   F+ F     A KA  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 284 EMNGQEIYGKHVVIEFSRP 302
           E++GQ   G+ + +  S  
Sbjct: 69  EVDGQVFQGRMLHVLPSTI 87

>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 = 56.9 bits (138), Expect = 1e-10
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            + V ++        ++E F  +G +K +     R T   K    +E+   + A  A + 
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NG EI G+ + +++   
Sbjct: 88  LNGAEIMGQTIQVDWCFV 105

>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 = 57.8 bits (139), Expect = 3e-10
 Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKH-QRFIEFYDVRDAAKALKEMNGQE 289
           I+V NL   V+   L +IF  FG V ++         Q  +++ D   A  A   ++GQ 
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 108

Query: 290 IY--GKHVVIEFSRPGGHSKKFFYANS 314
           IY     + I+FS+    + K+    S
Sbjct: 109 IYNACCTLRIDFSKLTSLNVKYNNDKS 135

>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 = 57.0 bits (138), Expect = 3e-10
 Identities = 14/78 (17%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            + V  +    +   + + F  +G +K +     R T   K    +E+   ++A  A++ 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NGQ++ G+ + +++   
Sbjct: 84  LNGQDLMGQPISVDWCFV 101

>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 = 56.1 bits (136), Expect = 3e-10
 Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 8/78 (10%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
           T+ V  L    +  TLKE   +F           RET   K   F++F    DA  A + 
Sbjct: 17  TLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73

Query: 285 MNGQEIYGKHVVIEFSRP 302
           M   EI G  V +++++P
Sbjct: 74  MEDGEIDGNKVTLDWAKP 91

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 18/79 (22%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
            + +  L    +   L+EI +A G VK+LR     +  +     ++E+ +   A++A+ +
Sbjct: 19  KLFISGLPFSCTKEELEEICKAHGTVKDLR-LVTNRAGKPKGLAYVEYENESQASQAVMK 77

Query: 285 MNGQEIYGKHVVIEFSRPG 303
           M+G  I    + +  S  G
Sbjct: 78  MDGMTIKENIIKVAISNSG 96

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 55.9 bits (135), Expect = 3e-10
 Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 5/73 (6%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALK 283
           G  V+ +    V    L  +F   G V  +       T   K   F+E   + DA K +K
Sbjct: 13  GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72

Query: 284 EMNGQEIYGKHVV 296
             +G+ +  KH +
Sbjct: 73  SFHGKRLDLKHRL 85

>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 = 56.1 bits (136), Expect = 3e-10
 Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 7/83 (8%)

Query: 223 PDGNNQGT-IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVR 276
             G   G  ++V NLD GVS + ++E+F  FG +K+       +  R      + F    
Sbjct: 23  GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAA-VHYDRSGRSLGTADVHFERKA 81

Query: 277 DAAKALKEMNGQEIYGKHVVIEF 299
           DA KA+K+ NG  + G+ + I+ 
Sbjct: 82  DALKAMKQYNGVPLDGRPMNIQL 104

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 56.6 bits (136), Expect = 4e-10
 Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 3/90 (3%)

Query: 216 VPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKH-QRFIEFYD 274
           V    A+   +    I+V NL   V+   L +IF  FG V ++         Q  +++ D
Sbjct: 16  VDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYAD 75

Query: 275 VRDAAKALKEMNGQEIY--GKHVVIEFSRP 302
              A  A   ++GQ IY     + I+FS+ 
Sbjct: 76  PVSAQHAKLSLDGQNIYNACCTLRIDFSKL 105

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 14/78 (17%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            + V  +    +   + + F  +G +K +     R T   K    +E+   ++A  A++ 
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NGQ++ G+ + +++   
Sbjct: 85  LNGQDLMGQPISVDWCFV 102

>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 = 55.7 bits (135), Expect = 4e-10
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 3/73 (4%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPV---KELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           V NLD G+    L++ F  FG +   K + E    K   F+ F    +A KA+ EMNG+ 
Sbjct: 20  VKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRI 79

Query: 290 IYGKHVVIEFSRP 302
           +  K + +  ++ 
Sbjct: 80  VATKPLYVALAQR 92

>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 = 54.8 bits (133), Expect = 4e-10
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 15/78 (19%)

Query: 235 NLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR-----FIEFYDVRDAAKALKE 284
           +L+  V   TL+  F+ F            +T            F+ F    DA  A+  
Sbjct: 8   DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQT-----GSSRGYGFVSFTSQDDAQNAMDS 62

Query: 285 MNGQEIYGKHVVIEFSRP 302
           M GQ++ G+ + I ++  
Sbjct: 63  MQGQDLNGRPLRINWAAK 80

>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 = 55.4 bits (134), Expect = 5e-10
 Identities = 13/81 (16%), Positives = 34/81 (41%), Gaps = 13/81 (16%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR---FIEFYDVRDAAKA 281
            + V N+        L+++F  FG + ++              +   F+ F +  DA +A
Sbjct: 17  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-----KGFGFVTFENSADADRA 71

Query: 282 LKEMNGQEIYGKHVVIEFSRP 302
            ++++G  + G+ + +  +  
Sbjct: 72  REKLHGTVVEGRKIEVNNATA 92

>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 = 57.2 bits (139), Expect = 5e-10
 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 7/84 (8%)

Query: 221 AVPDGNNQGTIVVF--NLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFY 273
                   G   +F   L + ++   +KE+  +FGP+K         T L K   F E+ 
Sbjct: 85  PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 144

Query: 274 DVRDAAKALKEMNGQEIYGKHVVI 297
           D+    +A+  +NG ++  K +++
Sbjct: 145 DINVTDQAIAGLNGMQLGDKKLLV 168

>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 = 56.1 bits (136), Expect = 1e-09
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 11/83 (13%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL----------RETPLKKHQRFIEFYDVRDAA 279
            + V N+  G++   + + F A   +  L           +    K+  F+EF  V +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 280 KALKEMNGQEIYGKHVVIEFSRP 302
           +A+   +G    G+ + I     
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHD 87

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 55.0 bits (133), Expect = 7e-10
 Identities = 13/73 (17%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR---FIEFYDVRDAAKALKEMNGQE 289
           V N+        L+++F  FG + ++     ++  +   F+ F +  DA +A ++++G  
Sbjct: 34  VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTV 93

Query: 290 IYGKHVVIEFSRP 302
           + G+ + +  +  
Sbjct: 94  VEGRKIEVNNATA 106

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 54.3 bits (131), Expect = 7e-10
 Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 9/75 (12%)

Query: 230 TIVVFNL------DSGVSSSTLKEIFQAFGPVKEL---RETPLKKHQRFIEFYDVRDAAK 280
            IVV N+            + + +IF  FG +       E    K   F+E+     A  
Sbjct: 3   VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 62

Query: 281 ALKEMNGQEIYGKHV 295
           A+K  +G ++  +H 
Sbjct: 63  AVKNADGYKLDKQHT 77

>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 = 55.3 bits (133), Expect = 7e-10
 Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 3/63 (4%)

Query: 230 TIVVFN--LDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           ++VV N  L +GVS + L  + +  G V  L   P K +  F  +    ++ +A   +NG
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYS-FARYRTTEESKRAYVTLNG 85

Query: 288 QEI 290
           +E+
Sbjct: 86  KEV 88

>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 = 54.1 bits (131), Expect = 9e-10
 Identities = 19/85 (22%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRD 277
           P G++   + V +L   ++++ +   F  FG + + R      T   K   F+ F++  D
Sbjct: 2   PLGSHF-HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRP 302
           A  A+++M GQ + G+ +   ++  
Sbjct: 61  AENAIQQMGGQWLGGRQIRTNWATR 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 = 54.2 bits (131), Expect = 1e-09
 Identities = 13/91 (14%), Positives = 28/91 (30%), Gaps = 5/91 (5%)

Query: 217 PTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIE 271
            +  A         I V N+   VS   + + F  +  +         +         + 
Sbjct: 4   GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 272 FYDVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
           F    +A  A+ ++N + I  + V +     
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94

>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 = 54.7 bits (132), Expect = 1e-09
 Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 5/85 (5%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRD 277
            D +N   + V +L   +++  +K  F  FG + +        T   K   F+ F++  D
Sbjct: 10  KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 69

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRP 302
           A  A+++M GQ + G+ +   ++  
Sbjct: 70  AENAIQQMGGQWLGGRQIRTNWATR 94

>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 = 54.6 bits (132), Expect = 1e-09
 Identities = 18/94 (19%), Positives = 44/94 (46%), Gaps = 12/94 (12%)

Query: 217 PTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR--- 268
           P  N  P+  +  T+    L + +    L++ F A G V+++     R +   +  +   
Sbjct: 14  PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNS---RRSKGIA 70

Query: 269 FIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
           ++EF +++    A+  + GQ + G  ++++ S+ 
Sbjct: 71  YVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA 103

>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 = 54.2 bits (131), Expect = 1e-09
 Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            + + ++    +   + ++    GPV  L      +T   K   FIEF D+  +A A++ 
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NG ++  + +   +S  
Sbjct: 64  LNGYQLGSRFLKCGYSSN 81

>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 = 53.7 bits (130), Expect = 1e-09
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL------RETPLKKHQRFIEFYDVRDAA 279
           +    I + NLD  +    L + F AFG + +        +T   K   FI F     + 
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62

Query: 280 KALKEMNGQEIYGKHVVIEFSRP 302
            A++ MNGQ +  + + + ++  
Sbjct: 63  AAIEAMNGQYLCNRPITVSYAFK 85

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            + V +L   ++   L+ IF+ FG +  +      +T   K   FI F D   A +AL++
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NG E+ G+ + +     
Sbjct: 67  LNGFELAGRPMRVGHVTE 84

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 54.7 bits (132), Expect = 1e-09
 Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 8/84 (9%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRD 277
           P+G N   + +++L    + + L   F  FG V        ++T L K   F+ F +   
Sbjct: 38  PEGCN---LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94

Query: 278 AAKALKEMNGQEIYGKHVVIEFSR 301
           A  A+K MNG ++  K + ++  +
Sbjct: 95  AQVAIKAMNGFQVGTKRLKVQLKK 118

>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 = 54.8 bits (132), Expect = 2e-09
 Identities = 21/110 (19%), Positives = 46/110 (41%), Gaps = 5/110 (4%)

Query: 198 PPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKE 257
           P      +       Q  +P     P+ +    ++V  + + V    L+++F+ +GP++ 
Sbjct: 12  PYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIES 71

Query: 258 L-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
           +     RET   +   F++F     A +A+  +NG  I  K + +  +  
Sbjct: 72  VKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS 121

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 53.3 bits (129), Expect = 2e-09
 Identities = 19/85 (22%), Positives = 31/85 (36%), Gaps = 3/85 (3%)

Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPV---KELRETPLKKHQRFIEFYDVRD 277
                +    I V NL    +   LK+ F   G V       E    K    ++F     
Sbjct: 1   GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEV 60

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRP 302
           A +A + MNG ++ G+ + +   R 
Sbjct: 61  AERACRMMNGMKLSGREIDVRIDRN 85

>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 = 53.9 bits (130), Expect = 2e-09
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 7/88 (7%)

Query: 221 AVPDGNNQGT-IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYD 274
                   G+ + V NLD  V    LKE+F   G V         K  +      + F  
Sbjct: 7   GALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRAD-ILEDKDGKSRGIGTVTFEQ 65

Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSRP 302
             +A +A+   NGQ ++ + + ++    
Sbjct: 66  SIEAVQAISMFNGQLLFDRPMHVKMDER 93

>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 = 53.1 bits (128), Expect = 2e-09
 Identities = 13/92 (14%), Positives = 29/92 (31%), Gaps = 5/92 (5%)

Query: 217 PTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIE 271
            +  +         I V N+   VS   + + F  +  +         +         + 
Sbjct: 4   GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 272 FYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG 303
           F    +A  A+ ++N + I  + V +     G
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLSGPSSG 95

>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 = 53.5 bits (129), Expect = 2e-09
 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            + V +L   ++   L+ IF+ FG ++ +      ET   K   FI F D   A KAL++
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NG E+ G+ + +     
Sbjct: 88  LNGFELAGRPMKVGHVTE 105

>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 = 53.3 bits (128), Expect = 3e-09
 Identities = 9/85 (10%), Positives = 28/85 (32%), Gaps = 9/85 (10%)

Query: 227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPV-------KELRETPLKKHQRFIEFYDVRDAA 279
               + +  +        + E                   +    +   F+E+   R AA
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 280 KALKEMNGQ--EIYGKHVVIEFSRP 302
            A +++     +++G  + ++++ P
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDWAEP 91

>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 = 53.0 bits (128), Expect = 3e-09
 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
           ++ V N+    +   LK+IF   GPV        RET   K   F E+ D   A  A++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NG+E  G+ + ++ +  
Sbjct: 70  LNGREFSGRALRVDNAAS 87

>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 = 52.2 bits (126), Expect = 4e-09
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
           T+ V NL   ++++ L  IF  +G V ++     ++T   K   FI F D   A    + 
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77

Query: 285 MNGQEIYGK 293
           +N ++++G+
Sbjct: 78  INNKQLFGR 86

>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 = 52.7 bits (127), Expect = 5e-09
 Identities = 19/90 (21%), Positives = 34/90 (37%), Gaps = 11/90 (12%)

Query: 224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDA 278
           D     T+ + NL        L E+ Q FG +K +      +T   K   F +F     A
Sbjct: 11  DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70

Query: 279 AKALKEMN------GQEIYGKHVVIEFSRP 302
            K L   +      G ++ G+ + ++ +  
Sbjct: 71  QKCLAAASLEAEGGGLKLDGRQLKVDLAVT 100

>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 = 53.0 bits (128), Expect = 5e-09
 Identities = 19/98 (19%), Positives = 31/98 (31%), Gaps = 11/98 (11%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDA 278
            D  N   + + NL   +    L+ + + FG V   R     +   +   F         
Sbjct: 23  QDPTN---LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKC 79

Query: 279 AKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSS 316
              +   NG+ I     V   + P     KF  +  SS
Sbjct: 80  EAVIGHFNGKFIKTPPGVSAPTEP--LLCKF--SGPSS 113

>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 = 52.3 bits (126), Expect = 5e-09
 Identities = 16/89 (17%), Positives = 32/89 (35%), Gaps = 15/89 (16%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQR-----FIEFY 273
            +      + + NL+   S + LK          +L      T            +++F 
Sbjct: 12  SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-----GTNRKFGYVDFE 66

Query: 274 DVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
              D  KAL E+ G +++G  + +E  + 
Sbjct: 67  SAEDLEKAL-ELTGLKVFGNEIKLEKPKG 94

>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 = 51.8 bits (125), Expect = 6e-09
 Identities = 14/85 (16%), Positives = 31/85 (36%), Gaps = 10/85 (11%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRD 277
              +    + +  L  G +   L ++ Q +G +        + T   K   F++F     
Sbjct: 3   SGSSG---LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSA 59

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRP 302
           A KA+  +    +  +  + + S P
Sbjct: 60  AQKAVTALKASGVQAQ--MAKQSGP 82

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 17/75 (22%), Positives = 27/75 (36%), Gaps = 3/75 (4%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK--EMNG 287
            I +  L   V+   +  +   FG V  L      K+Q FIE      A   +       
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVT 76

Query: 288 QEIYGKHVVIEFSRP 302
             + G+ + I+FS  
Sbjct: 77  PVLRGQPIYIQFSNH 91

>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 = 51.8 bits (124), Expect = 1e-08
 Identities = 17/75 (22%), Positives = 27/75 (36%), Gaps = 3/75 (4%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK--EMNG 287
            I +  L   V+   +  +   FG V  L      K+Q FIE      A   +       
Sbjct: 33  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVT 91

Query: 288 QEIYGKHVVIEFSRP 302
             + G+ + I+FS  
Sbjct: 92  PVLRGQPIYIQFSNH 106

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 51.2 bits (123), Expect = 2e-08
 Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 13/86 (15%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-------------RETPLKKHQRFIEFYDVR 276
           TI V  L   V+  ++ + F+  G +K               RET   K +  + F D  
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 277 DAAKALKEMNGQEIYGKHVVIEFSRP 302
            A  A+   +G+E  G  + + F+  
Sbjct: 69  SAKAAIDWFDGKEFSGNPIKVSFATR 94

>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 = 50.6 bits (121), Expect = 2e-08
 Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 3/74 (4%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK--EMNG 287
            + +  L   V+ + +  +   FG V  +      K+Q F+E      A   +       
Sbjct: 17  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-GKNQAFLELATEEAAITMVNYYSAVT 75

Query: 288 QEIYGKHVVIEFSR 301
             +  + + I++S 
Sbjct: 76  PHLRNQPIYIQYSN 89

>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 = 49.1 bits (118), Expect = 5e-08
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            I V NL    +S  +KE+F  FG V  +     RET   K   F+E  +    ++A+ +
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 285 MNGQEIYGKHVVIEFSRP 302
           ++  +  G+ + +  + P
Sbjct: 62  LDNTDFMGRTIRVTEANP 79

>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 = 49.0 bits (117), Expect = 9e-08
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 2/80 (2%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKAL 282
           P   ++  +VV  L    S   LK+  +  G V        +     +EF    D   A+
Sbjct: 10  PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV--YRDGTGVVEFVRKEDMTYAV 67

Query: 283 KEMNGQEIYGKHVVIEFSRP 302
           ++++  +         + R 
Sbjct: 68  RKLDNTKFRSHEGETAYIRV 87

>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 = 48.3 bits (116), Expect = 1e-07
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 12/81 (14%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR---FIEFYDVRDAAKA 281
           +I V N+D G ++  L+  F   G V  +     + +    H +   +IEF D      +
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFS---GHPKGFAYIEFSDKESVRTS 64

Query: 282 LKEMNGQEIYGKHVVIEFSRP 302
           L  ++     G+ + +   R 
Sbjct: 65  L-ALDESLFRGRQIKVIPKRT 84

>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 = 52.5 bits (125), Expect = 1e-07
 Identities = 29/157 (18%), Positives = 57/157 (36%), Gaps = 5/157 (3%)

Query: 217 PTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIE 271
           P  +    G+   T+ V  ++   + S L+  F+ +GP+K +     K+  +     FIE
Sbjct: 91  PHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIE 150

Query: 272 FYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTIYQTRN 331
           +   RD   A K  +G++I G+ V+++  R                  +         R+
Sbjct: 151 YEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRH 210

Query: 332 SDCPPPPLSADPPSYSPRSFASQAPHFRKKSPSNSFK 368
           S         + P  SP     +     ++    S +
Sbjct: 211 SGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRE 247

>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 = 48.1 bits (115), Expect = 2e-07
 Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 6/76 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFG-PVKELR-----ETPLKKHQRFIEFYDVRDAAKALK 283
           ++ + +L+  +  + +   F   G  V  ++      T +     F+EF D+  A K L 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 284 EMNGQEIYGKHVVIEF 299
           ++NG+ + G      F
Sbjct: 71  KINGKPLPGATPAKRF 86

>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 = 47.8 bits (114), Expect = 2e-07
 Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 6/85 (7%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRD 277
           PD  N G + +  L  G S   + + F     V      P+    R     F++F     
Sbjct: 10  PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEI 69

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRP 302
           A KAL + + + I  +++ I  S  
Sbjct: 70  AEKAL-KKHKERIGHRYIEIFKSSR 93

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 11/79 (13%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-------FIEFYDVRDAAKAL 282
           ++ +    +  +   +KE  +  G V  ++   +++          F+ F  +  A K +
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQ---MRRTLHKAFKGSIFVVFDSIESAKKFV 69

Query: 283 KEMNGQEIYGKHVVIEFSR 301
            E  GQ+     ++I F  
Sbjct: 70  -ETPGQKYKETDLLILFKD 87

>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 = 47.9 bits (114), Expect = 2e-07
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 2/80 (2%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKAL 282
           P   ++  +VV  L    S   LK+  +  G V        +     +EF    D   A+
Sbjct: 11  PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEFVRKEDMTYAV 68

Query: 283 KEMNGQEIYGKHVVIEFSRP 302
           ++++  +         + R 
Sbjct: 69  RKLDNTKFRSHEGETAYIRV 88

>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 = 47.2 bits (113), Expect = 3e-07
 Identities = 13/79 (16%), Positives = 29/79 (36%), Gaps = 7/79 (8%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGP--VKEL-----RETPLKKHQRFIEFYDVRDAAKALK 283
           + + NL    +   L E   + G   + E+     R     K    +       + K + 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 284 EMNGQEIYGKHVVIEFSRP 302
            +  +E++G++ V+  S  
Sbjct: 64  LLPKRELHGQNPVVTPSNK 82

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 48.8 bits (116), Expect = 3e-07
 Identities = 17/118 (14%), Positives = 37/118 (31%), Gaps = 9/118 (7%)

Query: 192 SYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQA 251
                 PP  +            I+ T + + +      + V +     +   L ++ ++
Sbjct: 21  QSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAA--VYVGSFSWWTTDQQLIQVIRS 78

Query: 252 FGP--VKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
            G   V EL     R     K    +         K L+ + G+ + G+ V +  +  
Sbjct: 79  IGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATR 136

>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 = 48.2 bits (115), Expect = 3e-07
 Identities = 15/87 (17%), Positives = 36/87 (41%), Gaps = 12/87 (13%)

Query: 224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR---FIEFYDV 275
              ++ ++ V N+D G ++  L+  F + G +  +     + +    H +   +IEF + 
Sbjct: 32  KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFS---GHPKGYAYIEFAER 88

Query: 276 RDAAKALKEMNGQEIYGKHVVIEFSRP 302
                A+  M+     G+ + +   R 
Sbjct: 89  NSVDAAV-AMDETVFRGRTIKVLPKRT 114

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 23/94 (24%), Positives = 35/94 (37%), Gaps = 7/94 (7%)

Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAK 280
                +   ++ V     GV S+ L E F AFGPV  +     K     +E  D   A +
Sbjct: 1   GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGD-VGARE 59

Query: 281 ALKEMNGQEIYGKHVVI------EFSRPGGHSKK 308
           A+   +   + G  + +      EF  P   S K
Sbjct: 60  AVLSQSQHSLGGHRLRVRPREQKEFQSPASKSPK 93

>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 = 46.7 bits (111), Expect = 7e-07
 Identities = 6/83 (7%), Positives = 31/83 (37%), Gaps = 6/83 (7%)

Query: 225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAA 279
            + +    + N+   ++   + +  +     +      +  + +      ++F +  DA 
Sbjct: 12  NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDAR 71

Query: 280 KALKEMNGQEIYGKHVVIEFSRP 302
           K+ + ++ +++ G+   +     
Sbjct: 72  KSER-LHRKKLNGREAFVHVVTL 93

>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 = 47.5 bits (114), Expect = 9e-07
 Identities = 14/89 (15%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 221 AVPDGNNQGTIVVF--NLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFY 273
           A+P      T  +F   +   V     +E F  +G + +      ++T   +   F+ + 
Sbjct: 78  AIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYD 137

Query: 274 DVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
              DA   + +    +   + + I+ + P
Sbjct: 138 SA-DAVDRVCQNKFIDFKDRKIEIKRAEP 165

>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 = 41.4 bits (98), Expect = 1e-04
 Identities = 17/94 (18%), Positives = 33/94 (35%), Gaps = 16/94 (17%)

Query: 228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR---FIEFYDVRDAA 279
              + +  L+   +   L+E F  +G V +L       T      R   F+ F       
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPAT---GRSRGFGFLSFEKPSSVD 59

Query: 280 KALKEMNGQEIYGKHVVIEFSRPGG---HSKKFF 310
           + +K  +   + GK +  + + P      + K F
Sbjct: 60  EVVKTQH--ILDGKVIDPKRAIPRDEQDKTGKIF 91

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 15/80 (18%), Positives = 28/80 (35%), Gaps = 2/80 (2%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR--FIEFYDVRDAAKALKEMNGQ 288
           I + NL  G S   LK++ +             +       +EF       +AL+ +N  
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90

Query: 289 EIYGKHVVIEFSRPGGHSKK 308
           E  G  + +E        ++
Sbjct: 91  EFRGSVITVERDDNPPPIRR 110

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 12/70 (17%), Positives = 27/70 (38%), Gaps = 1/70 (1%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           +++ NL + +   TL+ +    GP+       L +     ++    +A KA   +N   +
Sbjct: 10  LLLKNLTAQIDGPTLRTLCMQHGPLVSFH-PYLNQGIALCKYTTREEANKAQMALNNCVL 68

Query: 291 YGKHVVIEFS 300
               +  E  
Sbjct: 69  ANTTIFAESP 78

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 47.5 bits (112), Expect = 2e-06
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 1/82 (1%)

Query: 225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKE 284
           G   G +   +L      S ++ +F   G +  +R     K+  F++F    +A  A + 
Sbjct: 140 GGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIR-YVESKNCGFVKFKYQANAEFAKEA 198

Query: 285 MNGQEIYGKHVVIEFSRPGGHS 306
           M+ Q +          R  G  
Sbjct: 199 MSNQTLLLPSDKEWDDRREGTG 220

>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 = 44.7 bits (106), Expect = 3e-06
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 13/86 (15%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-------------RETPLKKHQRFIEFYDVR 276
            I V  L+  V+   L + F+  G VK               +ET   K    + + D  
Sbjct: 17  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76

Query: 277 DAAKALKEMNGQEIYGKHVVIEFSRP 302
            A  A++  +G++  G  + +  +R 
Sbjct: 77  TAKAAVEWFDGKDFQGSKLKVSLARK 102

>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 = 44.9 bits (106), Expect = 4e-06
 Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 6/85 (7%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRD 277
            D  N G + +  L  G +   + + F     V      P+    +     F++F     
Sbjct: 37  ADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQEL 96

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRP 302
           A KAL   + + I  +++ +  S  
Sbjct: 97  AEKAL-GKHKERIGHRYIEVFKSSQ 120

>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 = 44.2 bits (105), Expect = 4e-06
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGP-----VKELRETPLKKHQRFIEFYDVRDAAKALKE 284
           T  + NL   V+  ++KE F+          +E       K   + EF D+     AL  
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 75

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +N + +  K + ++ +  
Sbjct: 76  LNEESLGNKRIRVDVADQ 93

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 19/84 (22%), Positives = 32/84 (38%), Gaps = 13/84 (15%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-------------RETPLKKHQRF 269
              ++  TI V  L   V+  ++ + F+  G +K               RET   K +  
Sbjct: 8   HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 67

Query: 270 IEFYDVRDAAKALKEMNGQEIYGK 293
           + F D   A  A+   +G+E  G 
Sbjct: 68  VSFDDPPSAKAAIDWFDGKEFSGN 91

>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 = 46.2 bits (109), Expect = 6e-06
 Identities = 20/156 (12%), Positives = 49/156 (31%), Gaps = 11/156 (7%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGP--VKEL-----RETPLKKHQRFIEFYDV 275
                +  + + NL    +   L E   + G   + E+     R     K    +     
Sbjct: 63  TYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSE 122

Query: 276 RDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFFYANSSSCASSLNYSTIYQTRNSDCP 335
             + K +  +  +E++G++ V+        S+    +  ++ +  ++     + +     
Sbjct: 123 ASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMS----GEGKAGPPG 178

Query: 336 PPPLSADPPSYSPRSFASQAPHFRKKSPSNSFKGNP 371
               +A P     R     A     + P  +  G P
Sbjct: 179 GSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGP 214

>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 = 44.1 bits (104), Expect = 7e-06
 Identities = 10/85 (11%), Positives = 27/85 (31%), Gaps = 6/85 (7%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRD 277
                   + +  L     +  + + F+    V++        + +     F+EF +  D
Sbjct: 20  SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEAD 79

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRP 302
              AL   + Q +  + + +     
Sbjct: 80  YKAAL-CRHKQYMGNRFIQVHPITK 103

>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 = 43.4 bits (103), Expect = 9e-06
 Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 7/77 (9%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
           V  L+   S   +  +FQ FG + E           K   F++F    +A  A+  ++G 
Sbjct: 20  VGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS 79

Query: 289 EIY---GKHVVIEFSRP 302
           +        +V++F+  
Sbjct: 80  QTMPGASSSLVVKFADT 96

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 5/75 (6%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGP-VKELR----ETPLKKHQRFIEFYDVRD 277
                + ++ V +L   V    L E F    P  +  +    +T + K   F++F D  +
Sbjct: 4   GSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELE 63

Query: 278 AAKALKEMNGQEIYG 292
             +AL E  G    G
Sbjct: 64  QKRALTECQGAVGLG 78

>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 = 42.5 bits (100), Expect = 2e-05
 Identities = 11/79 (13%), Positives = 28/79 (35%), Gaps = 11/79 (13%)

Query: 233 VFNLDSGVSSSTL---KEIFQAFGPVKEL-----RETPLKKHQR---FIEFYDVRDAAKA 281
           V  L   ++   +    E F  FG + ++           +      ++ +    DA +A
Sbjct: 20  VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA 79

Query: 282 LKEMNGQEIYGKHVVIEFS 300
           ++ +N   + G+ +     
Sbjct: 80  IQCVNNVVVDGRTLKASLG 98

>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 = 42.6 bits (100), Expect = 2e-05
 Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 230 TIVVFNL-DSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK--EMN 286
            I + NL  SG S S + ++ + +G +K        K Q FIE     DA   +      
Sbjct: 27  VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-MKSQAFIEMETREDAMAMVDHCLKK 85

Query: 287 GQEIYGKHVVIEFSR 301
                G+ V ++ S 
Sbjct: 86  ALWFQGRCVKVDLSE 100

>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 = 42.2 bits (100), Expect = 2e-05
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 14/82 (17%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR---------FIEFYDVRDAAK 280
           T  + NL   V+  ++KE F+    +  +R   L +            + EF D+     
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVR---LPREPSNPERLKGFGYAEFEDLDSLLS 76

Query: 281 ALKEMNGQEIYGKHVVIEFSRP 302
           AL  +N + +  + + ++ +  
Sbjct: 77  AL-SLNEESLGNRRIRVDVADQ 97

>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 = 43.4 bits (103), Expect = 3e-05
 Identities = 16/103 (15%), Positives = 37/103 (35%), Gaps = 8/103 (7%)

Query: 207 GRPVWAQFIVPTCNAVPDGNNQGTIVVF--NLDSGVSSSTLKEIFQAFGPVKEL-----R 259
           GR V  +  V   ++   G +     +F   +        L++ F+ +G ++ +     R
Sbjct: 81  GRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR 140

Query: 260 ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
            +  K+   F+ F D     K +       + G +  +  +  
Sbjct: 141 GSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALS 182

>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 = 40.0 bits (94), Expect = 5e-04
 Identities = 19/101 (18%), Positives = 37/101 (36%), Gaps = 15/101 (14%)

Query: 224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQR---FIEFYDVRDA 278
           +      + +  L    +  +L+  F+ +G + +      P  K  R   F+ +  V + 
Sbjct: 9   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68

Query: 279 AKALKEMNGQEIYGKHVVI-------EFSRPGGH--SKKFF 310
             A+      ++ G+ V         +  RPG H   KK F
Sbjct: 69  DAAM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIF 108

>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 = 41.9 bits (99), Expect = 4e-05
 Identities = 22/114 (19%), Positives = 38/114 (33%), Gaps = 18/114 (15%)

Query: 217 PTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQR--- 268
              +          I V  L    + ++L++ F+ FG ++E      R+T      R   
Sbjct: 6   SGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQT---GKSRGYG 62

Query: 269 FIEFYDVRDAAKALKEMNGQEIYGKHVVI------EFSRPGGHSKKFFYANSSS 316
           F+   D   A +A K+ N   I G+   +         R          +  SS
Sbjct: 63  FVTMADRAAAERACKDPN-PIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSS 115

>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 = 41.5 bits (98), Expect = 4e-05
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 8/78 (10%)

Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNG 287
           +  +   +    LK +F+ FG + EL     R T + K   F+ + +   A KA   ++ 
Sbjct: 18  IGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHE 77

Query: 288 QEIY---GKHVVIEFSRP 302
           Q+      + + ++ +  
Sbjct: 78  QKTLPGMNRPIQVKPADS 95

>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 = 40.5 bits (95), Expect = 6e-05
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 13/78 (16%)

Query: 235 NLDSGVSSSTLKEIFQAFGPVKELRETPLK----------KHQRFIEFYDVRDAAKALKE 284
           N+  G++   + + F A   +  L + P            K+  F+EF  V +  +A+  
Sbjct: 13  NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-A 71

Query: 285 MNGQEIYGKHVVIEFSRP 302
            +G    G+   ++  RP
Sbjct: 72  FDGIIFQGQ--SLKIRRP 87

>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 = 41.8 bits (98), Expect = 6e-05
 Identities = 11/90 (12%), Positives = 28/90 (31%), Gaps = 8/90 (8%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRD 277
                   + +  L    + + +   F    PV+      +    R      +EF    +
Sbjct: 41  VQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR--VHIEIGPDGRVTGEADVEFATHEE 98

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPGGHSK 307
           A  A+   +   +  +++ +  +   G S 
Sbjct: 99  AVAAM-SKDRANMQHRYIELFLNSTTGASN 127

>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 = 42.1 bits (98), Expect = 1e-04
 Identities = 20/128 (15%), Positives = 46/128 (35%), Gaps = 8/128 (6%)

Query: 177 CYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNL 236
             D  V+ E+L    +    +      +   R   ++ +    +   +     ++ +   
Sbjct: 61  TTDFNVIVEALSKSKAELMEISEDKTKI---RRSPSKPLPEVTDEYKNDVKNRSVYIKGF 117

Query: 237 DSGVSSSTLKEIFQAFGPVKE--LRETPLKKHQ--RFIEFYDVRDAAKALKEMNGQEIYG 292
            +  +   +KE  +  G V    +R T  K  +   F+ F  +  A K ++   GQ+   
Sbjct: 118 PTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKE 176

Query: 293 KHVVIEFS 300
             ++I F 
Sbjct: 177 TDLLILFK 184

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 7/78 (8%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKE 284
           T  V NL        +  IF+    ++ +R     +T   K   ++EF +V    +AL  
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-T 74

Query: 285 MNGQEIYGKHVVIEFSRP 302
            +G  +  + + ++ +  
Sbjct: 75  YDGALLGDRSLRVDIAEG 92

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A* Length = 345

 Score = 41.3 bits (96), Expect = 3e-04
 Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 3/65 (4%)

Query: 231 IVVFN--LDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
           +VV N  L +GVS + L  + +  G V  L   P  K   F  +    ++ +A   +NG+
Sbjct: 21  LVVANGGLGNGVSRNQLLPVLEKCGLVDAL-LMPPNKPYSFARYRTTEESKRAYVTLNGK 79

Query: 289 EIYGK 293
           E+   
Sbjct: 80  EVVDD 84

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 4/53 (7%)

Query: 252 FGPVKELR-ETPLKKHQR---FIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS 300
           +G V+E+     L  H     +++F    DA KA+ ++N +   G+ +  E S
Sbjct: 51  YGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103

>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 = 38.8 bits (91), Expect = 4e-04
 Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 222 VPDGNNQ-GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVR 276
           +P+G     T+ V  +D  +  + ++  F  +G VKE++     T + K   F+ FY+  
Sbjct: 2   LPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDV 61

Query: 277 DAAKALKEMNGQEIYGKHVVIEFSRP 302
           D  K +   +    +GK + +  +  
Sbjct: 62  DVQKIV--ESQINFHGKKLKLGPAIR 85

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 38.3 bits (89), Expect = 5e-04
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 4/71 (5%)

Query: 235 NLDSGVSS-STLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK--EMNGQEIY 291
           +   G +    L ++ + FG +        K ++ FIE     DA  A+         ++
Sbjct: 22  DFQRGKNLRYQLLQLVEPFGVISNHLILN-KINEAFIEMATTEDAQAAVDYYTTTPALVF 80

Query: 292 GKHVVIEFSRP 302
           GK V +  S+ 
Sbjct: 81  GKPVRVHLSQK 91

>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 = 38.6 bits (90), Expect = 5e-04
 Identities = 10/86 (11%), Positives = 28/86 (32%), Gaps = 8/86 (9%)

Query: 222 VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVR 276
           +P   +   + V  +      + +++ F                  R      ++F   +
Sbjct: 10  LPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDA--VHLLKDHVGRNNGNGLVKFLSPQ 67

Query: 277 DAAKALKEMNGQEIYGKHVVIEFSRP 302
           D  +AL + N   +  ++V +  +  
Sbjct: 68  DTFEAL-KRNRMLMIQRYVEVSPATE 92

>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 = 38.1 bits (89), Expect = 5e-04
 Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 8/88 (9%)

Query: 224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDA 278
            G    T+ +      V+   + E      PV          H       F++F +  + 
Sbjct: 6   SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVA--IRIVRNAHGNKTGYIFVDFSNEEEV 63

Query: 279 AKALKEMNGQEIYGKHVVIEFSRPGGHS 306
            +ALK  N + + G+++ +   + G  S
Sbjct: 64  KQALK-CNREYMGGRYIEVFREKSGPSS 90

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 38.2 bits (88), Expect = 6e-04
 Identities = 14/50 (28%), Positives = 21/50 (42%)

Query: 239 GVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
           G S   L  + Q +G V  L  +  K     +EF  V+ A  A++   G 
Sbjct: 28  GYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVGL 77

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	408
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.98
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.97
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.97
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.97
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.97
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.97
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.96
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.96
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.95
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.95
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.95
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.86
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.83
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.82
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.79
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.76
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.76
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.75
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.74
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.74
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.73
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.73
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.73
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.72
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.72
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.72
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.72
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.72
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.72
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.72
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.72
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.72
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.71
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.71
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.71
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.71
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.71
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.71
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.71
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.71
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.71
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.71
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.71
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.7
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.7
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.7
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.7
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.7
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.7
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.7
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.7
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.7
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.7
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.7
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.7
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.7
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.7
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.7
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.7
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.7
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.7
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.7
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.7
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.69
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.69
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.69
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.69
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.69
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.69
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.69
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.69
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.69
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.69
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.69
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.69
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.69
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.69
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.69
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.69
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.69
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.69
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.69
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.68
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.68
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.68
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.68
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.68
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.68
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.68
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.68
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.68
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.68
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.68
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.68
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.68
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.68
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.67
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.67
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.67
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.67
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.67
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.67
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.67
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.67
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.67
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.67
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.67
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.67
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.67
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.67
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.67
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.67
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.67
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.67
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.67
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.67
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.67
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.66
2div_A	99	TRNA selenocysteine associated protein; structural	99.66
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.66
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.66
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.66
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.66
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.66
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.66
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.66
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.66
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.66
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.66
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.66
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.66
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.66
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.66
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.66
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.66
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.66
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.66
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.66
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.65
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.65
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.65
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.65
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.65
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.65
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.65
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.65
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.65
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.65
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.65
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.65
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.65
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.65
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.65
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.65
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.65
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.65
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.65
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.65
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.65
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.65
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.65
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.65
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.64
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.64
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.64
1x5p_A	97	Negative elongation factor E; structure genomics,	99.64
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.64
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.64
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.64
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.64
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.64
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.64
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.64
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.64
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.64
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.64
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.64
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.64
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.64
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.64
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.64
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.64
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.64
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.64
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.64
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.64
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.64
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.63
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.63
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.63
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.63
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.63
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.63
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.63
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.63
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.63
2div_A	99	TRNA selenocysteine associated protein; structural	99.63
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.63
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.63
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.63
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.63
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.63
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.63
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.63
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.62
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.62
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.62
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.62
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.62
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.62
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.62
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.62
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.62
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.62
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.62
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.62
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.62
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.62
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.62
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.62
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.62
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.61
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.61
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.61
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.61
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.61
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.61
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.61
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.61
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.61
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.61
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.61
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.61
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.6
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.6
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.6
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.6
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.6
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.6
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.6
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.6
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.6
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.6
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.6
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.6
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.6
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.6
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.59
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.59
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.59
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.59
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.59
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.59
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.59
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.59
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.59
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.59
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.58
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.58
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.58
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.58
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.58
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.58
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.58
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.58
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.58
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.57
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.57
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.35
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.57
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.57
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.57
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.56
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.56
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.56
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.56
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.56
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.56
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.56
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.56
1x5p_A	97	Negative elongation factor E; structure genomics,	99.56
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.56
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.56
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.56
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.56
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.56
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.55
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.55
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.55
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.55
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.55
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.55
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.55
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.55
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.55
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.54
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.54
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.54
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.54
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.54
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.54
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.54
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.53
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.53
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.53
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.53
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.53
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.53
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.53
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.53
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.52
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.52
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.52
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.52
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.52
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.52
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.51
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.5
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.5
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.5
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.49
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.49
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.49
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.49
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.49
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.49
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.48
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.48
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.48
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.48
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.22
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.47
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.47
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.47
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.46
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.44
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.44
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.44
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.43
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.43
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.43
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.41
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.41
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.4
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.4
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.38
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.37
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.37
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.36
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.35
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.35
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.35
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.34
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.33
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.32
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.31
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.29
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.26
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.21
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.21
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.16
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.03
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.0
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.99
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.81
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.79
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.72
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.63
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.46
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.45
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.2
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.87
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.72
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.43
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.32
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.18
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.18
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.02
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.98
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.92
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.75
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.72
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.43
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.41
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.91
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.68
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.6
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.22
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	89.18
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	89.13
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	84.37
1jgn_B	26	PAIP2, polyadenylate-binding protein-interacting p	82.75

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=2.4e-33  Score=252.58  Aligned_cols=163  Identities=20%  Similarity=0.305  Sum_probs=135.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ..+.++|||+|||+++||++|+++|++||+|.+|++++     +++|||||+|.+.++|++|++.+++..+.  |+.  +
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~--g~~--i   87 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIK--GKP--V   87 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEE--C
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcC--Ccc--c
Confidence            44678999999999999999999999999999999876     45899999999999999999999998765  563  3


Q ss_pred             eccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEE
Q 046223          154 KNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVV  233 (408)
Q Consensus       154 ~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V  233 (408)
                      ++.++...                 . .                                         .......+|||
T Consensus        88 ~~~~~~~~-----------------~-~-----------------------------------------~~~~~~~~l~v  108 (213)
T 4f02_A           88 RIMWSQRD-----------------P-S-----------------------------------------LRKSGVGNIFI  108 (213)
T ss_dssp             EEEECCCC-----------------T-H-----------------------------------------HHHHCTTEEEE
T ss_pred             cccccccc-----------------c-c-----------------------------------------ccccccccceE
Confidence            33222100                 0 0                                         00011378999


Q ss_pred             cCCCCCCcHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          234 FNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       234 ~nLp~~~t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      +||+..+|+++|+++|++||.|..++   ..+.++|||||+|.+.++|++|++.|||..|+|+.|+|.+++++.
T Consensus       109 ~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          109 KNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             ESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             CCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            99999999999999999999999883   344578999999999999999999999999999999999998754

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.98  E-value=1.8e-31  Score=229.80  Aligned_cols=157  Identities=18%  Similarity=0.314  Sum_probs=134.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      |+|||+|||.++|+++|+++|++||.|.+|++.+    +++|||||+|.+.++|++|++.|+|..+.  |+.  +++.++
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~--g~~--i~v~~~   76 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIE--NNI--VKINWA   76 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEET--TEE--CEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccC--CCe--eEEEEc
Confidence            6899999999999999999999999999999875    45899999999999999999999998876  663  333332


Q ss_pred             CccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCCC
Q 046223          159 SGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDS  238 (408)
Q Consensus       159 ~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp~  238 (408)
                      ...                                                           .........+|||+|||.
T Consensus        77 ~~~-----------------------------------------------------------~~~~~~~~~~l~v~nl~~   97 (166)
T 3md3_A           77 FQS-----------------------------------------------------------QQSSSDDTFNLFVGDLNV   97 (166)
T ss_dssp             CCC-----------------------------------------------------------CCCCCTTCEEEEEESCCT
T ss_pred             CCC-----------------------------------------------------------CCCCCCCCceEEECCCCC
Confidence            100                                                           001123358999999999


Q ss_pred             CCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          239 GVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       239 ~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .+++++|+++|++||.|..+.     .++.++|+|||+|.+.++|.+|++.|||..++|+.|+|.||++
T Consensus        98 ~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A           98 NVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             TCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             CCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            999999999999999999882     4577899999999999999999999999999999999999863

>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=99.97  E-value=9.7e-31  Score=231.83  Aligned_cols=169  Identities=14%  Similarity=0.209  Sum_probs=132.9

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ......++|||+|||.++|+++|+++|+.||.|.+|++.+     .++|||||+|.+.++|++|++. ++..|.  |+.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~--g~~l   84 (196)
T 1l3k_A            8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVD--GRVV   84 (196)
T ss_dssp             CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEET--TEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEEC--CEEe
Confidence            4456789999999999999999999999999999999876     3589999999999999999975 776654  6643


Q ss_pred             ceeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceE
Q 046223          152 GLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTI  231 (408)
Q Consensus       152 ~~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l  231 (408)
                      .+.  ++....                .                                       ..........++|
T Consensus        85 ~v~--~~~~~~----------------~---------------------------------------~~~~~~~~~~~~l  107 (196)
T 1l3k_A           85 EPK--RAVSRE----------------D---------------------------------------SQRPGAHLTVKKI  107 (196)
T ss_dssp             EEE--ECCC------------------------------------------------------------------CCSEE
T ss_pred             eee--cccCcc----------------c---------------------------------------ccccccCCCcceE
Confidence            333  222000                0                                       0000011234899


Q ss_pred             EEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCCC
Q 046223          232 VVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHS  306 (408)
Q Consensus       232 ~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~  306 (408)
                      ||+|||.++|+++|+++|+.||.|..++     .++.++|||||+|.+.++|.+|++. +|..|+|+.|.|.++.++...
T Consensus       108 ~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          108 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             EEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             EEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            9999999999999999999999999883     3677899999999999999999986 899999999999999887644

>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=99.97  E-value=1.7e-30  Score=224.40  Aligned_cols=155  Identities=17%  Similarity=0.314  Sum_probs=133.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ++++|||+|||.++|+++|+++|+.||.|.+|++.+     .++|||||+|.+.++|++|++.|+|..+.  |+.  +++
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~--g~~--l~v   77 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVR--NKR--LKV   77 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEET--TEE--CEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeC--CcE--EEE
Confidence            578999999999999999999999999999999876     24799999999999999999999998875  663  444


Q ss_pred             cccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcC
Q 046223          156 PYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFN  235 (408)
Q Consensus       156 ~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~n  235 (408)
                      .++...                                                             .......+|||+|
T Consensus        78 ~~~~~~-------------------------------------------------------------~~~~~~~~l~v~n   96 (168)
T 1b7f_A           78 SYARPG-------------------------------------------------------------GESIKDTNLYVTN   96 (168)
T ss_dssp             EECCCC-------------------------------------------------------------SSTTTTCEEEEES
T ss_pred             EecCCC-------------------------------------------------------------cccCCCCCEEEeC
Confidence            332200                                                             0112348999999


Q ss_pred             CCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEEe
Q 046223          236 LDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG--KHVVIEFS  300 (408)
Q Consensus       236 Lp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~a  300 (408)
                      ||..+++++|+++|++||.|..+.     .++.++|+|||+|.+.++|.+|++.|||..+.|  +.|+|+||
T Consensus        97 l~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A           97 LPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             CCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            999999999999999999998883     256778999999999999999999999999988  99999986

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.97  E-value=2.8e-30  Score=230.63  Aligned_cols=192  Identities=15%  Similarity=0.188  Sum_probs=135.4

Q ss_pred             CCCCEEEEcCCC-CCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           80 GPTRTLVLSYVP-GDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        80 ~~~rtlfV~nLp-~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      .++++|||+||+ .++|+++|+++|++||.|.+|++++.++|||||+|.+.++|++||+.|||..|.  ||  .|++.|+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~--g~--~l~v~~s   77 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMF--GQ--KMNVCVS   77 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEET--TE--ECEEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEEC--Cc--eEEEEEc
Confidence            357899999999 899999999999999999999999878999999999999999999999999876  67  4566565


Q ss_pred             CccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCc-CCCCCCCCCCceEEEcCCC
Q 046223          159 SGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPT-CNAVPDGNNQGTIVVFNLD  237 (408)
Q Consensus       159 ~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~-~~~~~~~~~~~~l~V~nLp  237 (408)
                      ..........  .....+...                     .+.. .+... ..+..+. ........+.++|||+|||
T Consensus        78 ~~~~~~p~~~--~~~~~~~~~---------------------~~~~-~~~~~-~r~~~~~~~~~~~~~~p~~~l~v~NLp  132 (205)
T 3tyt_A           78 KQPAIMPGQS--YGLEDGSCS---------------------YKDF-SESRN-NRFSTPEQAAKNRIQHPSNVLHFFNAP  132 (205)
T ss_dssp             SCSCCCCCSC--CBCTTSCBS---------------------EEEC-TTCTT-CSCSSHHHHTTSCCCCCCSEEEEEEEC
T ss_pred             cCCccCCCcc--cccccCCcc---------------------cccc-CCCcc-ccccCcccccccccCCCcceEEEeCCC
Confidence            4322100000  000000000                     0000 00000 0000000 0000011235899999999


Q ss_pred             CCCcHHHHHHHHhcCCCc--eeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCe----EEEEEEe
Q 046223          238 SGVSSSTLKEIFQAFGPV--KELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK----HVVIEFS  300 (408)
Q Consensus       238 ~~~t~~~L~~~F~~~G~v--~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~----~l~v~~a  300 (408)
                      .++|+++|+++|++||.|  ..++   ..+..+|+|||+|.+.++|.+|+..|||..|.|+    .+.|+|+
T Consensus       133 ~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          133 LEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             TTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            999999999999999998  6663   2234569999999999999999999999999986    5666665

>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=99.97  E-value=3.9e-30  Score=234.10  Aligned_cols=196  Identities=18%  Similarity=0.235  Sum_probs=144.6

Q ss_pred             CCCCCCCEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           77 PSTGPTRTLVLSYVPG-DVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~-~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ....++++|||+|||. ++|+++|+++|++||.|.+|++.+..+|||||+|.+.++|++|++.|||..|.  |+  .+++
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~--g~--~l~v  104 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLH--GK--PIRI  104 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCS--SS--BCEE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeEC--Ce--EEEE
Confidence            3455789999999999 99999999999999999999999877999999999999999999999998875  66  3555


Q ss_pred             cccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCC-CCCCCCCCceEEEc
Q 046223          156 PYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCN-AVPDGNNQGTIVVF  234 (408)
Q Consensus       156 ~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~-~~~~~~~~~~l~V~  234 (408)
                      .++.............   ....           ...+...  ...+           ...+... .........+|||+
T Consensus       105 ~~a~~~~~~~~~~~~~---~~~~-----------~~~~~~~--~~~~-----------~~~~~~~~~~~~~~~~~~l~V~  157 (229)
T 2adc_A          105 TLSKHQNVQLPREGQE---DQGL-----------TKDYGNS--PLHR-----------FKKPGSKNFQNIFPPSATLHLS  157 (229)
T ss_dssp             ECCSCCCCCCCCSSSS---TTTT-----------EEECTTC--SSCC-----------CCSTTSGGGTTCCCSCSEEEEE
T ss_pred             EEecCccccCcccccc---cccc-----------ccccccC--cccc-----------cCCccccccccCCCCCCEEEEe
Confidence            5554221110000000   0000           0000000  0000           0000000 00112346899999


Q ss_pred             CCCCCCcHHHHHHHHhcCC-CceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeC-CeEEEEEEecCC
Q 046223          235 NLDSGVSSSTLKEIFQAFG-PVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY-GKHVVIEFSRPG  303 (408)
Q Consensus       235 nLp~~~t~~~L~~~F~~~G-~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~l~v~~a~~~  303 (408)
                      ||+..+++++|+++|++|| .|..++.....+|+|||+|.+.++|.+|++.|||..++ |+.|+|.|++++
T Consensus       158 nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          158 NIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            9999999999999999999 99999765567999999999999999999999999999 999999999864

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.97  E-value=1.9e-30  Score=225.52  Aligned_cols=160  Identities=18%  Similarity=0.275  Sum_probs=131.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-------cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ++++|||+|||.++|+++|+++|++||+|.+|++.+       +++|||||+|.+.++|++|++.|+|..+.. ++...+
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~-~~~~~~   80 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLP-GMHHPI   80 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCT-TCSSCC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEcc-CCccce
Confidence            578999999999999999999999999999999875       358999999999999999999999977642 221122


Q ss_pred             eccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEE
Q 046223          154 KNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVV  233 (408)
Q Consensus       154 ~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V  233 (408)
                      .+.++...                                                            ........+|||
T Consensus        81 ~~~~~~~~------------------------------------------------------------~~~~~~~~~l~v  100 (175)
T 3nmr_A           81 QMKPADSE------------------------------------------------------------KNNAVEDRKLFI  100 (175)
T ss_dssp             EEEECGGG------------------------------------------------------------CCSCGGGSEEEE
T ss_pred             EEcccccc------------------------------------------------------------ccccCCCCeEEE
Confidence            22211100                                                            001123489999


Q ss_pred             cCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeC---CeEEEEEEec
Q 046223          234 FNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY---GKHVVIEFSR  301 (408)
Q Consensus       234 ~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~---g~~l~v~~a~  301 (408)
                      +|||..+|+++|+++|++||.|..++    ..+.++|||||+|.+.++|.+|++.|||..+.   |+.|+|.||.
T Consensus       101 ~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          101 GMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             ESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             cCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            99999999999999999999999883    35667999999999999999999999998776   4999999984

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.97  E-value=7.6e-30  Score=239.40  Aligned_cols=218  Identities=18%  Similarity=0.249  Sum_probs=144.2

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHH----HHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVR----RDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~----~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      ....++++|||+|||.++|+++|+    ++|++||.|.+|++.+  +++|||||+|.+.++|++|++.|||..|.  |+ 
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~-   80 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFY--DK-   80 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeC--Cc-
Confidence            455679999999999999999966    9999999999999876  56899999999999999999999998876  66 


Q ss_pred             cceeccccCcccc--ccCCCCCCCcc----cCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCC----------------
Q 046223          151 YGLKNPYSSGLML--MNNDNNNNNLA----TGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGR----------------  208 (408)
Q Consensus       151 l~~~~~~s~~~s~--~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~----------------  208 (408)
                       .+++.|+....-  ...........    ..+...........   ...............+.                
T Consensus        81 -~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (282)
T 3pgw_A           81 -PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKK---AVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHH  156 (282)
T ss_pred             -EEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhh---hccCcCCcccCCCCCCCCCCCCccccccccccc
Confidence             455656543321  00000000000    00000000000000   00000000000000000                


Q ss_pred             -----------------Cc-----------ccc---ccCCcCCCCCCCCCCceEEEcCCCCCCcHHHHHHHHhcCCCcee
Q 046223          209 -----------------PV-----------WAQ---FIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKE  257 (408)
Q Consensus       209 -----------------~~-----------~~~---~~~p~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~  257 (408)
                                       ..           ..+   ...+...........++|||+||+..+++++|+++|++||.|.+
T Consensus       157 ~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~  236 (282)
T 3pgw_A          157 MPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKE  236 (282)
T ss_pred             CCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEE
Confidence                             00           000   00000011123345789999999999999999999999999999


Q ss_pred             eccCCCCccEEEEEECCHHHHHHHHHHhCCceeC-CeEEEEEEec
Q 046223          258 LRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY-GKHVVIEFSR  301 (408)
Q Consensus       258 v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~l~v~~a~  301 (408)
                      |+.....+|||||+|.+.++|.+|++.|||..|+ |+.|+|+|++
T Consensus       237 v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          237 VRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            9655455799999999999999999999999999 9999999986

>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=99.97  E-value=2.7e-30  Score=222.69  Aligned_cols=155  Identities=22%  Similarity=0.408  Sum_probs=131.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ++++|||+|||.++|+++|+++|+.||.|.+|++.+     +++|||||+|.+.++|++|++.|+|..+.  |+.  +++
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~--g~~--l~v   76 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQ--TKT--IKV   76 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEE--CEE
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccC--Cce--EEE
Confidence            368999999999999999999999999999999876     23699999999999999999999998875  563  344


Q ss_pred             cccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcC
Q 046223          156 PYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFN  235 (408)
Q Consensus       156 ~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~n  235 (408)
                      .++...                                                             .......+|||+|
T Consensus        77 ~~~~~~-------------------------------------------------------------~~~~~~~~l~v~n   95 (167)
T 1fxl_A           77 SYARPS-------------------------------------------------------------SASIRDANLYVSG   95 (167)
T ss_dssp             EECCCC-------------------------------------------------------------CGGGTTCEEEEES
T ss_pred             EecCCC-------------------------------------------------------------cccCCCCcEEECC
Confidence            332200                                                             0011247899999


Q ss_pred             CCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeE--EEEEEe
Q 046223          236 LDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH--VVIEFS  300 (408)
Q Consensus       236 Lp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~--l~v~~a  300 (408)
                      ||..+++++|+++|++||.|..++     .++.++|||||+|.+.++|.+|++.|||..+.|+.  |+|+||
T Consensus        96 l~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A           96 LPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            999999999999999999998883     35667999999999999999999999999999975  888876

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.97  E-value=1.3e-30  Score=227.01  Aligned_cols=163  Identities=18%  Similarity=0.210  Sum_probs=135.5

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEe----ecCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQME----RLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~----~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ....+.++|||+|||.++|+++|+++|+.||.|..+.+.    ..++|||||+|.+.++|++|+ .|||..|.  |+.  
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~~--   82 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVF--GNE--   82 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEET--TEE--
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeC--CeE--
Confidence            345678999999999999999999999999976552221    257999999999999999999 49998876  664  


Q ss_pred             eeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEE
Q 046223          153 LKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIV  232 (408)
Q Consensus       153 ~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~  232 (408)
                      +++.++...                                                           .........+||
T Consensus        83 l~v~~~~~~-----------------------------------------------------------~~~~~~~~~~l~  103 (175)
T 1fje_B           83 IKLEKPKGR-----------------------------------------------------------DSKKVRAARTLL  103 (175)
T ss_dssp             EEEECCCCS-----------------------------------------------------------SCSTTGGGGEEE
T ss_pred             EEEecCCCc-----------------------------------------------------------cccccccCCEEE
Confidence            444332210                                                           000112248999


Q ss_pred             EcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       233 V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      |+|||..+++++|+++|++||.|..+..++.++|||||+|.+.++|.+|++.|||..++|+.|+|+|++++
T Consensus       104 v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          104 AKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             EESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             EeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            99999999999999999999999988667789999999999999999999999999999999999999875

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.97  E-value=9.9e-30  Score=225.70  Aligned_cols=179  Identities=20%  Similarity=0.304  Sum_probs=137.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcc----C-------CeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVF----G-------EVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQ  148 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~----G-------~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~g  148 (408)
                      ..+++|||+|||.++|+++|+++|++|    |       .|..+.+. +++|||||+|.+.++|++|+ .|||..|.  |
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~-~~~g~afV~F~~~~~A~~Al-~l~g~~~~--g   77 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETTQAM-AFDGIIFQ--G   77 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE-TTTTEEEEEESCSHHHHHHG-GGTTEEET--T
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec-CCCCEEEEEeCCHHHHHHHH-HhcCCEEc--C
Confidence            357999999999999999999999999    5       67777665 57999999999999999999 89998875  6


Q ss_pred             cccceeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCC
Q 046223          149 QSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQ  228 (408)
Q Consensus       149 r~l~~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~  228 (408)
                      +.  +++.++.......          ..                       .     ..   .....+...........
T Consensus        78 ~~--i~v~~~~~~~~~~----------~~-----------------------~-----~~---~~~~~~~~~~~~~~~~~  114 (198)
T 2yh0_A           78 QS--LKIRRPHDYQPLP----------GM-----------------------S-----EN---PSVYVPGVVSTVVPDSA  114 (198)
T ss_dssp             EE--EEEECCCCCCCCC----------CS-----------------------S-----SC---SSCCCTTSSCCCSSCCC
T ss_pred             ce--EEEeCCCCCCCCC----------CC-----------------------c-----CC---CcCCCCCCccCCCCCCC
Confidence            64  4444433110000          00                       0     00   00000111111123456


Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ++|||+|||..+++++|+++|++||.|..++     .++.++|||||+|.+.++|.+|++.|||..++|+.|+|++++++
T Consensus       115 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  194 (198)
T 2yh0_A          115 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG  194 (198)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            9999999999999999999999999998883     36677999999999999999999999999999999999999876


Q ss_pred             CC
Q 046223          304 GH  305 (408)
Q Consensus       304 ~~  305 (408)
                      ..
T Consensus       195 ~~  196 (198)
T 2yh0_A          195 AK  196 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.97  E-value=1.4e-30  Score=234.44  Aligned_cols=171  Identities=18%  Similarity=0.294  Sum_probs=137.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .+.++|||+|||.++|+++|+++|+.||.|.+|++.+     +++|||||+|.+.++|++|++.|+|..|.  |+.  ++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~--g~~--l~  101 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLG--GRN--IK  101 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC---CC--CE
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeC--Cee--EE
Confidence            3568999999999999999999999999999999975     36999999999999999999999998875  664  34


Q ss_pred             ccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEc
Q 046223          155 NPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVF  234 (408)
Q Consensus       155 ~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~  234 (408)
                      +.++....                ..........                                  .......+|||+
T Consensus       102 v~~~~~~~----------------~~~~~~~~~~----------------------------------~~~~~~~~l~v~  131 (216)
T 2qfj_A          102 VGRPSNIG----------------QAQPIIDQLA----------------------------------EEARAFNRIYVA  131 (216)
T ss_dssp             EECCSCCG----------------GGHHHHHHHH----------------------------------HHHTTSCEEEEE
T ss_pred             EecCCCcc----------------ccchhhhhhh----------------------------------cccCCCcEEEEe
Confidence            33322110                0000000000                                  001224899999


Q ss_pred             CCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          235 NLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       235 nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ||+.++++++|+++|++||.|..++     .++.++|||||+|.+.++|.+|++.|||..|+|+.|+|.|++++.
T Consensus       132 nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          132 SVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             CCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             CCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            9999999999999999999999883     356779999999999999999999999999999999999998764

>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=99.97  E-value=9.9e-30  Score=220.54  Aligned_cols=154  Identities=20%  Similarity=0.327  Sum_probs=131.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcc----C-------CeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVF----G-------EVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQ  148 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~----G-------~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~g  148 (408)
                      +++++|||+|||.++|+++|+++|++|    |       .|.++.+. .++|||||+|.+.++|++|+ .|||..|.  |
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~-~~~g~afV~f~~~~~A~~A~-~~~~~~~~--g   77 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETTQAM-AFDGIIFQ--G   77 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE-TTTTEEEEEESSHHHHHHHG-GGTTCEET--T
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec-CCCCEEEEEeCCHHHHHHHH-HhCCcEec--C
Confidence            357899999999999999999999999    6       77887776 57999999999999999999 89998875  6


Q ss_pred             cccceeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCC
Q 046223          149 QSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQ  228 (408)
Q Consensus       149 r~l~~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~  228 (408)
                      +.+.+.  ++...                                                             ......
T Consensus        78 ~~i~v~--~~~~~-------------------------------------------------------------~~~~~~   94 (172)
T 2g4b_A           78 QSLKIR--RPHDY-------------------------------------------------------------QPLPGA   94 (172)
T ss_dssp             EECEEE--CCSSC-------------------------------------------------------------CCCTTT
T ss_pred             ceeeec--CCccc-------------------------------------------------------------CCCCCC
Confidence            643333  21100                                                             001124


Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      .+|||+|||..+++++|+++|++||.|..++     .++.++|||||+|.+.++|.+|++.|||..++|+.|+|+||
T Consensus        95 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           95 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            8999999999999999999999999999883     36777999999999999999999999999999999999997

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.97  E-value=1.5e-29  Score=224.83  Aligned_cols=192  Identities=18%  Similarity=0.249  Sum_probs=141.7

Q ss_pred             CCCEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           81 PTRTLVLSYVPG-DVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        81 ~~rtlfV~nLp~-~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      .+++|||+|||. ++|+++|+++|++||.|.+|++.+..+|||||+|.+.++|++|++.|||..|.  |+.  +++.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~--g~~--l~v~~a~   77 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLH--GKP--IRITLSK   77 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCS--SCC--CEEEECC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeec--CeE--EEEEEec
Confidence            368999999999 99999999999999999999999877999999999999999999999998875  663  5555544


Q ss_pred             ccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCC-CCCCCCCCceEEEcCCCC
Q 046223          160 GLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCN-AVPDGNNQGTIVVFNLDS  238 (408)
Q Consensus       160 ~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~-~~~~~~~~~~l~V~nLp~  238 (408)
                      .......... ... ... .           ..+...  ...           .+..+... ......+..+|||+||+.
T Consensus        78 ~~~~~~~~~~-~~~-~~~-~-----------~~~~~~--~~~-----------r~~~~~~~~~~~~~~~~~~l~v~nl~~  130 (198)
T 1qm9_A           78 HQNVQLPREG-QED-QGL-T-----------KDYGNS--PLH-----------RFKKPGSKNFQNIFPPSATLHLSNIPP  130 (198)
T ss_dssp             CCSCCCSSSS-SSS-SSC-E-----------EESSCC--CTT-----------SSSSCCCCCCSCCCCCCCEEEECCCCT
T ss_pred             CCCcCCCCcC-Ccc-ccc-c-----------ccccCC--chh-----------hccCccccccccCCCCccEEEEeCCCC
Confidence            2211000000 000 000 0           000000  000           00000000 011123468999999999


Q ss_pred             CCcHHHHHHHHhcCC-CceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeC-CeEEEEEEecCC
Q 046223          239 GVSSSTLKEIFQAFG-PVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY-GKHVVIEFSRPG  303 (408)
Q Consensus       239 ~~t~~~L~~~F~~~G-~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~l~v~~a~~~  303 (408)
                      .+++++|+++|++|| .|..++.....+|+|||+|.+.++|.+|++.|||..++ |+.|+|.|++++
T Consensus       131 ~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          131 SVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             TCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            999999999999999 99998765567999999999999999999999999999 999999999764

>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=99.97  E-value=1.3e-30  Score=224.96  Aligned_cols=155  Identities=12%  Similarity=0.230  Sum_probs=128.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ++++|||+|||.++|+++|+++|+.||.|.+|++.+     +++|||||+|.+.++|++|++.  +..+  .|+.+  .+
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~--~g~~i--~v   75 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHIL--DGKVI--DP   75 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEE--TTEEC--CC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--cccc--CCeEc--cc
Confidence            578999999999999999999999999999999875     4589999999999999999985  3333  25532  22


Q ss_pred             cccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcC
Q 046223          156 PYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFN  235 (408)
Q Consensus       156 ~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~n  235 (408)
                      .++...                   .                                          ......+|||+|
T Consensus        76 ~~~~~~-------------------~------------------------------------------~~~~~~~l~V~n   94 (167)
T 2cjk_A           76 KRAIPR-------------------D------------------------------------------EQDKTGKIFVGG   94 (167)
T ss_dssp             EECCCH-------------------H------------------------------------------HHHHCEEEEEEE
T ss_pred             ccccch-------------------h------------------------------------------hccCCCeEEECC
Confidence            221100                   0                                          001137899999


Q ss_pred             CCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          236 LDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       236 Lp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ||.++++++|+++|++||.|..++     .++.++|||||+|.+.++|.+|++ ++|..++|+.|+|.|++++
T Consensus        95 lp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A           95 IGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             ECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             CCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            999999999999999999999883     357789999999999999999998 9999999999999999875

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.96  E-value=1.2e-27  Score=224.52  Aligned_cols=152  Identities=18%  Similarity=0.327  Sum_probs=133.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      .++++|||+|||.++|+++|+++|+.|| |..|.+ .+++|||||+|.+.++|++|++.|||..|.  |+.  +.+.++ 
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~~~~~~--g~~--i~v~~~-   92 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-DKYKGTAFVTLLNGEQAEAAINAFHQSRLR--ERE--LSVQLQ-   92 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTCEET--TEE--CEEEEC-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE-ecCCCEEEEEeCCHHHHHHHHHHcCCCeeC--CeE--EEEEec-
Confidence            3578999999999999999999999999 999988 468999999999999999999999998865  553  333211 


Q ss_pred             ccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCCCC
Q 046223          160 GLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSG  239 (408)
Q Consensus       160 ~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp~~  239 (408)
                                                                              .          ...+|||+|||.+
T Consensus        93 --------------------------------------------------------~----------~~~~l~v~nlp~~  106 (284)
T 3smz_A           93 --------------------------------------------------------P----------TDALLCVANLPPS  106 (284)
T ss_dssp             --------------------------------------------------------C----------CSCEEEEESCCTT
T ss_pred             --------------------------------------------------------C----------CCCEEEEcCCCCc
Confidence                                                                    0          1379999999999


Q ss_pred             CcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          240 VSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       240 ~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      +++++|+++|+.||.|..++     .++.++|||||+|.+.++|.+|++.|||..++|+.|.|.++.+..
T Consensus       107 ~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~  176 (284)
T 3smz_A          107 LTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ  176 (284)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGG
T ss_pred             CCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            99999999999999998882     467789999999999999999999999999999999999997654

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.96  E-value=1.3e-27  Score=224.51  Aligned_cols=164  Identities=15%  Similarity=0.189  Sum_probs=138.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ..++|||+|||.++|+++|+++|+.||.|..|++.+     .++|||||+|.+.++|.+|++.|+|..|.  |+.  +.+
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~--g~~--i~v  169 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLG--PRT--LYV  169 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEE--CEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeC--CcE--EEE
Confidence            457999999999999999999999999999998875     35899999999999999999999998875  663  444


Q ss_pred             cccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcC
Q 046223          156 PYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFN  235 (408)
Q Consensus       156 ~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~n  235 (408)
                      .++....                                                          .........+|||+|
T Consensus       170 ~~a~~~~----------------------------------------------------------~~~~~~~~~~l~v~n  191 (284)
T 3smz_A          170 HWTDAGQ----------------------------------------------------------LTPALLHSRCLCVDR  191 (284)
T ss_dssp             EECCGGG----------------------------------------------------------CCTTTTSCSEEEEEC
T ss_pred             EECCCCC----------------------------------------------------------CCcccCCccEEEEec
Confidence            4433110                                                          001112358999999


Q ss_pred             CCCCC-cHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCCC
Q 046223          236 LDSGV-SSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHS  306 (408)
Q Consensus       236 Lp~~~-t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~  306 (408)
                      ||..+ ++++|+++|+.||.|..++    ..+.++|+|||+|.+.++|.+|++.|||..++|+.|+|.|++++..+
T Consensus       192 lp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~  267 (284)
T 3smz_A          192 LPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG  267 (284)
T ss_dssp             CCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSCH
T ss_pred             CCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCcc
Confidence            99995 9999999999999998883    45677999999999999999999999999999999999999887653

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.95  E-value=1e-27  Score=222.50  Aligned_cols=155  Identities=23%  Similarity=0.326  Sum_probs=133.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      .....++|||+|||.++|+++|+++|+.||.|..|.+. +++|||||+|.+.++|++|++.|+|..|.  |+.  +++.+
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~-~~kg~afV~f~~~~~A~~A~~~l~g~~i~--g~~--l~v~~   92 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN-RDRGFGFIRLESRTLAEIAKAELDGTILK--SRP--LRIRF   92 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEET--TEE--CEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCcEEEEEECCHHHHHHHHHHcCCcEEC--Cce--eEeee
Confidence            34567899999999999999999999999999999987 47999999999999999999999998875  563  33322


Q ss_pred             cCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCC
Q 046223          158 SSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLD  237 (408)
Q Consensus       158 s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp  237 (408)
                      +.                                                                   ...+|||+||+
T Consensus        93 a~-------------------------------------------------------------------~~~~l~v~nl~  105 (261)
T 3sde_A           93 AT-------------------------------------------------------------------HGAALTVKNLS  105 (261)
T ss_dssp             CC-------------------------------------------------------------------CSSEEEEESCC
T ss_pred             cc-------------------------------------------------------------------cCCcccccCCC
Confidence            11                                                                   13789999999


Q ss_pred             CCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhC-CceeC---CeEEEEEEecCCC
Q 046223          238 SGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMN-GQEIY---GKHVVIEFSRPGG  304 (408)
Q Consensus       238 ~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~-g~~~~---g~~l~v~~a~~~~  304 (408)
                      ..+|+++|+++|+.||.|..|.    .++.++|||||+|.+.++|.+|++.|| |..+.   |+.|.|.++....
T Consensus       106 ~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          106 PVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             TTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             CCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            9999999999999999999883    467789999999999999999999995 55555   8999999997653

>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=99.95  E-value=1.3e-27  Score=225.23  Aligned_cols=156  Identities=15%  Similarity=0.208  Sum_probs=128.5

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec---CccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL---MEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~---~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ......++|||+|||.++|+++|+++|+.||.|..|++.+.   ++|||||+|.+.++|++|++ ++|..|.  |+.  +
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~--g~~--i  110 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVG--QNE--I  110 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEET--TEE--C
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeC--CcE--E
Confidence            45677899999999999999999999999999999999863   58999999999999999995 8997765  553  2


Q ss_pred             eccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEE
Q 046223          154 KNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVV  233 (408)
Q Consensus       154 ~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V  233 (408)
                      .+.++                                                                    ...+|||
T Consensus       111 ~v~~~--------------------------------------------------------------------~~~~l~v  122 (292)
T 2ghp_A          111 IVSHL--------------------------------------------------------------------TECTLWM  122 (292)
T ss_dssp             EEEEC--------------------------------------------------------------------CSCEEEE
T ss_pred             EEEEC--------------------------------------------------------------------CCCEEEE
Confidence            32110                                                                    1489999


Q ss_pred             cCCCCCCcHHHHHHHHhcCC-Cceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCC
Q 046223          234 FNLDSGVSSSTLKEIFQAFG-PVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGH  305 (408)
Q Consensus       234 ~nLp~~~t~~~L~~~F~~~G-~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  305 (408)
                      +|||..+++++|+++|+.|| .|..++    ..+.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.+...
T Consensus       123 ~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          123 TNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK  199 (292)
T ss_dssp             ECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC--
T ss_pred             ECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcc
Confidence            99999999999999999999 999883    2356799999999999999999999999999999999999986643

>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=99.95  E-value=1.8e-27  Score=224.29  Aligned_cols=164  Identities=15%  Similarity=0.245  Sum_probs=133.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccC-CeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFG-EVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G-~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ..++|||+|||.++|+++|+++|+.|| .|..|++.+    .++|||||+|.+.++|.+|++.|+|..|.  |+.  +.+
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~--l~v  191 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIE--GYT--LVT  191 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEET--TEE--CEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeC--CcE--EEE
Confidence            578999999999999999999999999 999999875    46999999999999999999999998876  563  444


Q ss_pred             cccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcC
Q 046223          156 PYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFN  235 (408)
Q Consensus       156 ~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~n  235 (408)
                      .++....              + .                     .      +            .........+|||+|
T Consensus       192 ~~a~~~~--------------~-~---------------------~------~------------~~~~~~~~~~l~v~n  217 (292)
T 2ghp_A          192 KVSNPLE--------------K-S---------------------K------R------------TDSATLEGREIMIRN  217 (292)
T ss_dssp             EECCCC---------------------------------------------------------------CCTTTEEEEEE
T ss_pred             EECCCCc--------------c-c---------------------c------c------------ccccCCCCceEEEEC
Confidence            4433110              0 0                     0      0            001123358999999


Q ss_pred             CCCC-CcHHHHHHHHhcCCCceeecc------CCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          236 LDSG-VSSSTLKEIFQAFGPVKELRE------TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       236 Lp~~-~t~~~L~~~F~~~G~v~~v~~------~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ||.. +++++|+++|+.||.|..|+.      ++.++|||||+|.+.++|.+|+ .|||..|+|+.|+|.|++++
T Consensus       218 lp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          218 LSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             ECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             CCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            9999 999999999999999999832      2778999999999999999999 99999999999999999875

>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=99.86  E-value=3.1e-21  Score=164.91  Aligned_cols=80  Identities=28%  Similarity=0.461  Sum_probs=73.5

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ....+|||+|||.++++++|+++|+.||.|..++     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|.++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3458999999999999999999999999999883     36788999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 046223          301 RPGGH  305 (408)
Q Consensus       301 ~~~~~  305 (408)
                      +++..
T Consensus       148 ~~~~~  152 (158)
T 2kn4_A          148 RYGRP  152 (158)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            87653

>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=99.83  E-value=1.6e-20  Score=159.02  Aligned_cols=138  Identities=21%  Similarity=0.258  Sum_probs=106.1

Q ss_pred             cCccEEEEEECCHHHHHHHHHHh-cCccccccccccceeccccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCC
Q 046223          117 LMEGIVTVHFYDLRHAEMAFKEI-REQHMQLQQQSYGLKNPYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAP  195 (408)
Q Consensus       117 ~~kG~afV~F~~~~~A~~Ai~~l-ng~~i~~~gr~l~~~~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  195 (408)
                      +-+|+++|+|.+.++|++|++.+ ||..+.  |   .+++.++.......          ...                 
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~--G---~~~~~~a~~~~~~~----------~~~-----------------   58 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVD--G---EWTYDDATKTFTVT----------EGS-----------------   58 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCC--C---EEEEETTTTEEEEE----------CSS-----------------
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCC--C---ceecccccCccccc----------ccc-----------------
Confidence            45999999999999999999999 998877  3   25555443221000          000                 


Q ss_pred             CCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCH
Q 046223          196 VLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDV  275 (408)
Q Consensus       196 ~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~  275 (408)
                                        ...............++|||+|||.++++++|+++|++||.|.+|+....++|||||+|.+.
T Consensus        59 ------------------~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~  120 (150)
T 2i2y_A           59 ------------------HHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDP  120 (150)
T ss_dssp             ------------------SSCCCCSCSSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSH
T ss_pred             ------------------ccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCH
Confidence                              00000001112334689999999999999999999999999999976555799999999999


Q ss_pred             HHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          276 RDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       276 ~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ++|.+|++.|||..|+|+.|+|+|++++.
T Consensus       121 ~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A          121 RDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            99999999999999999999999998764

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.82  E-value=2.1e-20  Score=150.93  Aligned_cols=73  Identities=12%  Similarity=0.187  Sum_probs=64.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      .+.+|||+|||+++||++|+++|++||.|.+|++.+   .++|||||+|.+.++|++|++.|+|..|.  ||.  |++.+
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~--g~~--i~V~~   79 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN--DRK--VFVGR   79 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEET--TEE--CEEEE
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEEC--CEE--EEEEE
Confidence            356899999999999999999999999999999886   35899999999999999999999998876  674  44444

>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=99.79  E-value=4.8e-19  Score=138.80  Aligned_cols=75  Identities=20%  Similarity=0.465  Sum_probs=70.7

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..+|||+|||.++|+++|+++|++||.|.+++     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|+||+|
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            57899999999999999999999999999883     4678899999999999999999999999999999999999976

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.76  E-value=2.3e-18  Score=133.76  Aligned_cols=80  Identities=18%  Similarity=0.133  Sum_probs=71.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ...++++|||+|||.++||++|+++|++||.|.+|++. +.||||||+|.+.++|.+|++.|+|..+.+.||  .+++.|
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~-~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr--~i~V~~   93 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM-PKKRQALVEFEDVLGACNAVNYAADNQIYIAGH--PAFVNY   93 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTE--EEEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCc--EEEEEe
Confidence            44578999999999999999999999999999999987 479999999999999999999999988666788  577777


Q ss_pred             cCc
Q 046223          158 SSG  160 (408)
Q Consensus       158 s~~  160 (408)
                      ++.
T Consensus        94 S~~   96 (100)
T 3r27_A           94 STS   96 (100)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            763

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.76  E-value=7e-19  Score=146.02  Aligned_cols=80  Identities=28%  Similarity=0.459  Sum_probs=73.0

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ..++|||+|||.++++++|+++|++||.|..|+     .++.++|||||+|.+.++|++|++.|||..|.|+.|+|+|++
T Consensus        46 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~  125 (135)
T 2lea_A           46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR  125 (135)
T ss_dssp             GCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            358999999999999999999999999999883     356789999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 046223          302 PGGHS  306 (408)
Q Consensus       302 ~~~~~  306 (408)
                      ++...
T Consensus       126 ~~~~~  130 (135)
T 2lea_A          126 YGRPP  130 (135)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.75  E-value=3.9e-18  Score=131.49  Aligned_cols=78  Identities=19%  Similarity=0.402  Sum_probs=70.0

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCC-Cceeec-----cCCCCccEEEEEECCHHHHHHHHHHhC-CceeCCeEEEEEEe
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFG-PVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMN-GQEIYGKHVVIEFS  300 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G-~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~-g~~~~g~~l~v~~a  300 (408)
                      +++|||+|||.++|+++|+++|++|| .|.+|+     .++.++|||||+|.+.++|++|++.++ +..++|++|+|+||
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            37899999999999999999999999 788873     467889999999999999999999874 56899999999999


Q ss_pred             cCCCC
Q 046223          301 RPGGH  305 (408)
Q Consensus       301 ~~~~~  305 (408)
                      +++..
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1e-17  Score=131.38  Aligned_cols=81  Identities=20%  Similarity=0.143  Sum_probs=68.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ...+.++|||+|||+++||++|+++|++||+|.+|++++ .||||||+|.+.++|++|++.|++....+.||  .|++.|
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~-~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr--~l~V~~   88 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ--PIYIQF   88 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTSCCEETTE--ECCBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHhccCCceECCE--EEEEEE
Confidence            345678999999999999999999999999999999985 59999999999999999999987643334477  566767


Q ss_pred             cCcc
Q 046223          158 SSGL  161 (408)
Q Consensus       158 s~~~  161 (408)
                      +..+
T Consensus        89 A~~~   92 (105)
T 1sjq_A           89 SNHK   92 (105)
T ss_dssp             CSSS
T ss_pred             cCCC
Confidence            6533

>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=99.74  E-value=9e-18  Score=135.39  Aligned_cols=79  Identities=24%  Similarity=0.412  Sum_probs=71.1

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ..+|||+|||+++|+++|+++|++||.|.+|+   ..+.++|||||+|.+.++|++|++.|||..|+|+.|+|.+++++.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~   84 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   84 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCcc
Confidence            47899999999999999999999999999883   344578999999999999999999999999999999999998765


Q ss_pred             CC
Q 046223          305 HS  306 (408)
Q Consensus       305 ~~  306 (408)
                      .+
T Consensus        85 ~~   86 (115)
T 4f25_A           85 ER   86 (115)
T ss_dssp             C-
T ss_pred             cc
Confidence            43

>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=99.73  E-value=7.8e-18  Score=131.86  Aligned_cols=76  Identities=21%  Similarity=0.365  Sum_probs=66.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ..+++|||+|||.++||++|+++|++||+|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  ||  .|+
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~--gr--~l~   92 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQ--SK--TIK   92 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TE--ECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEEC--CE--EEE
Confidence            3567899999999999999999999999999999875     45899999999999999999999998876  67  455


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      |.|++
T Consensus        93 V~~Ak   97 (99)
T 4fxv_A           93 VSYAR   97 (99)
T ss_dssp             EEECC
T ss_pred             EEEee
Confidence            55543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.73  E-value=1.4e-17  Score=133.02  Aligned_cols=78  Identities=18%  Similarity=0.304  Sum_probs=72.2

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+||++++++++|+++|++||.|.+|+     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|+++..
T Consensus         6 ~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~   85 (110)
T 3s8s_A            6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIK   85 (110)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECST
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            58999999999999999999999999999983     4578899999999999999999999999999999999999976


Q ss_pred             CCC
Q 046223          303 GGH  305 (408)
Q Consensus       303 ~~~  305 (408)
                      ...
T Consensus        86 ~~~   88 (110)
T 3s8s_A           86 GQQ   88 (110)
T ss_dssp             THH
T ss_pred             CcH
Confidence            543

>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=99.73  E-value=3.5e-17  Score=129.10  Aligned_cols=81  Identities=17%  Similarity=0.133  Sum_probs=70.1

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ....++++|||+|||+++||++|+++|++||.|..|.+.+ .||||||+|.+.++|++|++.|++..+.+.||  .+++.
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr--~l~V~   86 (104)
T 1wex_A           10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-FKRQALVEFENIDSAKECVTFAADVPVYIAGQ--QAFFN   86 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSS--BCEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCE--EEEEE
Confidence            3445789999999999999999999999999999998875 69999999999999999999998876555677  46666


Q ss_pred             ccCc
Q 046223          157 YSSG  160 (408)
Q Consensus       157 ~s~~  160 (408)
                      |+..
T Consensus        87 ~a~~   90 (104)
T 1wex_A           87 YSTS   90 (104)
T ss_dssp             ECSS
T ss_pred             EccC
Confidence            6653

>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=99.72  E-value=2.7e-17  Score=132.75  Aligned_cols=81  Identities=27%  Similarity=0.478  Sum_probs=73.6

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ...++|||+||+.++++++|+++|++||.|..|.    .++.++|||||+|.+.++|++|++.|||..|+|+.|+|++++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   84 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK   84 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3458999999999999999999999999999883    366788999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 046223          302 PGGHS  306 (408)
Q Consensus       302 ~~~~~  306 (408)
                      ++...
T Consensus        85 ~~~~~   89 (116)
T 2fy1_A           85 KPSFQ   89 (116)
T ss_dssp             CSSCS
T ss_pred             CCCCC
Confidence            76543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.72  E-value=1.9e-17  Score=128.57  Aligned_cols=79  Identities=27%  Similarity=0.374  Sum_probs=71.3

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCce--eCCeEEEEEEecC
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE--IYGKHVVIEFSRP  302 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~--~~g~~l~v~~a~~  302 (408)
                      ..++++|||+|||.++|+++|+++|++||.|.+++.. +.+|||||+|++.++|.+|++.|+|..  +.|+.|.|+|++.
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~-~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~   96 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM-PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS   96 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccc
Confidence            3456999999999999999999999999999999644 468999999999999999999999875  8899999999987


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      +.
T Consensus        97 k~   98 (100)
T 3r27_A           97 QK   98 (100)
T ss_dssp             SC
T ss_pred             cc
Confidence            54

>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=99.72  E-value=6.3e-17  Score=127.68  Aligned_cols=82  Identities=33%  Similarity=0.540  Sum_probs=73.4

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ....++|||+|||..+++++|+++|++||.|..|+   ....++|||||+|.+.++|++|++.|||..|.|+.|+|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   91 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECC
Confidence            34569999999999999999999999999999883   233468999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 046223          302 PGGHS  306 (408)
Q Consensus       302 ~~~~~  306 (408)
                      ++..+
T Consensus        92 ~~~~~   96 (103)
T 2cqi_A           92 TPSSQ   96 (103)
T ss_dssp             CTTCC
T ss_pred             CCccc
Confidence            86644

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.72  E-value=9.6e-17  Score=129.28  Aligned_cols=82  Identities=23%  Similarity=0.426  Sum_probs=74.6

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ....++|||+||+..+++++|+++|+.||.|..|+     .++..+|||||+|.+.++|++|++.|||..|+|+.|+|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34569999999999999999999999999999883     3667789999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 046223          300 SRPGGHS  306 (408)
Q Consensus       300 a~~~~~~  306 (408)
                      ++++...
T Consensus        92 a~~~~~~   98 (115)
T 2dgo_A           92 ATRKPPA   98 (115)
T ss_dssp             SSCCCCC
T ss_pred             ccCCCCC
Confidence            9877644

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.72  E-value=2.1e-17  Score=128.11  Aligned_cols=76  Identities=17%  Similarity=0.386  Sum_probs=68.1

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCC--ceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCc----eeCCeEE
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGP--VKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQ----EIYGKHV  295 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~--v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~----~~~g~~l  295 (408)
                      .-.+|||+||++++|+++|+++|++||.  |.+|     +.++.++|||||+|.+.++|++|++.|||.    .++||+|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            3489999999999999999999999995  4455     246788999999999999999999999997    5999999


Q ss_pred             EEEEecC
Q 046223          296 VIEFSRP  302 (408)
Q Consensus       296 ~v~~a~~  302 (408)
                      .|+||+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999974

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.8e-17  Score=130.00  Aligned_cols=79  Identities=22%  Similarity=0.235  Sum_probs=71.0

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhC--CceeCCeEEEEEEecCCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMN--GQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~--g~~~~g~~l~v~~a~~~~  304 (408)
                      ...+|||+|||+++|+++|+++|++||.|.+|+.. ..+|||||+|.+.++|++|++.|+  +..|.|+.|+|+|++++.
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~-~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~   93 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML-KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE   93 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCC
Confidence            45899999999999999999999999999999644 358999999999999999999986  479999999999998765


Q ss_pred             CC
Q 046223          305 HS  306 (408)
Q Consensus       305 ~~  306 (408)
                      .+
T Consensus        94 ~~   95 (105)
T 1sjq_A           94 LK   95 (105)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.72  E-value=8.5e-17  Score=128.31  Aligned_cols=81  Identities=28%  Similarity=0.497  Sum_probs=73.1

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec--cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~--~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ....++|||+|||.++++++|+++|++||.|..|+  ..+.++|||||+|.+.++|++|++.|||..|.|+.|+|+|+++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   98 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   98 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEccc
Confidence            34568999999999999999999999999998883  4455789999999999999999999999999999999999987


Q ss_pred             CCC
Q 046223          303 GGH  305 (408)
Q Consensus       303 ~~~  305 (408)
                      +..
T Consensus        99 ~~~  101 (109)
T 1x4a_A           99 GRG  101 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.72  E-value=2.9e-17  Score=125.31  Aligned_cols=77  Identities=22%  Similarity=0.440  Sum_probs=69.9

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      +..+|||+|||.++++++|+++|++||.|..++     .++.++|||||+|.+.++|++|++.|||..++|+.|+|++++
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            358999999999999999999999999999883     366789999999999999999999999999999999999997


Q ss_pred             CC
Q 046223          302 PG  303 (408)
Q Consensus       302 ~~  303 (408)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            64

>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=99.72  E-value=6e-17  Score=126.79  Aligned_cols=80  Identities=30%  Similarity=0.402  Sum_probs=73.5

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||.++++++|+++|++||.|..|+     .++.++|||||+|.+.++|++|++.|||..|.|+.|+|+++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            3468999999999999999999999999999984     26778899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 046223          301 RPGGH  305 (408)
Q Consensus       301 ~~~~~  305 (408)
                      +++..
T Consensus        86 ~~~~~   90 (99)
T 1whw_A           86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCcc
Confidence            88754

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.71  E-value=2e-17  Score=123.94  Aligned_cols=73  Identities=16%  Similarity=0.264  Sum_probs=68.7

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      +..|||+||++.+|+++|+++|.+||+|.+++.. .++|||||+|.+.++|.+|++.|||..++|+.|+|++|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~-~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPY-LNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEc-CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            4789999999999999999999999999999643 589999999999999999999999999999999999984

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=5.8e-17  Score=127.62  Aligned_cols=81  Identities=26%  Similarity=0.470  Sum_probs=73.7

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||..+++++|+++|++||.|..|+     .++..+|||||+|.+.++|++|++.|||..|+|+.|+|+++
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            3468999999999999999999999999999883     34668999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 046223          301 RPGGHS  306 (408)
Q Consensus       301 ~~~~~~  306 (408)
                      +++..+
T Consensus        90 ~~~~~~   95 (102)
T 2cqb_A           90 KPMRIK   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            877643

>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=99.71  E-value=4.3e-17  Score=123.22  Aligned_cols=76  Identities=24%  Similarity=0.360  Sum_probs=70.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      .+|||+|||.++++++|+++|++||.|..+.     .++.++|||||+|.+.++|++|++.|||..++|+.|+|++++++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            6899999999999999999999999999883     45777999999999999999999999999999999999999875


Q ss_pred             C
Q 046223          304 G  304 (408)
Q Consensus       304 ~  304 (408)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.71  E-value=5e-17  Score=126.54  Aligned_cols=77  Identities=21%  Similarity=0.375  Sum_probs=71.7

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      +++|||+||+.++++++|+++|++||.|..++     .++.++|||||+|.+.++|++|++.|||..++|+.|+|+++++
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            48999999999999999999999999999983     3467799999999999999999999999999999999999987


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      +.
T Consensus        82 ~~   83 (96)
T 2x1f_A           82 SD   83 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>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=99.71  E-value=7.5e-17  Score=129.91  Aligned_cols=81  Identities=23%  Similarity=0.425  Sum_probs=73.8

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ....++|||+||+.++++++|+++|++||.|..|+     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|+|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999883     3677889999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 046223          300 SRPGGH  305 (408)
Q Consensus       300 a~~~~~  305 (408)
                      ++++..
T Consensus       102 a~~~~~  107 (115)
T 2cpz_A          102 KRSKND  107 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCc
Confidence            987654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.71  E-value=2.9e-17  Score=131.11  Aligned_cols=75  Identities=19%  Similarity=0.274  Sum_probs=66.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .+.++|||+||++++||++|+++|++||.|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  ||.  |+
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~--gr~--i~   79 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVM--GNI--IH   79 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEE--CE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEEC--CeE--EE
Confidence            4678999999999999999999999999999999875     46899999999999999999999999876  774  44


Q ss_pred             cccc
Q 046223          155 NPYS  158 (408)
Q Consensus       155 ~~~s  158 (408)
                      +.++
T Consensus        80 V~~a   83 (110)
T 3s8s_A           80 AQLD   83 (110)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            4443

>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=99.71  E-value=6.1e-17  Score=126.92  Aligned_cols=81  Identities=22%  Similarity=0.217  Sum_probs=68.4

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ....++++|||+|||+++||++|+++|++||.|..|.+.+ .+|||||+|.+.++|++|++.|++..+.+.||  .+++.
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr--~l~V~   86 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-GKNQAFLELATEEAAITMVNYYSAVTPHLRNQ--PIYIQ   86 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCEETTE--ECEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCc--EEEEE
Confidence            3445789999999999999999999999999999998875 59999999999999999999887554445577  46666


Q ss_pred             ccCc
Q 046223          157 YSSG  160 (408)
Q Consensus       157 ~s~~  160 (408)
                      |+..
T Consensus        87 ~a~~   90 (101)
T 2cq1_A           87 YSNH   90 (101)
T ss_dssp             ECSC
T ss_pred             EcCc
Confidence            6653

>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=99.71  E-value=4.6e-17  Score=123.65  Aligned_cols=75  Identities=27%  Similarity=0.501  Sum_probs=69.9

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ..++|||+|||.++++++|+++|++||.|..+.     .++..+|||||+|.+.++|++|++.|||..++|+.|+|+|++
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            469999999999999999999999999999983     456679999999999999999999999999999999999985

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=4e-17  Score=128.80  Aligned_cols=82  Identities=28%  Similarity=0.441  Sum_probs=74.0

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ....++|||+|||.++++++|+++|++||.|..|.     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34569999999999999999999999999999883     3467899999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 046223          300 SRPGGHS  306 (408)
Q Consensus       300 a~~~~~~  306 (408)
                      ++.....
T Consensus        90 a~~~~~~   96 (103)
T 2dnm_A           90 ARYGRRD   96 (103)
T ss_dssp             CSSCCSC
T ss_pred             CCcCCCC
Confidence            9876543

>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=99.71  E-value=3.1e-17  Score=131.97  Aligned_cols=81  Identities=19%  Similarity=0.138  Sum_probs=68.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ...++++|||+|||+++||++|+++|++||.|.+|++.+ .+|||||+|.+.++|++|++.|++..+.+.||  .|++.|
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~-~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr--~l~V~~  103 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ--PIYIQF  103 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEG-GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTB--CCEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhccCCceECCe--EEEEEE
Confidence            445689999999999999999999999999999999885 59999999999999999999998654444577  466666


Q ss_pred             cCcc
Q 046223          158 SSGL  161 (408)
Q Consensus       158 s~~~  161 (408)
                      +..+
T Consensus       104 a~~k  107 (119)
T 2ad9_A          104 SNHK  107 (119)
T ss_dssp             CSSS
T ss_pred             ccCC
Confidence            6533

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=7.5e-17  Score=126.50  Aligned_cols=81  Identities=23%  Similarity=0.374  Sum_probs=73.4

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ....++|||+|||.++++++|+++|++||.|..++    .++..+|||||+|.+.++|++|++.|||..++|+.|+|+++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            34568999999999999999999999999999883    35677899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 046223          301 RPGGH  305 (408)
Q Consensus       301 ~~~~~  305 (408)
                      +++..
T Consensus        94 ~~~~~   98 (100)
T 2do4_A           94 NSGPS   98 (100)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            87653

>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=99.71  E-value=1.1e-17  Score=134.72  Aligned_cols=76  Identities=16%  Similarity=0.231  Sum_probs=66.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      .++++|||+|||.++|+++|+++|+.||.|..|.+.+  .++|||||+|.+.++|++|++.|||..|.  |+  .+++.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~--~l~v~~   81 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVS--NR--YLVVLY   81 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSS--SC--BCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEEC--Ce--EEEEEE
Confidence            3578999999999999999999999999999999875  45899999999999999999999998875  66  355544


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus        82 a~   83 (115)
T 3lqv_A           82 YN   83 (115)
T ss_dssp             CC
T ss_pred             ec
Confidence            43

>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=99.70  E-value=3.9e-17  Score=140.34  Aligned_cols=81  Identities=20%  Similarity=0.372  Sum_probs=72.5

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||..+++++|+++|++||.|..|.     .++.++|||||+|.+.++|++|++.|||..|.|+.|.|.|+
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  149 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  149 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            3468999999999999999999999999999883     46667999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 046223          301 RPGGHS  306 (408)
Q Consensus       301 ~~~~~~  306 (408)
                      +++..+
T Consensus       150 ~~~~~~  155 (165)
T 1rk8_A          150 FVKGPK  155 (165)
T ss_dssp             EECC--
T ss_pred             cCCCCC
Confidence            877654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.5e-17  Score=128.02  Aligned_cols=82  Identities=28%  Similarity=0.448  Sum_probs=74.3

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ....++|||+|||.++++++|+++|++||.|..|.     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            34569999999999999999999999999999883     3667899999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 046223          300 SRPGGHS  306 (408)
Q Consensus       300 a~~~~~~  306 (408)
                      ++++..+
T Consensus        92 a~~~~~~   98 (103)
T 2cq0_A           92 AKPSTNS   98 (103)
T ss_dssp             SSCCCCS
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.70  E-value=7.2e-17  Score=127.77  Aligned_cols=81  Identities=31%  Similarity=0.398  Sum_probs=74.0

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ....++|||+|||..+++++|+++|++||.|..|+     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            34569999999999999999999999999999883     3667889999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 046223          300 SRPGGH  305 (408)
Q Consensus       300 a~~~~~  305 (408)
                      ++++..
T Consensus        92 a~~~~~   97 (105)
T 1x5u_A           92 ASAHNK   97 (105)
T ss_dssp             TTTTSC
T ss_pred             CCCCCc
Confidence            987654

>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=99.70  E-value=1.6e-17  Score=130.16  Aligned_cols=78  Identities=9%  Similarity=0.006  Sum_probs=68.2

Q ss_pred             CCCCCEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           79 TGPTRTLVLSYVPG-DVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        79 ~~~~rtlfV~nLp~-~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ..++++|||+|||+ ++||++|+++|++||.|.+|++++ .+|||||+|.+.++|++|++.||+....+.||  .|+|.|
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr--~l~V~~   88 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN-KINEAFIEMATTEDAQAAVDYYTTTPALVFGK--PVRVHL   88 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS-SSSCEEEEESSHHHHHHHHHHHHHSCCEETTE--ECEEEE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHHcCCCceECCc--EEEEEE
Confidence            44789999999999 999999999999999999999884 68999999999999999999999876555688  456666


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus        89 a~   90 (102)
T 1x4d_A           89 SQ   90 (102)
T ss_dssp             EC
T ss_pred             CC
Confidence            54

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=8.3e-17  Score=126.01  Aligned_cols=80  Identities=26%  Similarity=0.416  Sum_probs=72.7

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||..+++++|+++|++||.|..|+     .++.++|||||+|.+.++|++|++ |||..|+|+.|+|+++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            4469999999999999999999999999999883     356789999999999999999999 9999999999999999


Q ss_pred             cCCCCC
Q 046223          301 RPGGHS  306 (408)
Q Consensus       301 ~~~~~~  306 (408)
                      +++..+
T Consensus        87 ~~~~~~   92 (99)
T 2dgs_A           87 EPRDSK   92 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            876543

>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=99.70  E-value=1.6e-16  Score=125.34  Aligned_cols=82  Identities=17%  Similarity=0.317  Sum_probs=73.1

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ....++|||+|||.++++++|+++|++||.|..|+   ....++|||||+|.+.++|++|++.|||..|+|+.|+|++++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   91 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   91 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            34569999999999999999999999999999883   223468999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 046223          302 PGGHS  306 (408)
Q Consensus       302 ~~~~~  306 (408)
                      ++...
T Consensus        92 ~~~~~   96 (103)
T 2cq3_A           92 ARVMT   96 (103)
T ss_dssp             SSCCC
T ss_pred             cCCCC
Confidence            76543

>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=99.70  E-value=1.3e-16  Score=125.79  Aligned_cols=80  Identities=30%  Similarity=0.559  Sum_probs=72.6

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGH  305 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  305 (408)
                      ...++|||+||+.++++++|+++|++||.|..|..   .++||||+|.+.++|++|++.|||..|.|+.|+|++++++..
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~---~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   85 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK---LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQ   85 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEE---CSSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE---ECCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCcc
Confidence            34589999999999999999999999999999864   377999999999999999999999999999999999988765


Q ss_pred             CCC
Q 046223          306 SKK  308 (408)
Q Consensus       306 ~~~  308 (408)
                      +..
T Consensus        86 ~~~   88 (103)
T 2dgu_A           86 KRK   88 (103)
T ss_dssp             CCC
T ss_pred             cch
Confidence            443

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

Probab=99.70  E-value=3.2e-17  Score=128.86  Aligned_cols=73  Identities=19%  Similarity=0.265  Sum_probs=65.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      ++|||+|||.++|+++|+++|++||+|..|.+.+.++|||||+|.+.++|++|++.|||..|.  |+.  +++.++.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~--l~V~~a~   73 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVIC--GSR--VRVELST   73 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSS--SCC--CEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeEC--CcE--EEEEEcc
Confidence            489999999999999999999999999999998767999999999999999999999998876  663  5555543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.70  E-value=4.8e-17  Score=129.69  Aligned_cols=77  Identities=21%  Similarity=0.142  Sum_probs=69.9

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCC-Cceeecc-CCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFG-PVKELRE-TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G-~v~~v~~-~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ..+|||+|||+++++++|+++|++|| .|..+.. ...++|||||+|.+.++|++|++.|||..|+|+.|+|++++...
T Consensus        28 ~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~p  106 (111)
T 2jvr_A           28 RYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPP  106 (111)
T ss_dssp             CEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC--
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            58999999999999999999999999 8988854 35689999999999999999999999999999999999987543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.70  E-value=4.7e-17  Score=121.97  Aligned_cols=73  Identities=11%  Similarity=0.098  Sum_probs=65.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      .+..|||+||++.+||++|+++|.+||+|.++++.. ++|||||+|.+.++|++|++.|||..+.  ||.  |++.++
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-~kGfaFVey~~~~eA~~Ai~~Ln~~~l~--gr~--I~V~~A   78 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-NQGIALCKYTTREEANKAQMALNNCVLA--NTT--IFAESP   78 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTEEET--TEE--EEEECC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-CCcEEEEEECCHHHHHHHHHHhcCCEEC--CcE--EEEEEC
Confidence            467899999999999999999999999999999874 8999999999999999999999998876  774  555443

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=7.3e-17  Score=125.28  Aligned_cols=79  Identities=25%  Similarity=0.398  Sum_probs=72.6

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ..++|||+||+.++++++|+++|++||.|..++     .++.++|||||+|.+.++|++|++.|||..+.|+.|+|++++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            358999999999999999999999999999883     356789999999999999999999999999999999999998


Q ss_pred             CCCC
Q 046223          302 PGGH  305 (408)
Q Consensus       302 ~~~~  305 (408)
                      ++..
T Consensus        84 ~~~~   87 (95)
T 2dnz_A           84 ERLD   87 (95)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            7654

>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=99.70  E-value=1.4e-16  Score=124.90  Aligned_cols=80  Identities=15%  Similarity=0.186  Sum_probs=71.1

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHh--CCceeCCeEEEEEEecCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEM--NGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l--~g~~~~g~~l~v~~a~~~  303 (408)
                      .+.++|||+|||+++++++|+++|++||.|.+|... ..+|||||+|.+.++|++|++.|  ++..+.|+.|+|.|++.+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   91 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML-KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   91 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-CCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcc
Confidence            346899999999999999999999999999998543 35999999999999999999987  477899999999999876


Q ss_pred             CCC
Q 046223          304 GHS  306 (408)
Q Consensus       304 ~~~  306 (408)
                      ..+
T Consensus        92 ~~~   94 (101)
T 2cq1_A           92 ELK   94 (101)
T ss_dssp             SCC
T ss_pred             cCc
Confidence            644

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=7.8e-17  Score=125.35  Aligned_cols=80  Identities=24%  Similarity=0.403  Sum_probs=72.6

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-c-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-R-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ..++|||+|||.++++++|+++|++||.|..+ +     .++.++|||||+|.+.++|++|++.|||..++|+.|+|+++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35899999999999999999999999999776 3     45667899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 046223          301 RPGGHS  306 (408)
Q Consensus       301 ~~~~~~  306 (408)
                      +++..+
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            877644

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=6.4e-17  Score=127.36  Aligned_cols=81  Identities=22%  Similarity=0.484  Sum_probs=73.5

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||.++++++|+++|++||.|..|+     .++..+|||||+|.+.++|++|++.|||..|+|+.|+|+++
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   89 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   89 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3468999999999999999999999999999883     35567899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 046223          301 RPGGHS  306 (408)
Q Consensus       301 ~~~~~~  306 (408)
                      +++...
T Consensus        90 ~~~~~~   95 (102)
T 1x5s_A           90 GKSSDN   95 (102)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            877643

>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=99.70  E-value=4.8e-17  Score=127.48  Aligned_cols=78  Identities=18%  Similarity=0.270  Sum_probs=70.0

Q ss_pred             CCCceEEEcCCCC-CCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCc--eeCCeEEEEEEecC
Q 046223          226 NNQGTIVVFNLDS-GVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ--EIYGKHVVIEFSRP  302 (408)
Q Consensus       226 ~~~~~l~V~nLp~-~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~--~~~g~~l~v~~a~~  302 (408)
                      .+.++|||+|||+ ++|++||+++|++||.|.+|+.. ..+|||||+|++.++|.+|++.||+.  .|.|+.|.|.||+.
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   91 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   91 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCC
Confidence            3568999999999 99999999999999999999644 46799999999999999999999864  59999999999986


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      ..
T Consensus        92 ~~   93 (102)
T 1x4d_A           92 YK   93 (102)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=7.2e-17  Score=127.35  Aligned_cols=82  Identities=26%  Similarity=0.404  Sum_probs=74.2

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ....++|||+|||.++++++|+++|++||.|..|+   .++..+|||||+|.+.++|++|++.|||..|.|+.|+|++++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ   91 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEec
Confidence            34568999999999999999999999999999883   256789999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 046223          302 PGGHS  306 (408)
Q Consensus       302 ~~~~~  306 (408)
                      ++..+
T Consensus        92 ~~~~~   96 (103)
T 2d9p_A           92 RKEER   96 (103)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87643

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.70  E-value=5.5e-17  Score=129.15  Aligned_cols=80  Identities=28%  Similarity=0.449  Sum_probs=72.1

Q ss_pred             CCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       224 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      .....++|||+||+.++++++|+++|++||.|..+...   +|||||+|.+.++|++|++.|||..++|+.|+|+|++++
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            34567999999999999999999999999999998654   899999999999999999999999999999999999876


Q ss_pred             CCC
Q 046223          304 GHS  306 (408)
Q Consensus       304 ~~~  306 (408)
                      ..+
T Consensus       104 ~~r  106 (108)
T 2jvo_A          104 AKR  106 (108)
T ss_dssp             C--
T ss_pred             CCC
Confidence            543

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

Probab=99.70  E-value=1.8e-16  Score=122.35  Aligned_cols=78  Identities=23%  Similarity=0.413  Sum_probs=71.2

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ....++|||+|||.++++++|+++|++||.|..+...   ++||||+|.+.++|++|++.|||..+.|+.|+|++++++.
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            3456999999999999999999999999999998643   6699999999999999999999999999999999998765


Q ss_pred             C
Q 046223          305 H  305 (408)
Q Consensus       305 ~  305 (408)
                      .
T Consensus        84 ~   84 (92)
T 2dgt_A           84 R   84 (92)
T ss_dssp             S
T ss_pred             C
Confidence            3

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=7.6e-17  Score=128.62  Aligned_cols=80  Identities=18%  Similarity=0.348  Sum_probs=72.3

Q ss_pred             CCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       224 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      .....++|||+||+.++++++|+++|++||.|..++   ..+.++|||||+|.+.++|++|++.|||..++|+.|+|+++
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  104 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA  104 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            345579999999999999999999999999998883   23457899999999999999999999999999999999999


Q ss_pred             cCC
Q 046223          301 RPG  303 (408)
Q Consensus       301 ~~~  303 (408)
                      +++
T Consensus       105 ~~~  107 (109)
T 2err_A          105 TAR  107 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            765

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=1e-16  Score=124.22  Aligned_cols=76  Identities=24%  Similarity=0.424  Sum_probs=70.0

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||.++++++|+++|++||.|..+.     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|+||
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            3468999999999999999999999999999883     34667899999999999999999999999999999999998


Q ss_pred             c
Q 046223          301 R  301 (408)
Q Consensus       301 ~  301 (408)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=1.4e-16  Score=126.53  Aligned_cols=81  Identities=25%  Similarity=0.496  Sum_probs=73.6

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeecc------CCCCccEEEEEECCHHHHHHHHHHh-CCceeCCeEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRE------TPLKKHQRFIEFYDVRDAAKALKEM-NGQEIYGKHVVI  297 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~------~~~~~g~afV~F~~~~~A~~A~~~l-~g~~~~g~~l~v  297 (408)
                      ....++|||+|||..+++++|+++|++||.|..|+.      ++..+|||||+|.+.++|++|++.| ||..|.|+.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            445699999999999999999999999999999842      5567999999999999999999999 999999999999


Q ss_pred             EEecCCCC
Q 046223          298 EFSRPGGH  305 (408)
Q Consensus       298 ~~a~~~~~  305 (408)
                      +|++++..
T Consensus        92 ~~a~~~~~   99 (107)
T 2cph_A           92 EWADSEVT   99 (107)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99987654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.1e-16  Score=124.15  Aligned_cols=77  Identities=23%  Similarity=0.448  Sum_probs=70.9

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||..+++++|+++|++||.|..+.     .++..+|||||+|.+.++|++|++.|||..++|+.|+|+|+
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP   92 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            4468999999999999999999999999999883     34677899999999999999999999999999999999998


Q ss_pred             cC
Q 046223          301 RP  302 (408)
Q Consensus       301 ~~  302 (408)
                      ++
T Consensus        93 ~~   94 (95)
T 2cqc_A           93 SS   94 (95)
T ss_dssp             SC
T ss_pred             CC
Confidence            75

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=2.7e-16  Score=126.39  Aligned_cols=80  Identities=23%  Similarity=0.284  Sum_probs=72.2

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ...++|||+||+.++++++|+++|++||.|..|+    .++.++|||||+|.+.++|++|++.|||..|+|+.|+|++++
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   92 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDE   92 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcc
Confidence            3468999999999999999999999999998882    346678999999999999999999999999999999999997


Q ss_pred             CCCC
Q 046223          302 PGGH  305 (408)
Q Consensus       302 ~~~~  305 (408)
                      ....
T Consensus        93 ~~~~   96 (114)
T 2do0_A           93 RALP   96 (114)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            6543

>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=99.69  E-value=9.5e-17  Score=122.67  Aligned_cols=77  Identities=26%  Similarity=0.399  Sum_probs=70.0

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeecc-----C-CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRE-----T-PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~-----~-~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      .++|||+|||.++++++|+++|++||.|..+..     + +..+|||||+|.+.++|++|++.|||..++|+.|+|+++.
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   83 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL   83 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECC
Confidence            489999999999999999999999999998832     1 2278999999999999999999999999999999999997


Q ss_pred             CCC
Q 046223          302 PGG  304 (408)
Q Consensus       302 ~~~  304 (408)
                      +..
T Consensus        84 ~~~   86 (88)
T 4a8x_A           84 APW   86 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.69  E-value=9.1e-17  Score=128.34  Aligned_cols=80  Identities=20%  Similarity=0.377  Sum_probs=73.2

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||..+++++|+++|++||.|..+.     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|+|+
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            3458999999999999999999999999999883     35677899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 046223          301 RPGGH  305 (408)
Q Consensus       301 ~~~~~  305 (408)
                      +++..
T Consensus       104 ~~~~~  108 (110)
T 1oo0_B          104 FVKGP  108 (110)
T ss_dssp             EESSC
T ss_pred             ccCCC
Confidence            87654

>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=99.69  E-value=1.5e-16  Score=127.23  Aligned_cols=81  Identities=23%  Similarity=0.395  Sum_probs=73.7

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhC------CceeCCeE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMN------GQEIYGKH  294 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~------g~~~~g~~  294 (408)
                      ...++|||+|||.++++++|+++|++||.|..|+     .++.++|||||+|.+.++|++|++.||      |..|+|+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            4468999999999999999999999999999883     346789999999999999999999999      99999999


Q ss_pred             EEEEEecCCCCC
Q 046223          295 VVIEFSRPGGHS  306 (408)
Q Consensus       295 l~v~~a~~~~~~  306 (408)
                      |+|++++++...
T Consensus        93 l~v~~a~~~~~~  104 (111)
T 1x4h_A           93 LKVDLAVTRDEA  104 (111)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEEECCCCccC
Confidence            999999877544

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.69  E-value=1.5e-16  Score=132.63  Aligned_cols=84  Identities=21%  Similarity=0.474  Sum_probs=75.5

Q ss_pred             CCCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q 046223          223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVI  297 (408)
Q Consensus       223 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  297 (408)
                      ......++|||+||+.++++++|+++|+.||.|.+|+     .++.++|||||+|.+.++|.+|++.|||..|+|+.|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            3445679999999999999999999999999999883     34667999999999999999999999999999999999


Q ss_pred             EEecCCCCC
Q 046223          298 EFSRPGGHS  306 (408)
Q Consensus       298 ~~a~~~~~~  306 (408)
                      ++++++..+
T Consensus       117 ~~a~~~~~~  125 (139)
T 1u6f_A          117 ALAASGHQR  125 (139)
T ss_dssp             EESSCCCCC
T ss_pred             EECCCCCCC
Confidence            999887644

>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=99.69  E-value=1.9e-16  Score=126.06  Aligned_cols=78  Identities=17%  Similarity=0.200  Sum_probs=70.7

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCC-----eEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG-----KHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g-----~~l~v~~a  300 (408)
                      ....+|||+|||+++++++|+++|++||.|..|.....  |||||+|.+.++|++|++.|||..|.|     +.|+|+++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a   90 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   90 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeC
Confidence            34689999999999999999999999999999864332  999999999999999999999999999     99999999


Q ss_pred             cCCCC
Q 046223          301 RPGGH  305 (408)
Q Consensus       301 ~~~~~  305 (408)
                      +++..
T Consensus        91 ~~~~~   95 (108)
T 1x4c_A           91 GPRSP   95 (108)
T ss_dssp             SCCSC
T ss_pred             CCCCC
Confidence            88653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.7e-16  Score=124.63  Aligned_cols=80  Identities=31%  Similarity=0.453  Sum_probs=72.4

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ...++|||+|||.++++++|+++|++||.|.-+. .++..+|||||+|.+.++|++|++.|||..|.|+.|+|++++++.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRG   92 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCC
Confidence            4469999999999999999999999999985543 466789999999999999999999999999999999999998765


Q ss_pred             C
Q 046223          305 H  305 (408)
Q Consensus       305 ~  305 (408)
                      .
T Consensus        93 ~   93 (101)
T 2fc9_A           93 S   93 (101)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.69  E-value=1e-16  Score=123.19  Aligned_cols=77  Identities=18%  Similarity=0.333  Sum_probs=71.3

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGH  305 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  305 (408)
                      ...++|||+|||.++++++|+++|++||.|..++..   +|||||+|.+.++|++|++.|||..++|+.|+|++++++..
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            346999999999999999999999999999998644   89999999999999999999999999999999999987654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.69  E-value=5.4e-17  Score=126.32  Aligned_cols=81  Identities=27%  Similarity=0.405  Sum_probs=74.6

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGH  305 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  305 (408)
                      ...++|||+|||..+++++|+++|+.||.|..+..++.++|||||+|.+.++|++|++.|||..++|+.|+|++++++..
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            34689999999999999999999999999988866778899999999999999999999999999999999999987654


Q ss_pred             C
Q 046223          306 S  306 (408)
Q Consensus       306 ~  306 (408)
                      +
T Consensus        94 ~   94 (96)
T 1fjc_A           94 T   94 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.7e-16  Score=127.39  Aligned_cols=82  Identities=22%  Similarity=0.358  Sum_probs=73.4

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCce--------ee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeC
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVK--------EL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY  291 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~--------~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~  291 (408)
                      ....++|||+|||.++++++|+++|++||.|.        .|     +.++.++|||||+|.+.++|++|++.|||..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            34569999999999999999999999999998        35     245678999999999999999999999999999


Q ss_pred             CeEEEEEEecCCCCC
Q 046223          292 GKHVVIEFSRPGGHS  306 (408)
Q Consensus       292 g~~l~v~~a~~~~~~  306 (408)
                      |+.|+|++++++...
T Consensus        92 g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           92 GSKLKVSLARKKPPM  106 (113)
T ss_dssp             TEECEEECSSCCCCS
T ss_pred             CCEEEEEECCCCCCC
Confidence            999999999876543

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

Probab=99.69  E-value=1.5e-16  Score=122.22  Aligned_cols=77  Identities=30%  Similarity=0.451  Sum_probs=70.7

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGH  305 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  305 (408)
                      ...++|||+|||.++++++|+++|++||.|..++..   ++||||+|.+.++|++|++.|||..++|+.|+|+++++...
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   83 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQK   83 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCC
Confidence            446899999999999999999999999999998643   66999999999999999999999999999999999987653

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=9.6e-17  Score=125.38  Aligned_cols=79  Identities=24%  Similarity=0.399  Sum_probs=71.5

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeecc--------CCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRE--------TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE  298 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~--------~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  298 (408)
                      +.++|||+|||.++++++|+++|++||.|..|+.        ++.++|||||+|.+.++|++|++.|||..|+|+.|+|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            3589999999999999999999999999998832        23678999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 046223          299 FSRPGGH  305 (408)
Q Consensus       299 ~a~~~~~  305 (408)
                      +++++..
T Consensus        84 ~a~~~~~   90 (98)
T 2cpf_A           84 ISERATK   90 (98)
T ss_dssp             CSSCSSC
T ss_pred             EccCCCC
Confidence            9987653

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.69  E-value=8.2e-17  Score=124.20  Aligned_cols=79  Identities=24%  Similarity=0.282  Sum_probs=72.6

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ..++|||+|||.++++++|+++|++||.|..++   .++.++|||||+|.+.++|++|++.|||..++|+.|+|+++++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   86 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNA   86 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            458999999999999999999999999999883   45678999999999999999999999999999999999999876


Q ss_pred             CC
Q 046223          304 GH  305 (408)
Q Consensus       304 ~~  305 (408)
                      ..
T Consensus        87 ~~   88 (92)
T 2dgv_A           87 SG   88 (92)
T ss_dssp             SS
T ss_pred             CC
Confidence            53

>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=99.69  E-value=1.6e-16  Score=125.73  Aligned_cols=81  Identities=21%  Similarity=0.351  Sum_probs=73.4

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCC---eEEEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG---KHVVIE  298 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g---~~l~v~  298 (408)
                      ...++|||+|||..+++++|+++|++||.|..|+    .++.++|||||+|.+.++|++|++.|||..+.|   +.|+|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            3469999999999999999999999999999883    356678999999999999999999999999998   999999


Q ss_pred             EecCCCCC
Q 046223          299 FSRPGGHS  306 (408)
Q Consensus       299 ~a~~~~~~  306 (408)
                      +++++..+
T Consensus        93 ~a~~~~~~  100 (105)
T 2dnh_A           93 FADTDKES  100 (105)
T ss_dssp             ESCSSCCC
T ss_pred             ECccCccc
Confidence            99887654

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

Probab=99.69  E-value=3.1e-16  Score=122.76  Aligned_cols=77  Identities=22%  Similarity=0.416  Sum_probs=70.9

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcC--CCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAF--GPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~--G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ...++|||+|||..+++++|+++|++|  |.|..+.   ..+|||||+|.+.++|++|++.|||..|.|+.|+|++++++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   89 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE---ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEE---EeCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            456899999999999999999999999  8998886   35889999999999999999999999999999999999876


Q ss_pred             CC
Q 046223          304 GH  305 (408)
Q Consensus       304 ~~  305 (408)
                      ..
T Consensus        90 ~~   91 (99)
T 2cpd_A           90 DK   91 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.69  E-value=3.3e-17  Score=130.34  Aligned_cols=79  Identities=16%  Similarity=0.186  Sum_probs=68.6

Q ss_pred             CCCCCCEEEEcCCCCC-CCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           78 STGPTRTLVLSYVPGD-VSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~-vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ...++++|||+|||++ +||++|+++|++||+|.+|++. +++|||||+|.+.++|++|++.|++..+.+.||  .|++.
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr--~l~V~   97 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGR--CVKVD   97 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSS--CCEEE
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhccCCceECCE--EEEEE
Confidence            3557899999999998 9999999999999999999987 479999999999999999999998766555678  46666


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        98 ~a~  100 (112)
T 1x4f_A           98 LSE  100 (112)
T ss_dssp             EEC
T ss_pred             ECc
Confidence            654

>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=99.69  E-value=1.4e-16  Score=125.62  Aligned_cols=80  Identities=19%  Similarity=0.229  Sum_probs=70.8

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCc--eeCCeEEEEEEecCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ--EIYGKHVVIEFSRPG  303 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~--~~~g~~l~v~~a~~~  303 (408)
                      .+.++|||+||++++++++|+++|++||.|..|... ..+|||||+|.+.++|.+|++.|++.  .+.|+.|+|+|++.+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~   91 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM-PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-CCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCc
Confidence            346899999999999999999999999999998643 35899999999999999999999764  599999999999876


Q ss_pred             CCC
Q 046223          304 GHS  306 (408)
Q Consensus       304 ~~~  306 (408)
                      ..+
T Consensus        92 ~~~   94 (104)
T 1wex_A           92 RIT   94 (104)
T ss_dssp             SCC
T ss_pred             ccc
Confidence            543

>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=99.68  E-value=1.8e-16  Score=123.65  Aligned_cols=77  Identities=22%  Similarity=0.395  Sum_probs=71.1

Q ss_pred             CCCCceEEEcCCCC-CCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          225 GNNQGTIVVFNLDS-GVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       225 ~~~~~~l~V~nLp~-~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ....++|||+||+. ++++++|+++|++||.|..++.   .+|||||+|.+.++|.+|++.|||..++|+.|+|++++++
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE---CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            34579999999998 9999999999999999999874   4899999999999999999999999999999999999765


Q ss_pred             C
Q 046223          304 G  304 (408)
Q Consensus       304 ~  304 (408)
                      .
T Consensus        96 ~   96 (97)
T 2xnq_A           96 A   96 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.68  E-value=2e-16  Score=123.17  Aligned_cols=78  Identities=21%  Similarity=0.331  Sum_probs=70.0

Q ss_pred             CCceEEEcCCCCCCcHHHHH----HHHhcCCCceeeccC--CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          227 NQGTIVVFNLDSGVSSSTLK----EIFQAFGPVKELRET--PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~----~~F~~~G~v~~v~~~--~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      +..+|||+|||.++++++|+    ++|++||.|.+|+..  ...+|||||+|.+.++|++|++.|||..++|+.|+|+++
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   87 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA   87 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            45899999999999999999    999999999998422  122899999999999999999999999999999999999


Q ss_pred             cCCC
Q 046223          301 RPGG  304 (408)
Q Consensus       301 ~~~~  304 (408)
                      ++..
T Consensus        88 ~~~~   91 (96)
T 2dgx_A           88 TGAS   91 (96)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7764

>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=99.68  E-value=9.3e-17  Score=127.84  Aligned_cols=81  Identities=27%  Similarity=0.408  Sum_probs=73.5

Q ss_pred             CCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q 046223          224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE  298 (408)
Q Consensus       224 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  298 (408)
                      .....++|||+||+..+++++|+++|++||.|..+.     .++.++|||||+|.+.++|++|++.|||..++|+.|+|+
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345569999999999999999999999999999883     456778999999999999999999999999999999999


Q ss_pred             EecCCC
Q 046223          299 FSRPGG  304 (408)
Q Consensus       299 ~a~~~~  304 (408)
                      +++++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            998764

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=1.7e-16  Score=123.90  Aligned_cols=78  Identities=17%  Similarity=0.237  Sum_probs=70.7

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ..++|||+|||.++++++|+++|++||.|..+     +.++.++|||||+|.+.++|++|++.|||..|+|+.|+|++++
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   93 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGS   93 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcC
Confidence            45899999999999999999999999998755     3466789999999999999999999999999999999999987


Q ss_pred             CCC
Q 046223          302 PGG  304 (408)
Q Consensus       302 ~~~  304 (408)
                      .+.
T Consensus        94 ~~~   96 (98)
T 2cqp_A           94 GPS   96 (98)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.68  E-value=1.1e-16  Score=130.42  Aligned_cols=84  Identities=26%  Similarity=0.340  Sum_probs=73.6

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccE-EEEEECCHHHHHHHHHHhCCceeCC--eEEEEEEecCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQ-RFIEFYDVRDAAKALKEMNGQEIYG--KHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~-afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~a~~~~  304 (408)
                      -..|||+||++.+|+++|+++|++||.|.+|+...+.+|| |||+|.+.++|++|++.|||..|.|  +.|+|+|+++..
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  107 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSS
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCc
Confidence            3678899999999999999999999999999644456788 9999999999999999999999988  999999999876


Q ss_pred             CCCCccc
Q 046223          305 HSKKFFY  311 (408)
Q Consensus       305 ~~~~~~~  311 (408)
                      ...+..+
T Consensus       108 l~v~~n~  114 (130)
T 3zzy_A          108 LNVKYNN  114 (130)
T ss_dssp             CCCCCCS
T ss_pred             eeEEecC
Confidence            5544433

>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=99.68  E-value=1.7e-16  Score=125.87  Aligned_cols=81  Identities=17%  Similarity=0.319  Sum_probs=73.1

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCcee---CCeEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEI---YGKHVV  296 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~---~g~~l~  296 (408)
                      ....++|||+|||.++++++|+++|++||.|..|+     .++.++|||||+|.+.++|++|++.|||..+   .|+.|+
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            34468999999999999999999999999999983     3467899999999999999999999999988   899999


Q ss_pred             EEEecCCCC
Q 046223          297 IEFSRPGGH  305 (408)
Q Consensus       297 v~~a~~~~~  305 (408)
                      |++++++..
T Consensus        90 v~~a~~~~~   98 (106)
T 2dgp_A           90 VKPADSESR   98 (106)
T ss_dssp             EEECCCCSC
T ss_pred             EEECCcccc
Confidence            999987654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=8.9e-17  Score=127.47  Aligned_cols=79  Identities=18%  Similarity=0.407  Sum_probs=72.4

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+||+..+++++|+++|++||.|..|.     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|+++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            3458999999999999999999999999999983     34677999999999999999999999999999999999999


Q ss_pred             cCCC
Q 046223          301 RPGG  304 (408)
Q Consensus       301 ~~~~  304 (408)
                      +++.
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            8764

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1.3e-16  Score=124.52  Aligned_cols=79  Identities=18%  Similarity=0.214  Sum_probs=71.0

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ...++|||+||+.++++++|+++|++||.|......+.++|||||+|.+.++|++|++.|||..|+|+.|+|++++++.
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEEEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            4468999999999999999999999999986223355789999999999999999999999999999999999998764

>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=99.68  E-value=1.5e-16  Score=122.98  Aligned_cols=78  Identities=21%  Similarity=0.320  Sum_probs=69.7

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCC-ceeeccCCCCccEEEEEECCHHHHHHHHHHhCC-ceeCCeEEEEEEecCCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGP-VKELRETPLKKHQRFIEFYDVRDAAKALKEMNG-QEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~-v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g-~~~~g~~l~v~~a~~~~  304 (408)
                      ..++|||+|||.++++++|+++|++||. |..+..  .++|||||+|.+.++|++|++.||| ..++|+.|+|++++++.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~   84 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL--LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   84 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE--EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE--cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcc
Confidence            4589999999999999999999999999 555433  4689999999999999999999999 99999999999998765


Q ss_pred             CC
Q 046223          305 HS  306 (408)
Q Consensus       305 ~~  306 (408)
                      .+
T Consensus        85 ~~   86 (93)
T 2cqh_A           85 LR   86 (93)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>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=99.68  E-value=1.1e-16  Score=128.60  Aligned_cols=80  Identities=21%  Similarity=0.229  Sum_probs=71.3

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCC--ceeCCeEEEEEEecCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNG--QEIYGKHVVIEFSRPG  303 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g--~~~~g~~l~v~~a~~~  303 (408)
                      .+.++|||+|||+++++++|+++|++||.|.+|+.. ..+|||||+|++.++|++|++.|++  ..|.|+.|+|.|++++
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~-~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k  107 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML-KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK  107 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEE-GGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCC
Confidence            346899999999999999999999999999998643 3589999999999999999999984  6899999999999876


Q ss_pred             CCC
Q 046223          304 GHS  306 (408)
Q Consensus       304 ~~~  306 (408)
                      ..+
T Consensus       108 ~~~  110 (119)
T 2ad9_A          108 ELK  110 (119)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>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=99.68  E-value=1.4e-16  Score=124.16  Aligned_cols=79  Identities=19%  Similarity=0.349  Sum_probs=71.7

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeC--CeEEEEEEecCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY--GKHVVIEFSRPG  303 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~--g~~l~v~~a~~~  303 (408)
                      ...++|||+|||.++++++|+++|++||.|..++.. ..+|||||+|.+.++|++|++.|||..+.  |+.|+|+|++++
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~   93 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEEC-SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe-CCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCC
Confidence            345899999999999999999999999999999644 34899999999999999999999999999  999999999876


Q ss_pred             CC
Q 046223          304 GH  305 (408)
Q Consensus       304 ~~  305 (408)
                      ..
T Consensus        94 ~~   95 (97)
T 1why_A           94 PS   95 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.68  E-value=2.1e-17  Score=127.06  Aligned_cols=76  Identities=16%  Similarity=0.165  Sum_probs=65.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCC--Cceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFG--PVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G--~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      .+|||+||++++++++|+++|++||  .|.+++     .++.++|||||+|.+.++|++|++.|||..++|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  888873     477889999999999999999999999999999999999998


Q ss_pred             CCC
Q 046223          302 PGG  304 (408)
Q Consensus       302 ~~~  304 (408)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            764

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.68  E-value=9.6e-17  Score=126.14  Aligned_cols=76  Identities=17%  Similarity=0.255  Sum_probs=70.8

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ..++|||+||+.++++++|+++|++||.|.+++.. .++|||||+|.+.++|.+|++.|||..++|+.|+|+|++++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            35899999999999999999999999999999644 67999999999999999999999999999999999999764

>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=99.68  E-value=1.5e-16  Score=123.53  Aligned_cols=76  Identities=24%  Similarity=0.375  Sum_probs=70.1

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..++|||+|||..+++++|+++|++||.|..|+    ..+.++|||||+|.+.++|++|++.|||..++|+.|+|++++.
T Consensus        15 ~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           15 ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             GGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcCC
Confidence            458999999999999999999999999999883    3466789999999999999999999999999999999999864

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.68  E-value=1.6e-16  Score=124.39  Aligned_cols=76  Identities=26%  Similarity=0.437  Sum_probs=69.9

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCcee--------e-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKE--------L-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG  292 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~--------v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g  292 (408)
                      ....+|||+||+.++++++|+++|++||.|..        +     +.++.++|||||+|.+.++|++|++.|||..++|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            34699999999999999999999999999988        6     2457789999999999999999999999999999


Q ss_pred             eEEEEEEec
Q 046223          293 KHVVIEFSR  301 (408)
Q Consensus       293 ~~l~v~~a~  301 (408)
                      +.|+|++|+
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999984

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.67  E-value=6.9e-17  Score=125.19  Aligned_cols=80  Identities=10%  Similarity=0.220  Sum_probs=66.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCC--eEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcc--ccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGE--VRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQH--MQLQQ  148 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~--V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~--i~~~g  148 (408)
                      ....-.||||+|||+++||++|+++|++||.  |.+|++.+     +++|||||+|.+.++|++|++.|||..  +.++|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            3445679999999999999999999999995  56788865     569999999999999999999999975  33457


Q ss_pred             cccceeccccC
Q 046223          149 QSYGLKNPYSS  159 (408)
Q Consensus       149 r~l~~~~~~s~  159 (408)
                      |  .+++.|++
T Consensus        85 r--~i~V~~Ak   93 (95)
T 2lkz_A           85 K--TIGVDFAK   93 (95)
T ss_dssp             E--EEEEEECC
T ss_pred             E--EEEEEEcc
Confidence            8  45665543

>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=99.67  E-value=2.5e-16  Score=125.63  Aligned_cols=78  Identities=24%  Similarity=0.401  Sum_probs=71.6

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGH  305 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  305 (408)
                      ..++|||+||+..+++++|+++|++||.|..|+.. ..+|||||+|.+.++|++|++.|||..|+|+.|+|.|++++..
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF-PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            35899999999999999999999999999999644 3389999999999999999999999999999999999987654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.67  E-value=1.2e-16  Score=130.71  Aligned_cols=80  Identities=16%  Similarity=0.290  Sum_probs=71.8

Q ss_pred             CCCceEEEcCCCCCCcHHHHH----HHHhcCCCceeec--cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLK----EIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~----~~F~~~G~v~~v~--~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ...++|||+||++.+++++|+    ++|++||.|.+|.  .++.++|||||+|.+.++|.+|++.|||..|.|+.|+|.|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~  106 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF  106 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEE
Confidence            346899999999999999876    7999999998883  3567899999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 046223          300 SRPGGH  305 (408)
Q Consensus       300 a~~~~~  305 (408)
                      ++.+..
T Consensus       107 a~~~~~  112 (127)
T 2a3j_A          107 SETPQS  112 (127)
T ss_dssp             CCCCCH
T ss_pred             ccCcch
Confidence            987653

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.8e-16  Score=123.62  Aligned_cols=82  Identities=28%  Similarity=0.407  Sum_probs=73.2

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec--cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~--~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ....++|||+||+.++++++|+++|+.|+.|..+.  .++.++|||||+|.+.++|++|++.|||..|.|+.|+|+|+++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   91 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKP   91 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            34569999999999999999999999998776663  4677899999999999999999999999999999999999988


Q ss_pred             CCCC
Q 046223          303 GGHS  306 (408)
Q Consensus       303 ~~~~  306 (408)
                      +...
T Consensus        92 ~~~~   95 (102)
T 2fc8_A           92 KGEG   95 (102)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7643

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

Probab=99.67  E-value=1.3e-16  Score=125.45  Aligned_cols=78  Identities=28%  Similarity=0.440  Sum_probs=71.0

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHS  306 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~  306 (408)
                      ++|||+|||.++++++|+++|++||.|..+.....++|||||+|.+.++|++|++.|||..++|+.|+|++++++..+
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   78 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRR   78 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCc
Confidence            479999999999999999999999999998543337999999999999999999999999999999999999887643

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.67  E-value=1.3e-16  Score=129.05  Aligned_cols=77  Identities=25%  Similarity=0.450  Sum_probs=70.4

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ....++|||+||+.++++++|+++|++||.|..++     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|+|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            44568999999999999999999999999999883     3567799999999999999999999999999999999999


Q ss_pred             ec
Q 046223          300 SR  301 (408)
Q Consensus       300 a~  301 (408)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            85

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.67  E-value=2e-16  Score=128.82  Aligned_cols=79  Identities=13%  Similarity=0.068  Sum_probs=70.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccE-EEEEECCHHHHHHHHHHhcCccccccccccceeccccCc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGI-VTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSG  160 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~-afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~~  160 (408)
                      -..|||+||++.+||++|+++|++||+|.+|++..+.+|| |||+|.+.++|++|++.|||..|.+.++  .|++.|++.
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~--~LrI~~ak~  105 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACC--TLRIDFSKL  105 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEE--EEEEEECSC
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCc--EEEEEecCC
Confidence            3467899999999999999999999999999998878898 9999999999999999999999985435  578888875


Q ss_pred             cc
Q 046223          161 LM  162 (408)
Q Consensus       161 ~s  162 (408)
                      ..
T Consensus       106 ~~  107 (130)
T 3zzy_A          106 TS  107 (130)
T ss_dssp             SS
T ss_pred             Cc
Confidence            54

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=5.2e-16  Score=125.16  Aligned_cols=79  Identities=23%  Similarity=0.328  Sum_probs=71.8

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ....++|||+|||.++++++|+++|++||.|..|+     .++.++|||||+|.+.++|++|++.|++ .|.|+.|+|++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            44569999999999999999999999999999883     3567899999999999999999999998 89999999999


Q ss_pred             ecCCC
Q 046223          300 SRPGG  304 (408)
Q Consensus       300 a~~~~  304 (408)
                      ++...
T Consensus        93 a~~~~   97 (116)
T 2cqd_A           93 AYLGA   97 (116)
T ss_dssp             STTTC
T ss_pred             cccCC
Confidence            97654

>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=99.67  E-value=3e-16  Score=123.96  Aligned_cols=79  Identities=20%  Similarity=0.299  Sum_probs=71.3

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeecc-----C-CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRE-----T-PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~-----~-~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ...++|||+|||.++++++|+++|+.|| |..|+.     + +.++|||||+|.+.++|++|+ .|||..|+|+.|+|++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            3458999999999999999999999999 988832     2 678999999999999999999 8999999999999999


Q ss_pred             ecCCCCC
Q 046223          300 SRPGGHS  306 (408)
Q Consensus       300 a~~~~~~  306 (408)
                      ++++..+
T Consensus        91 a~~~~~~   97 (104)
T 1wi8_A           91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9887644

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.3e-16  Score=127.20  Aligned_cols=81  Identities=15%  Similarity=0.202  Sum_probs=69.6

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           75 PPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        75 p~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      +.......++|||+|||.++|+++|+++|++||+|..|++.+   .++|||||+|.+.++|++|++.|||..|.  |+  
T Consensus        22 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~--g~--   97 (109)
T 2err_A           22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVE--GR--   97 (109)
T ss_dssp             CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEET--TE--
T ss_pred             CccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEEC--CE--
Confidence            345566789999999999999999999999999999999875   35899999999999999999999998876  66  


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                      .+++.++.
T Consensus        98 ~l~V~~a~  105 (109)
T 2err_A           98 KIEVNNAT  105 (109)
T ss_dssp             ECEEEECC
T ss_pred             EEEEEECC
Confidence            35555544

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=1.4e-16  Score=125.79  Aligned_cols=81  Identities=22%  Similarity=0.320  Sum_probs=73.6

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhc-CCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCce-eCCeEEEEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQA-FGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQE-IYGKHVVIEF  299 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~-~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~-~~g~~l~v~~  299 (408)
                      ....+|||+||+.++++++|+++|+. ||.|..|+    .++.++|||||+|.+.++|.+|++.|||.. ++|+.|+|++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~   86 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSV   86 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEE
Confidence            44689999999999999999999999 99999883    267789999999999999999999999999 9999999999


Q ss_pred             ecCCCCC
Q 046223          300 SRPGGHS  306 (408)
Q Consensus       300 a~~~~~~  306 (408)
                      ++++..+
T Consensus        87 a~~~~~~   93 (104)
T 2dhg_A           87 AIPKASR   93 (104)
T ss_dssp             CCCCCSC
T ss_pred             ccCCCcC
Confidence            9876644

>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=99.67  E-value=5e-16  Score=122.47  Aligned_cols=79  Identities=20%  Similarity=0.357  Sum_probs=69.2

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ......++|||+|||.++|+++|+++|++||.|..|++.+   .++|||||+|.+.++|++|++.|||..|.  |+  .|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~--~l   85 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKIL--GK--EV   85 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEET--TE--EE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcC--CC--eE
Confidence            4556789999999999999999999999999999999886   35899999999999999999999998876  66  45


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.|+.
T Consensus        86 ~V~~a~   91 (103)
T 2cqi_A           86 KVNWAT   91 (103)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            565554

>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=99.67  E-value=1.4e-16  Score=130.45  Aligned_cols=81  Identities=17%  Similarity=0.394  Sum_probs=73.8

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+||+..+|+++|+++|++||.|..|.     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|+|+
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            3468999999999999999999999999999883     36677999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 046223          301 RPGGHS  306 (408)
Q Consensus       301 ~~~~~~  306 (408)
                      +++...
T Consensus       100 ~~~~~~  105 (126)
T 3ex7_B          100 FVRGPP  105 (126)
T ss_dssp             EESSSC
T ss_pred             cCCCCC
Confidence            876544

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.67  E-value=4.9e-17  Score=127.64  Aligned_cols=76  Identities=22%  Similarity=0.242  Sum_probs=70.8

Q ss_pred             CceEEEcCCCC------CCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCC-eEE
Q 046223          228 QGTIVVFNLDS------GVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG-KHV  295 (408)
Q Consensus       228 ~~~l~V~nLp~------~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g-~~l  295 (408)
                      .++|||+|||.      ++++++|+++|++||.|.+|+     .++.++|||||+|.+.++|++|++.|||..|.| +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            58999999999      999999999999999999983     447889999999999999999999999999999 999


Q ss_pred             EEEEecCC
Q 046223          296 VIEFSRPG  303 (408)
Q Consensus       296 ~v~~a~~~  303 (408)
                      +|.++++.
T Consensus        86 ~V~~a~~~   93 (100)
T 3ns6_A           86 FLYTMKDV   93 (100)
T ss_dssp             EEEESHHH
T ss_pred             EEEECchh
Confidence            99999764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.67  E-value=3.4e-17  Score=126.20  Aligned_cols=74  Identities=23%  Similarity=0.360  Sum_probs=63.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccC-CeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhc-Ccccccccccccee
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFG-EVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIR-EQHMQLQQQSYGLK  154 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G-~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~ln-g~~i~~~gr~l~~~  154 (408)
                      +++|||+|||.++||++|+++|++|| +|.+|++++     .++|||||+|.+.++|++|++.++ +..|.  ||  .++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~--gr--~i~   76 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNIL--GQ--KVS   76 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEET--TE--EEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEEC--CE--EEE
Confidence            57999999999999999999999999 899998875     469999999999999999999875 43443  67  466


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.|+.
T Consensus        77 V~~a~   81 (91)
T 2lxi_A           77 MHYSD   81 (91)
T ss_dssp             EECCC
T ss_pred             EEEcC
Confidence            66765

>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=99.67  E-value=3.1e-16  Score=125.25  Aligned_cols=77  Identities=22%  Similarity=0.355  Sum_probs=71.1

Q ss_pred             CCCceEEEcCCCCC-CcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          226 NNQGTIVVFNLDSG-VSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       226 ~~~~~l~V~nLp~~-~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ...++|||+||+.. +++++|+++|++||.|..|..   .+|||||+|.+.++|++|++.|||..|+|+.|+|++++...
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            34589999999999 999999999999999999875   78999999999999999999999999999999999998654


Q ss_pred             C
Q 046223          305 H  305 (408)
Q Consensus       305 ~  305 (408)
                      .
T Consensus       102 ~  102 (110)
T 1wf1_A          102 P  102 (110)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.67  E-value=5.1e-16  Score=123.77  Aligned_cols=79  Identities=16%  Similarity=0.226  Sum_probs=68.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ....+.++|||+|||.++|+++|+++|++||.|..|++..  +++|||||+|.+.++|++|++.||+..|.  ++  .|+
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~--~l~   92 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYD--GY--RLR   92 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEET--TE--ECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEEC--Ce--EEE
Confidence            4455789999999999999999999999999999999875  45899999999999999999999998876  66  455


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.|+.
T Consensus        93 V~~a~   97 (109)
T 1x4a_A           93 VEFPR   97 (109)
T ss_dssp             EECCC
T ss_pred             EEEcc
Confidence            55554

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.67  E-value=3e-16  Score=122.85  Aligned_cols=75  Identities=16%  Similarity=0.236  Sum_probs=64.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEE--------EEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRG--------VQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~--------v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ..+..+|||+|||.++|+++|+++|++||.|..        |++..     +++|||||+|.+.++|++|++.|||..|.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            345789999999999999999999999999999        88875     34899999999999999999999998876


Q ss_pred             ccccccceeccc
Q 046223          146 LQQQSYGLKNPY  157 (408)
Q Consensus       146 ~~gr~l~~~~~~  157 (408)
                        |+.  +++.+
T Consensus        90 --g~~--l~V~~   97 (99)
T 2la6_A           90 --GNP--IKVSF   97 (99)
T ss_dssp             --SSB--CEEEE
T ss_pred             --CcE--EEEEe
Confidence              663  44433

>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=99.67  E-value=3.4e-16  Score=124.27  Aligned_cols=76  Identities=30%  Similarity=0.473  Sum_probs=70.4

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ...++|||+||+..+++++|+++|++||.|..|.    .++.++|||||+|.+.++|++|++.|||..|.|+.|+|+++.
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            4569999999999999999999999999998882    366779999999999999999999999999999999999985

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.67  E-value=1.3e-16  Score=135.50  Aligned_cols=76  Identities=5%  Similarity=0.061  Sum_probs=64.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccC--CeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFG--EVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G--~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ...++|||+|||+++||++|+++|+.||  .|.+|+++.     +++|||||+|.+.++|++||+.|||..|.  ||.  
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~--Gr~--  128 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLN--GEK--  128 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEET--TEE--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC--CeE--
Confidence            4578999999999999999999999999  999999875     45899999999999999999999998876  774  


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |+|.++.
T Consensus       129 l~V~~a~  135 (156)
T 3n9u_C          129 VDVRPAT  135 (156)
T ss_dssp             CEEEECC
T ss_pred             eEEEEcC
Confidence            5554544

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.67  E-value=2.3e-16  Score=125.79  Aligned_cols=82  Identities=23%  Similarity=0.284  Sum_probs=70.3

Q ss_pred             CCCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q 046223          224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE  298 (408)
Q Consensus       224 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  298 (408)
                      .....++|||+||+.++++++|+++|+.||.|..|+     .++.++|||||+|.+.++|++|++.+ +..++|+.|+|+
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            345579999999999999999999999999999983     35778999999999999999999976 599999999999


Q ss_pred             EecCCCCC
Q 046223          299 FSRPGGHS  306 (408)
Q Consensus       299 ~a~~~~~~  306 (408)
                      ++.++..+
T Consensus       100 ~a~~~~~~  107 (109)
T 2rs2_A          100 VAFPRRAQ  107 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99877644

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.66  E-value=5.1e-16  Score=122.41  Aligned_cols=78  Identities=19%  Similarity=0.284  Sum_probs=70.6

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||.++++++|+++|++|| |..|+     .++.++|||||+|.+.++|++|+ .|||..|.|+.|+|+++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEe
Confidence            3469999999999999999999999997 88883     35678999999999999999999 89999999999999999


Q ss_pred             cCCCC
Q 046223          301 RPGGH  305 (408)
Q Consensus       301 ~~~~~  305 (408)
                      +++..
T Consensus        91 ~~~~~   95 (103)
T 2dng_A           91 EGRKQ   95 (103)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=1.9e-16  Score=123.92  Aligned_cols=78  Identities=19%  Similarity=0.367  Sum_probs=71.7

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCce-eec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeE----EE
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVK-ELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH----VV  296 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~-~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~----l~  296 (408)
                      ..++|||+|||.++++++|+++|++||.|. .++     .++.++|||||+|.+.++|++|++.|||..+.|+.    |+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~   87 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFK   87 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEE
Confidence            459999999999999999999999999998 772     36678899999999999999999999999999999    99


Q ss_pred             EEEecCCC
Q 046223          297 IEFSRPGG  304 (408)
Q Consensus       297 v~~a~~~~  304 (408)
                      |+|+++..
T Consensus        88 v~~a~~~~   95 (99)
T 2div_A           88 LNYATYSG   95 (99)
T ss_dssp             EEETTCCS
T ss_pred             EeecCCCC
Confidence            99998764

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.66  E-value=5.9e-16  Score=125.19  Aligned_cols=73  Identities=16%  Similarity=0.178  Sum_probs=65.0

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....+.++|||+|||.++|+++|+++|++||+|..|++.+     +++|||||+|.+.++|++|++.|||..|.  |+.|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l  112 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVG--TKRL  112 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEET--TEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEEC--CEEE
Confidence            3455789999999999999999999999999999999875     44899999999999999999999998876  6643

>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=99.66  E-value=2.3e-16  Score=119.76  Aligned_cols=75  Identities=20%  Similarity=0.374  Sum_probs=69.2

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHh-CCceeCCeEEEEEEec
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEM-NGQEIYGKHVVIEFSR  301 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l-~g~~~~g~~l~v~~a~  301 (408)
                      ...++|||+|||..+++++|+++|++||.|..++.. .++|||||+|.+.++|++|++.| +|..++|+.|+|+|++
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~-~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV-QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEE-CCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            446899999999999999999999999999998643 46899999999999999999999 9999999999999985

>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=99.66  E-value=2.8e-16  Score=120.30  Aligned_cols=76  Identities=22%  Similarity=0.332  Sum_probs=70.2

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+|||.++++++|+++|++||.|..++     .++.++|||||+|.+.++|++|+ .|||..+.|+.|+|.++++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            38999999999999999999999999999882     36778999999999999999999 8999999999999999976


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      ..
T Consensus        85 ~~   86 (89)
T 3ucg_A           85 NR   86 (89)
T ss_dssp             TS
T ss_pred             CC
Confidence            53

>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=99.66  E-value=2.9e-16  Score=119.16  Aligned_cols=75  Identities=16%  Similarity=0.301  Sum_probs=65.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ..+.++|||+|||.++++++|+++|++||.|..|.+.+     +++|||||+|.+.++|++|++.|||..|.  |+.  +
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~--l   79 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF--GRT--I   79 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEET--TEE--C
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEEC--CcE--E
Confidence            34689999999999999999999999999999999865     35999999999999999999999998876  663  4


Q ss_pred             eccc
Q 046223          154 KNPY  157 (408)
Q Consensus       154 ~~~~  157 (408)
                      ++.|
T Consensus        80 ~v~~   83 (85)
T 3mdf_A           80 RVNL   83 (85)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            4433

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.66  E-value=1.7e-16  Score=130.87  Aligned_cols=80  Identities=21%  Similarity=0.403  Sum_probs=72.0

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCcee--e-----ccCCCCccEEEEEECCHHHHHHHHHHhCCc----eeCCe
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKE--L-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQ----EIYGK  293 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~--v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~----~~~g~  293 (408)
                      ....++|||+||++++|+++|+++|++||.|..  |     +.++.++|||||+|.+. +|.+|++.|||.    .++|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            345689999999999999999999999999955  4     24778899999999999 999999999999    99999


Q ss_pred             EEEEEEecCCCC
Q 046223          294 HVVIEFSRPGGH  305 (408)
Q Consensus       294 ~l~v~~a~~~~~  305 (408)
                      .|+|+++++...
T Consensus        99 ~l~V~~a~~~~~  110 (131)
T 2m2b_A           99 TINVEFAKGSKR  110 (131)
T ss_dssp             CCCCEECCCSCC
T ss_pred             EEEEEECCCCCC
Confidence            999999987653

>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=99.66  E-value=1.2e-16  Score=131.28  Aligned_cols=80  Identities=25%  Similarity=0.474  Sum_probs=73.1

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ....++|||+|||.++++++|+++|++||.|..|+     .++..+|||||+|.+.++|++|++.|||..|+|+.|+|+|
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999883     3567899999999999999999999999999999999999


Q ss_pred             ecCCC
Q 046223          300 SRPGG  304 (408)
Q Consensus       300 a~~~~  304 (408)
                      ++++.
T Consensus       123 a~~~~  127 (129)
T 2kxn_B          123 SITKR  127 (129)
T ss_dssp             CSSSS
T ss_pred             ecCCC
Confidence            98764

>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=99.66  E-value=5.2e-16  Score=120.95  Aligned_cols=79  Identities=16%  Similarity=0.304  Sum_probs=68.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ...++++|||+|||.++|+++|+++|++||.|..|.+.+ .+|||||+|.+.++|++|++.|||..|.+.++  .|++.|
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~-~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~--~l~V~~   89 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-GDSFAYIQYESLDAAQAACAKMRGFPLGGPDR--RLRVDF   89 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSC--BCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeC-CCCEEEEEECCHHHHHHHHHHHCCCEeCCCCc--EEEEEE
Confidence            344678999999999999999999999999999999885 48999999999999999999999988764356  355555


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus        90 a~   91 (97)
T 1why_A           90 AK   91 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=3.5e-16  Score=121.15  Aligned_cols=77  Identities=17%  Similarity=0.260  Sum_probs=66.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....+.++|||+|||.++++++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|||..|.  |+. 
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~-   87 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLF--GRV-   87 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEET--TEE-
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeC--CcE-
Confidence            3445678999999999999999999999999999999875     35899999999999999999999998876  663 


Q ss_pred             ceeccc
Q 046223          152 GLKNPY  157 (408)
Q Consensus       152 ~~~~~~  157 (408)
                       +++.|
T Consensus        88 -l~v~~   92 (94)
T 2e5h_A           88 -IKASI   92 (94)
T ss_dssp             -EEEEE
T ss_pred             -EEEEe
Confidence             45444

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

Probab=99.66  E-value=1.2e-16  Score=124.29  Aligned_cols=78  Identities=22%  Similarity=0.374  Sum_probs=70.9

Q ss_pred             CCCceEEEcCCCC-CCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          226 NNQGTIVVFNLDS-GVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       226 ~~~~~l~V~nLp~-~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ...++|||+|||. .+++++|+++|++||.|..+..   .+|||||+|.+.++|++|++.|||..+.|+.|+|++++++.
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE---ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            3469999999998 9999999999999999999874   48999999999999999999999999999999999998765


Q ss_pred             CC
Q 046223          305 HS  306 (408)
Q Consensus       305 ~~  306 (408)
                      ..
T Consensus        85 ~~   86 (96)
T 2kvi_A           85 RP   86 (96)
T ss_dssp             C-
T ss_pred             CC
Confidence            43

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=4.7e-16  Score=120.65  Aligned_cols=76  Identities=14%  Similarity=0.260  Sum_probs=66.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .++++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|||..|.  |+.  |+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~--l~   78 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELA--GRP--MR   78 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSS--SSC--CE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeC--CcE--EE
Confidence            4678999999999999999999999999999999876     35899999999999999999999998876  663  55


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.++.
T Consensus        79 V~~a~   83 (95)
T 2dnz_A           79 VGHVT   83 (95)
T ss_dssp             EEESS
T ss_pred             EEEcc
Confidence            55544

>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=99.66  E-value=4.5e-16  Score=121.83  Aligned_cols=78  Identities=19%  Similarity=0.310  Sum_probs=71.9

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ...++|||+|||..+++++|+++|++||.|..++.. ..+|||||+|.+.++|++|++.|||..|.|+.|+|++++++.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            446899999999999999999999999999998644 568999999999999999999999999999999999998754

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.66  E-value=3.2e-16  Score=124.05  Aligned_cols=78  Identities=21%  Similarity=0.235  Sum_probs=70.9

Q ss_pred             CCCceEEEcCCCCCC------cHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCe-EE
Q 046223          226 NNQGTIVVFNLDSGV------SSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK-HV  295 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~------t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~-~l  295 (408)
                      ...++|||+|||..+      ++++|+++|++||.|..|.   .++.++|||||+|.+.++|.+|++.|||..|+|+ .|
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            346899999999999      8899999999999999883   4567899999999999999999999999999998 99


Q ss_pred             EEEEecCC
Q 046223          296 VIEFSRPG  303 (408)
Q Consensus       296 ~v~~a~~~  303 (408)
                      +|.++...
T Consensus        93 ~V~~a~~~  100 (105)
T 2nlw_A           93 RVNLFTDF  100 (105)
T ss_dssp             EEECSCCC
T ss_pred             EEEEcchH
Confidence            99998654

>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=99.66  E-value=2e-16  Score=123.29  Aligned_cols=80  Identities=28%  Similarity=0.485  Sum_probs=72.4

Q ss_pred             CCCceEEEcCCCCCCcHHHHH----HHHhcCCCceeecc--CCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLK----EIFQAFGPVKELRE--TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~----~~F~~~G~v~~v~~--~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ...++|||+|||.++++++|+    ++|++||.|..+..  ++.++|||||+|.+.++|.+|++.|||..++|+.|+|+|
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   85 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   85 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            446899999999999999999    99999999999842  346789999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 046223          300 SRPGGH  305 (408)
Q Consensus       300 a~~~~~  305 (408)
                      ++++..
T Consensus        86 a~~~~~   91 (97)
T 1nu4_A           86 AKTDSD   91 (97)
T ss_dssp             CSSCCT
T ss_pred             ccCCCc
Confidence            987653

>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=99.66  E-value=2.6e-16  Score=119.95  Aligned_cols=76  Identities=13%  Similarity=0.315  Sum_probs=65.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec-----CccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL-----MEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~-----~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .+.++|||+|||.++|+++|+++|++||.|.+|++.+.     ++|||||+|.+.++|++|++.|||..|.  |+  .++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~--~l~   79 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG--GR--QIR   79 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TE--ECE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC--Ce--EEE
Confidence            35789999999999999999999999999999998763     4899999999999999999999998876  66  355


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.|+.
T Consensus        80 v~~a~   84 (87)
T 3bs9_A           80 TNWAT   84 (87)
T ss_dssp             EEEEC
T ss_pred             EEecC
Confidence            55543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.66  E-value=1.3e-15  Score=126.93  Aligned_cols=79  Identities=23%  Similarity=0.364  Sum_probs=68.5

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ......++|||+|||.++||++|+++|+.||+|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  |+  
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~--  112 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNIL--NK--  112 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECS--SC--
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--Ce--
Confidence            3456789999999999999999999999999999999875     34899999999999999999999998876  66  


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                      .|++.++.
T Consensus       113 ~l~v~~a~  120 (139)
T 1u6f_A          113 RLKVALAA  120 (139)
T ss_dssp             EEEEEESS
T ss_pred             EEEEEECC
Confidence            45555544

>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=99.66  E-value=1.1e-15  Score=120.39  Aligned_cols=79  Identities=16%  Similarity=0.222  Sum_probs=68.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ......++|||+|||.++|+++|+++|++||.|..|++.+   .++|||||+|.+.++|++|++.|||..|.  |+.  |
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~--l   85 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVE--GRK--I   85 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEET--TEE--C
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEEC--CEE--E
Confidence            4456789999999999999999999999999999999986   34899999999999999999999998876  664  5


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.++.
T Consensus        86 ~v~~a~   91 (103)
T 2cq3_A           86 EVNNAT   91 (103)
T ss_dssp             EEEECC
T ss_pred             EEEEcc
Confidence            555544

>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=99.66  E-value=2.3e-16  Score=122.45  Aligned_cols=75  Identities=17%  Similarity=0.239  Sum_probs=68.5

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+|||.++++++|+++|++||.|..+     +.++..+|||||+|.+.++|++|++.|||..|+|+.|+|+++.+
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~s   94 (95)
T 2ek1_A           15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS   94 (95)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC-
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEeccC
Confidence            4899999999999999999999999998765     24567899999999999999999999999999999999999864

>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=99.66  E-value=5.1e-16  Score=122.85  Aligned_cols=79  Identities=18%  Similarity=0.186  Sum_probs=68.2

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ......++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|||..|.  |+. 
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~-   86 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLY--GKP-   86 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCS--SCB-
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeEC--CeE-
Confidence            4455789999999999999999999999999999999876     35899999999999999999999998876  664 


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                       |++.++.
T Consensus        87 -l~v~~a~   93 (105)
T 1x5u_A           87 -IRVNKAS   93 (105)
T ss_dssp             -CEEEETT
T ss_pred             -EEEEECC
Confidence             5554543

>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=99.66  E-value=4.4e-16  Score=121.39  Aligned_cols=75  Identities=15%  Similarity=0.166  Sum_probs=65.0

Q ss_pred             CCCCCCEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           78 STGPTRTLVLSYVPG-DVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~-~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ...++++|||+|||. ++++++|+++|++||.|..|++   .+|||||+|.+.++|++|++.|||..+.  |+.  +++.
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~--l~V~   90 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIEXESQEMNF--GKK--LILE   90 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE---CSSEEEEEESSHHHHHHHHHHHTTSEET--TEE--CEEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEEC--CEE--EEEE
Confidence            344688999999998 9999999999999999999988   4899999999999999999999998876  663  5555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        91 ~a~   93 (97)
T 2xnq_A           91 VSS   93 (97)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            543

>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=99.65  E-value=2.5e-16  Score=133.11  Aligned_cols=81  Identities=30%  Similarity=0.382  Sum_probs=71.7

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeecc-CCCCccEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEEecCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRE-TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG--KHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~-~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~a~~~~  304 (408)
                      ..+|||+||++.+|+++|+++|++||.|++|+. ....+|||||+|.+.++|++|++.|||..|.|  +.|+|+|++++.
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            467999999999999999999999999999953 23467899999999999999999999999965  999999999876


Q ss_pred             CCCC
Q 046223          305 HSKK  308 (408)
Q Consensus       305 ~~~~  308 (408)
                      ...+
T Consensus       126 l~vk  129 (164)
T 1sjr_A          126 LNVK  129 (164)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            5433

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=3.5e-16  Score=123.35  Aligned_cols=80  Identities=24%  Similarity=0.287  Sum_probs=68.9

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           76 PPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        76 ~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      +....+.++|||+|||.++|+++|+++|++||.|..|.+..     +++|||||+|.+.++|++|++.|||..|.  |+.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~   84 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELD--GRE   84 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBT--TBC
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEEC--CcE
Confidence            34556789999999999999999999999999999999875     35899999999999999999999998876  663


Q ss_pred             cceeccccC
Q 046223          151 YGLKNPYSS  159 (408)
Q Consensus       151 l~~~~~~s~  159 (408)
                        |++.++.
T Consensus        85 --l~V~~a~   91 (103)
T 2dnm_A           85 --LRVQVAR   91 (103)
T ss_dssp             --CEEEECS
T ss_pred             --EEEEECC
Confidence              5555544

>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=99.65  E-value=3.5e-16  Score=125.94  Aligned_cols=82  Identities=30%  Similarity=0.418  Sum_probs=73.1

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCcee----e-ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKE----L-RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~----v-~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ....++|||+|||.++|+++|+++|+.||.|..    + ..++.++|||||+|.+.++|++|++.|||..|+|+.|+|+|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            345689999999999999999999999999843    3 24678899999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 046223          300 SRPGGHS  306 (408)
Q Consensus       300 a~~~~~~  306 (408)
                      ++++..+
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9876543

>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=99.65  E-value=4.5e-16  Score=118.15  Aligned_cols=76  Identities=18%  Similarity=0.260  Sum_probs=65.8

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHh-cCccccccccccceec
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEI-REQHMQLQQQSYGLKN  155 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~l-ng~~i~~~gr~l~~~~  155 (408)
                      ......++|||+|||.++|+++|+++|++||.|..|++.+ ++|||||+|.+.++|++|++.| +|..+.  |+.  +++
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~-~kg~afV~f~~~~~A~~a~~~l~~~~~~~--g~~--l~v   81 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-RQQCAFIQFATRQAAEVAAEKSFNKLIVN--GRR--LNV   81 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG-GGTEEEEEESSHHHHHHHHHTTTTTCEET--TEE--CCE
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC-CCCEEEEEECCHHHHHHHHHHhcCCeeEC--CCE--EEE
Confidence            3445678999999999999999999999999999999885 6999999999999999999988 887766  563  444


Q ss_pred             cc
Q 046223          156 PY  157 (408)
Q Consensus       156 ~~  157 (408)
                      .|
T Consensus        82 ~~   83 (85)
T 2ytc_A           82 KW   83 (85)
T ss_dssp             EE
T ss_pred             Ee
Confidence            43

>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=99.65  E-value=3.7e-16  Score=121.57  Aligned_cols=75  Identities=25%  Similarity=0.330  Sum_probs=66.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ++++|||+|||.++++++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|||..|.  |+  .+++
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~--~l~V   76 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLG--SR--FLKC   76 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEET--TE--ECEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeEC--Ce--EEEE
Confidence            478999999999999999999999999999999875     34899999999999999999999998876  66  3555


Q ss_pred             cccC
Q 046223          156 PYSS  159 (408)
Q Consensus       156 ~~s~  159 (408)
                      .|+.
T Consensus        77 ~~a~   80 (96)
T 2x1f_A           77 GYSS   80 (96)
T ss_dssp             EECS
T ss_pred             EEcC
Confidence            5554

>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=99.65  E-value=4.6e-16  Score=131.46  Aligned_cols=82  Identities=13%  Similarity=0.073  Sum_probs=70.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec-CccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL-MEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~-~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      .....+|||+||++++||++|+++|++||+|.+|++..+ ++|||||+|.+.++|++|++.|||..|.++++  .|++.|
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~--~L~V~~  120 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACC--TLRIDF  120 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCS--CEEEEE
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCc--EEEEEE
Confidence            344567999999999999999999999999999998754 58899999999999999999999999975556  577778


Q ss_pred             cCccc
Q 046223          158 SSGLM  162 (408)
Q Consensus       158 s~~~s  162 (408)
                      ++...
T Consensus       121 Ak~~~  125 (164)
T 1sjr_A          121 SKLTS  125 (164)
T ss_dssp             CSSSS
T ss_pred             ecCCc
Confidence            77543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.65  E-value=5.8e-16  Score=119.38  Aligned_cols=77  Identities=13%  Similarity=0.167  Sum_probs=67.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ..+.++|||+|||.++|+++|+++|++||.|..|++.+   +++|||||+|.+.++|++|++.|||..|.  |+  .|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~--g~--~l~v   80 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLS--GR--EIDV   80 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBT--TB--CCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--Cc--EEEE
Confidence            44678999999999999999999999999999999886   35899999999999999999999998876  66  3555


Q ss_pred             cccC
Q 046223          156 PYSS  159 (408)
Q Consensus       156 ~~s~  159 (408)
                      .++.
T Consensus        81 ~~a~   84 (92)
T 2dgv_A           81 RIDR   84 (92)
T ss_dssp             EECS
T ss_pred             EEcC
Confidence            5544

>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=99.65  E-value=6.1e-16  Score=124.56  Aligned_cols=79  Identities=14%  Similarity=0.143  Sum_probs=68.2

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....+.++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|||..|.  |+  
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~--   95 (115)
T 2cpz_A           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIG--MK--   95 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET--TE--
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEEC--CE--
Confidence            4455678999999999999999999999999999999875     34799999999999999999999998876  66  


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                      .|++.|+.
T Consensus        96 ~l~V~~a~  103 (115)
T 2cpz_A           96 RLKVQLKR  103 (115)
T ss_dssp             ECEEECCC
T ss_pred             EEEEEEcC
Confidence            45555544

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=3.2e-16  Score=124.02  Aligned_cols=81  Identities=21%  Similarity=0.336  Sum_probs=72.9

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ....++|||+|||..+++++|+++|++||.|..|+     .++.++|||||+|.+.++|++|++. ||..|+|+.|+|++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            34569999999999999999999999999999882     4567889999999999999999998 99999999999999


Q ss_pred             ecCCCCC
Q 046223          300 SRPGGHS  306 (408)
Q Consensus       300 a~~~~~~  306 (408)
                      ++++...
T Consensus        92 a~~~~~~   98 (105)
T 2dh8_A           92 CTPRGMQ   98 (105)
T ss_dssp             SCCSSCC
T ss_pred             ccCCCCC
Confidence            9876543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=3.9e-16  Score=121.91  Aligned_cols=76  Identities=14%  Similarity=0.246  Sum_probs=66.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--------cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      .++++|||+|||.++|+++|+++|++||.|..|.+.+        .++|||||+|.+.++|++|++.|||..|.  |+  
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~--   78 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVD--GH--   78 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEET--TE--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeC--Ce--
Confidence            4678999999999999999999999999999998875        34799999999999999999999998876  66  


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                      .|++.++.
T Consensus        79 ~l~V~~a~   86 (98)
T 2cpf_A           79 KLEVRISE   86 (98)
T ss_dssp             ECEEECSS
T ss_pred             EEEEEEcc
Confidence            35555544

>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=99.65  E-value=7e-16  Score=122.75  Aligned_cols=79  Identities=16%  Similarity=0.244  Sum_probs=68.0

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....++++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|||..|.  |+  
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~--g~--   96 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELA--GR--   96 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSS--SS--
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC--CE--
Confidence            3455678999999999999999999999999999999875     34899999999999999999999998876  66  


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                      .|++.++.
T Consensus        97 ~l~V~~a~  104 (108)
T 2jrs_A           97 PMKVGHVT  104 (108)
T ss_dssp             CCEEECSC
T ss_pred             EEEEEEcc
Confidence            35555544

>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=99.65  E-value=8.7e-16  Score=121.50  Aligned_cols=80  Identities=20%  Similarity=0.251  Sum_probs=67.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccc-ccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQ-QQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~-gr~l~  152 (408)
                      ...+.++|||+|||.++|+++|+++|++||.|..|++.+    +++|||||+|.+.++|++|++.|||..+.+. ++  .
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~--~   88 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASS--S   88 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSS--C
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCc--c
Confidence            345689999999999999999999999999999999886    3489999999999999999999999887631 15  3


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.|+.
T Consensus        89 l~V~~a~   95 (105)
T 2dnh_A           89 LVVKFAD   95 (105)
T ss_dssp             CEEEESC
T ss_pred             EEEEECc
Confidence            5555544

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=1e-15  Score=117.75  Aligned_cols=77  Identities=17%  Similarity=0.222  Sum_probs=70.2

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ....+|||+|||.++++++|+++|+.| .|..++    .++.++|||||+|.+.++|++|++ |||..|+|+.|+|.+++
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEES
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECC
Confidence            446899999999999999999999999 888883    456779999999999999999999 99999999999999998


Q ss_pred             CCC
Q 046223          302 PGG  304 (408)
Q Consensus       302 ~~~  304 (408)
                      ++.
T Consensus        86 ~~~   88 (91)
T 2dgw_A           86 SGP   88 (91)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            764

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=6e-16  Score=120.00  Aligned_cols=78  Identities=14%  Similarity=0.151  Sum_probs=67.4

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....++++|||+|||.++|+++|+++|++||.|..|.+.+     +++|||||+|.+.++|++|++.|||..|.  |+  
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~--   85 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD--GR--   85 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEET--TE--
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEEC--CE--
Confidence            3445688999999999999999999999999999999875     44899999999999999999999998876  66  


Q ss_pred             ceecccc
Q 046223          152 GLKNPYS  158 (408)
Q Consensus       152 ~~~~~~s  158 (408)
                      .|++.|+
T Consensus        86 ~l~v~~a   92 (95)
T 2cqc_A           86 RIRVSGP   92 (95)
T ss_dssp             EEEEECC
T ss_pred             EEEEEec
Confidence            3555444

>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=99.65  E-value=4.1e-16  Score=120.99  Aligned_cols=78  Identities=13%  Similarity=0.111  Sum_probs=67.1

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ....+.++|||+|||.++++++|+++|++||+|..|++.+    +++|||||+|.+.++|++|++.|||..|.  |+.  
T Consensus        11 ~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~--   86 (95)
T 2ywk_A           11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLY--GRP--   86 (95)
T ss_dssp             -CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEET--TEE--
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEEC--CCE--
Confidence            4455789999999999999999999999999999999886    34899999999999999999999998876  663  


Q ss_pred             eecccc
Q 046223          153 LKNPYS  158 (408)
Q Consensus       153 ~~~~~s  158 (408)
                      |++.|+
T Consensus        87 l~V~~a   92 (95)
T 2ywk_A           87 INVSGP   92 (95)
T ss_dssp             CEEECC
T ss_pred             EEEEEc
Confidence            455443

>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=99.65  E-value=8.3e-16  Score=130.74  Aligned_cols=81  Identities=20%  Similarity=0.283  Sum_probs=74.0

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||..+|+++|+++|++||.|..|.     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|+|+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            4568999999999999999999999999999983     35678899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 046223          301 RPGGHS  306 (408)
Q Consensus       301 ~~~~~~  306 (408)
                      ++....
T Consensus       117 ~~~~~~  122 (156)
T 1h2v_Z          117 AGFKEG  122 (156)
T ss_dssp             SCCCTT
T ss_pred             CCCCCc
Confidence            876544

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=4.9e-16  Score=123.15  Aligned_cols=78  Identities=14%  Similarity=0.315  Sum_probs=67.4

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....++++|||+|||.++|+++|+++|++||.|..|.+.+     .++|||||+|.+.++|++|++.|||..|.  |+. 
T Consensus        18 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~-   94 (106)
T 1p27_B           18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM--GQP-   94 (106)
T ss_dssp             CCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSS--SSB-
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEEC--CcE-
Confidence            3455678999999999999999999999999999999875     34899999999999999999999998876  664 


Q ss_pred             ceecccc
Q 046223          152 GLKNPYS  158 (408)
Q Consensus       152 ~~~~~~s  158 (408)
                       |++.|+
T Consensus        95 -l~V~~a  100 (106)
T 1p27_B           95 -ISVDWC  100 (106)
T ss_dssp             -CEEEES
T ss_pred             -EEEEee
Confidence             455444

>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=99.65  E-value=2.4e-16  Score=125.41  Aligned_cols=80  Identities=16%  Similarity=0.131  Sum_probs=67.0

Q ss_pred             CCCCCEEEE--cCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccc-cccccccceec
Q 046223           79 TGPTRTLVL--SYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHM-QLQQQSYGLKN  155 (408)
Q Consensus        79 ~~~~rtlfV--~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i-~~~gr~l~~~~  155 (408)
                      ..++++|||  +||++++||++|+++|++||+|..|.+. ..+|||||+|.+.++|++|++.|||+.| ...+....+.+
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~-~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v  100 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL  100 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEE
Confidence            446889999  7799999999999999999999999887 4699999999999999999999999987 32222335666


Q ss_pred             cccC
Q 046223          156 PYSS  159 (408)
Q Consensus       156 ~~s~  159 (408)
                      .|+.
T Consensus       101 ~~a~  104 (114)
T 2cq2_A          101 NFVE  104 (114)
T ss_dssp             EEES
T ss_pred             Eecc
Confidence            6654

>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=99.65  E-value=5.5e-16  Score=121.26  Aligned_cols=77  Identities=19%  Similarity=0.198  Sum_probs=67.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ..++++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|||..|.  |+  .+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~--~l   80 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQ--GR--ML   80 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESS--SC--EE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEEC--Cc--EE
Confidence            45689999999999999999999999999999999875     35899999999999999999999998876  66  35


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.++.
T Consensus        81 ~V~~a~   86 (99)
T 1whw_A           81 HVLPST   86 (99)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            555544

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.65  E-value=4.4e-16  Score=127.25  Aligned_cols=78  Identities=13%  Similarity=0.190  Sum_probs=67.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHH----HHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVR----RDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~----~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ..++++|||+||++++++++|+    ++|++||.|.+|.+.+  +++|||||+|.+.++|++|++.|||..|.  ||  .
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~--gr--~  101 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQ--GN--P  101 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCT--TS--C
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeC--CC--E
Confidence            3457899999999999999876    7999999999998865  67999999999999999999999998876  67  4


Q ss_pred             eeccccCc
Q 046223          153 LKNPYSSG  160 (408)
Q Consensus       153 ~~~~~s~~  160 (408)
                      |+|.|+..
T Consensus       102 l~V~~a~~  109 (127)
T 2a3j_A          102 LVITFSET  109 (127)
T ss_dssp             CEEEECCC
T ss_pred             EEEEEccC
Confidence            66666653

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=1e-15  Score=120.02  Aligned_cols=79  Identities=14%  Similarity=0.202  Sum_probs=67.8

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ....+.++|||+|||.++|+++|+++|++||.|..|++..    +++|||||+|.+.++|++|++.|||..|.  |+  .
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~--~   87 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIK--EN--I   87 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESS--SC--E
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEEC--CE--E
Confidence            3445678999999999999999999999999999999876    34799999999999999999999998876  66  3


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.|+.
T Consensus        88 l~v~~a~   94 (100)
T 2do4_A           88 IKVAISN   94 (100)
T ss_dssp             EEEEECC
T ss_pred             EEEEECC
Confidence            5555544

>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=99.65  E-value=2.6e-16  Score=125.96  Aligned_cols=78  Identities=14%  Similarity=0.286  Sum_probs=70.3

Q ss_pred             CCceEEEcCCCCCCcHHHHH---HHHhcCCCceeecc--------CCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEE
Q 046223          227 NQGTIVVFNLDSGVSSSTLK---EIFQAFGPVKELRE--------TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHV  295 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~---~~F~~~G~v~~v~~--------~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l  295 (408)
                      ..++|||+|||.++++++|+   ++|++||.|..+..        .+.++|||||+|.+.++|++|++.|||..|+|+.|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l   93 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   93 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEE
Confidence            35899999999999999999   99999999999831        12456999999999999999999999999999999


Q ss_pred             EEEEecCCC
Q 046223          296 VIEFSRPGG  304 (408)
Q Consensus       296 ~v~~a~~~~  304 (408)
                      +|++++++.
T Consensus        94 ~V~~a~~k~  102 (111)
T 2cpi_A           94 KASLGTTKY  102 (111)
T ss_dssp             EEESCCCCS
T ss_pred             EEEeccccc
Confidence            999998765

>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=99.65  E-value=7.3e-16  Score=117.52  Aligned_cols=75  Identities=24%  Similarity=0.325  Sum_probs=67.9

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ....++|||+|||.++++++|+++|++||.|..++     .++.++|||||+|.+.++|++|++ +++..++|+.|+|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            34568999999999999999999999999999883     457789999999999999999996 688999999999998


Q ss_pred             e
Q 046223          300 S  300 (408)
Q Consensus       300 a  300 (408)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            6

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=3.9e-16  Score=118.48  Aligned_cols=68  Identities=13%  Similarity=0.141  Sum_probs=62.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQ  149 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr  149 (408)
                      .++++|||+|||.++++++|+++|++||.|..|++..     .++|||||+|.+.++|++|++.|||..|.  |+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~   75 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQ--AQ   75 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCC--EE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEe--eE
Confidence            4678999999999999999999999999999999875     34899999999999999999999998876  55

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

Probab=99.64  E-value=8.5e-16  Score=118.01  Aligned_cols=74  Identities=19%  Similarity=0.269  Sum_probs=65.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      ..+.++|||+|||.++|+++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|||..|.  |+  .+++.|+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~--g~--~l~v~~a   77 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLH--GV--NINVEAS   77 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCS--SC--BCEEECS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccC--Cc--EEEEEEC
Confidence            3467899999999999999999999999999999987   899999999999999999999998876  66  3555554


Q ss_pred             C
Q 046223          159 S  159 (408)
Q Consensus       159 ~  159 (408)
                      .
T Consensus        78 ~   78 (90)
T 2dnq_A           78 K   78 (90)
T ss_dssp             S
T ss_pred             C
Confidence            4

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=5e-16  Score=122.45  Aligned_cols=80  Identities=14%  Similarity=0.202  Sum_probs=69.1

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           76 PPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        76 ~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      .....+.++|||+|||.++|+++|+++|++||.|..|.+.+     .++|||||+|.+.++|++|++.|||..|.  |+ 
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~-   85 (103)
T 2cq0_A            9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYD--HL-   85 (103)
T ss_dssp             CCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEET--TE-
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeC--Cc-
Confidence            34556789999999999999999999999999999999875     34899999999999999999999998876  66 


Q ss_pred             cceeccccC
Q 046223          151 YGLKNPYSS  159 (408)
Q Consensus       151 l~~~~~~s~  159 (408)
                       .|++.|+.
T Consensus        86 -~l~v~~a~   93 (103)
T 2cq0_A           86 -ILNVEWAK   93 (103)
T ss_dssp             -ECEEEESS
T ss_pred             -EEEEEECC
Confidence             45555544

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.64  E-value=3.7e-16  Score=132.70  Aligned_cols=77  Identities=16%  Similarity=0.188  Sum_probs=70.5

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCC--Cceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFG--PVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G--~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ...+|||+||++++++++|+++|+.||  .|.+|+     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            458999999999999999999999999  888883     4788899999999999999999999999999999999999


Q ss_pred             ecCC
Q 046223          300 SRPG  303 (408)
Q Consensus       300 a~~~  303 (408)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.8e-15  Score=117.90  Aligned_cols=77  Identities=18%  Similarity=0.394  Sum_probs=70.5

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGH  305 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  305 (408)
                      ...++|||+||  ++++++|+++|++||.|..|.. ...+|||||+|.+.++|++|++.|||..|+|+.|+|.|++++..
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i-~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~   89 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM   89 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEe-cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCC
Confidence            34689999996  8999999999999999999964 47899999999999999999999999999999999999987654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=8.7e-16  Score=120.13  Aligned_cols=77  Identities=18%  Similarity=0.246  Sum_probs=66.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ...+.++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++ |+|..|.  |+.  
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~--g~~--   80 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIM--GKK--   80 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSS--SCB--
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEEC--CeE--
Confidence            345679999999999999999999999999999999975     358999999999999999998 9998876  663  


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.++.
T Consensus        81 l~V~~a~   87 (99)
T 2dgs_A           81 VEVKRAE   87 (99)
T ss_dssp             CEEEECC
T ss_pred             EEEEECC
Confidence            5555544

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.64  E-value=3.1e-15  Score=122.10  Aligned_cols=80  Identities=26%  Similarity=0.371  Sum_probs=72.8

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ....++|||+||+..+++++|+++|++||.|..|+    .++.++|||||+|.+.++|++|++.|||..++|+.|+|++|
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEe
Confidence            34568999999999999999999999999999883    25668999999999999999999999999999999999999


Q ss_pred             cCCC
Q 046223          301 RPGG  304 (408)
Q Consensus       301 ~~~~  304 (408)
                      .+..
T Consensus       112 ~~~~  115 (124)
T 2kt5_A          112 ASQI  115 (124)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            7654

>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=99.64  E-value=7.2e-16  Score=120.63  Aligned_cols=78  Identities=18%  Similarity=0.284  Sum_probs=68.1

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ....+.++|||+|||.++|+++|+++|++||+|..|++. +++|||||+|.+.++|++|++.|||..|.  |+.  |++.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-~~kg~afV~f~~~~~a~~a~~~l~g~~~~--g~~--l~v~   84 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLR--GKQ--LRVR   84 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBT--TBC--CEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCEeC--Cce--EEEE
Confidence            344577899999999999999999999999999999988 46999999999999999999999998876  663  5555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        85 ~a~   87 (99)
T 2cpj_A           85 FAC   87 (99)
T ss_dssp             ESS
T ss_pred             EcC
Confidence            554

>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=99.64  E-value=1.5e-16  Score=157.09  Aligned_cols=80  Identities=25%  Similarity=0.468  Sum_probs=73.0

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+||+..+|+++|+++|++||.|..|.     .++.++|||||+|.+.++|.+||+.|||..|+|+.|.|.|+
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            3458999999999999999999999999999883     36778999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 046223          301 RPGGH  305 (408)
Q Consensus       301 ~~~~~  305 (408)
                      ++...
T Consensus       180 ~~~~~  184 (437)
T 3pgw_S          180 RGRTV  184 (437)
T ss_pred             CCCCC
Confidence            87543

>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=99.64  E-value=5.7e-16  Score=116.98  Aligned_cols=74  Identities=16%  Similarity=0.198  Sum_probs=64.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      +.+|||+|||.++++++|+++|++||.|.+|.+.+     +++|||||+|.+.++|++|++.|||..|.  |+  .+++.
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~--g~--~l~v~   76 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN--GR--PLRIN   76 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEET--TE--ECEEE
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeC--Cc--EEEEE
Confidence            46899999999999999999999999999999875     34899999999999999999999999876  66  35555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        77 ~a~   79 (83)
T 3md1_A           77 WAA   79 (83)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=9.8e-16  Score=121.58  Aligned_cols=79  Identities=20%  Similarity=0.395  Sum_probs=68.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec------CccEEEEEECCHHHHHHHHHHh-cCcccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL------MEGIVTVHFYDLRHAEMAFKEI-REQHMQLQQQ  149 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~------~kG~afV~F~~~~~A~~Ai~~l-ng~~i~~~gr  149 (408)
                      ......++|||+|||.++|+++|+++|++||.|..|++.+.      ++|||||+|.+.++|++|++.| ||..|.  |+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~--g~   87 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY--GR   87 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSS--SC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeEC--CC
Confidence            45567899999999999999999999999999999998754      4899999999999999999999 898876  66


Q ss_pred             ccceeccccC
Q 046223          150 SYGLKNPYSS  159 (408)
Q Consensus       150 ~l~~~~~~s~  159 (408)
                        .|++.|+.
T Consensus        88 --~l~v~~a~   95 (107)
T 2cph_A           88 --RLVLEWAD   95 (107)
T ss_dssp             --BCEEEECC
T ss_pred             --EEEEEeCC
Confidence              45555544

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.64  E-value=7.9e-16  Score=123.85  Aligned_cols=79  Identities=13%  Similarity=0.280  Sum_probs=68.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec-----CccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL-----MEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~-----~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....+.++|||+|||.++|+++|+++|++||.|..|++.+.     ++|||||+|.+.++|++|++.|||..|.  |+  
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~--   85 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG--GR--   85 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEET--TE--
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--CE--
Confidence            45567899999999999999999999999999999998763     3899999999999999999999998876  66  


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                      .|+|.|+.
T Consensus        86 ~l~V~~a~   93 (115)
T 2dgo_A           86 QIRTNWAT   93 (115)
T ss_dssp             ECEEEESS
T ss_pred             EEEEEEcc
Confidence            45555554

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.64  E-value=1.2e-15  Score=123.68  Aligned_cols=77  Identities=16%  Similarity=0.122  Sum_probs=67.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccE-EEEEECCHHHHHHHHHHhcCccccccccccceeccccCcc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGI-VTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSSGL  161 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~-afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~~~  161 (408)
                      ..|||+||++.+|+++|+++|++||+|.+|++..+ .|| |||+|.+.++|++|++.|||..|.+.++  .|++.|+...
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~--~l~V~~Ak~~  102 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCC--TLKIEYARPT  102 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBS--EEEEECCSCS
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCe--EEEEEEecCC
Confidence            34689999999999999999999999999998765 596 9999999999999999999999874434  5788888765


Q ss_pred             c
Q 046223          162 M  162 (408)
Q Consensus       162 s  162 (408)
                      +
T Consensus       103 ~  103 (124)
T 2e5i_A          103 R  103 (124)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.64  E-value=7.3e-16  Score=122.66  Aligned_cols=76  Identities=14%  Similarity=0.163  Sum_probs=65.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccc---cccceecc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQ---QSYGLKNP  156 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~g---r~l~~~~~  156 (408)
                      ....+|||+|||+++|+++|+++|++||+|..|++...  |||||+|.+.++|++||+.|||..|.+..   +  .|+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~--~i~V~   88 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA--YIRVK   88 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEE--EEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCccCCcCcce--EEEEE
Confidence            45789999999999999999999999999999999865  99999999999999999999999886310   5  45665


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      ++.
T Consensus        89 ~a~   91 (108)
T 1x4c_A           89 VDG   91 (108)
T ss_dssp             ESS
T ss_pred             eCC
Confidence            554

>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=99.64  E-value=1.4e-16  Score=126.69  Aligned_cols=78  Identities=22%  Similarity=0.210  Sum_probs=69.9

Q ss_pred             CCCceEEEcCCCCC-CcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCC--ceeCCeEEEEEEecC
Q 046223          226 NNQGTIVVFNLDSG-VSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNG--QEIYGKHVVIEFSRP  302 (408)
Q Consensus       226 ~~~~~l~V~nLp~~-~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g--~~~~g~~l~v~~a~~  302 (408)
                      ...++|||+||+++ +++++|+++|++||.|.+|+.. ..+|||||+|.+.++|++|++.|++  ..|.|+.|+|.|++.
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  101 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK  101 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcc
Confidence            34689999999998 9999999999999999999643 5799999999999999999998864  569999999999976


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      +.
T Consensus       102 ~~  103 (112)
T 1x4f_A          102 YK  103 (112)
T ss_dssp             CS
T ss_pred             cc
Confidence            54

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=7.2e-16  Score=116.59  Aligned_cols=73  Identities=19%  Similarity=0.437  Sum_probs=65.6

Q ss_pred             Cce-EEEcCCCCCCcHHH----HHHHHhcC-CCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          228 QGT-IVVFNLDSGVSSST----LKEIFQAF-GPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       228 ~~~-l~V~nLp~~~t~~~----L~~~F~~~-G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ..+ |||+||++.+++++    |+++|++| |.|.+|.  +   |+|||+|.+.++|++|++.|||..+.||.|+|+||+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt--g---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~   82 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT--G---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTP   82 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC--T---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSC
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe--c---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecC
Confidence            355 99999999999887    55899999 5999983  2   999999999999999999999999999999999998


Q ss_pred             CCCC
Q 046223          302 PGGH  305 (408)
Q Consensus       302 ~~~~  305 (408)
                      .+..
T Consensus        83 ~~sd   86 (96)
T 2diu_A           83 KNRE   86 (96)
T ss_dssp             CSCC
T ss_pred             CCcc
Confidence            7653

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.64  E-value=2.9e-16  Score=118.10  Aligned_cols=64  Identities=16%  Similarity=0.250  Sum_probs=59.3

Q ss_pred             CCEEEEcCCCCCC------CHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           82 TRTLVLSYVPGDV------SETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        82 ~rtlfV~nLp~~v------te~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      +++|||+|||.++      |+++|+++|++||.|.+|.+.+   +++|||||+|.+.++|++|++.|||..|.
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~   73 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD   73 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccC
Confidence            4789999999999      7899999999999999999875   46899999999999999999999998876

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.64  E-value=6e-16  Score=121.53  Aligned_cols=74  Identities=12%  Similarity=0.166  Sum_probs=65.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      ..++|||+|||.++|+++|+++|++||.|.+|++. +++|||||+|.+.++|++|++.|||..|.  |+  .+++.|+.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~--~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-PEKGCCFIKYDTHEQAAVCIVALANFPFQ--GR--NLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEET--TE--ECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCeEC--Ce--EEEEEecc
Confidence            46899999999999999999999999999999988 58999999999999999999999998876  66  45555543

>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=99.64  E-value=5.3e-16  Score=129.97  Aligned_cols=82  Identities=34%  Similarity=0.432  Sum_probs=73.2

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceee----------ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----------RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH  294 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v----------~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~  294 (408)
                      ....++|||+||++.+|+++|+++|+.||.|..+          ..++.++|||||+|.+.++|.+|++.|||..|.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            3456899999999999999999999999998763          357889999999999999999999999999999999


Q ss_pred             EEEEEecCCCCC
Q 046223          295 VVIEFSRPGGHS  306 (408)
Q Consensus       295 l~v~~a~~~~~~  306 (408)
                      |+|.++++...+
T Consensus       122 l~V~~a~~~~~~  133 (143)
T 3egn_A          122 MVVQFARSARPK  133 (143)
T ss_dssp             CEEEECCCSCC-
T ss_pred             EEEEECCCCCCc
Confidence            999999876543

>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=99.64  E-value=2.5e-16  Score=124.42  Aligned_cols=78  Identities=28%  Similarity=0.452  Sum_probs=72.0

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+|||..+++++|+++|++||.|..+.     .++.++|||||+|.+.++|++|++.|||..++|+.|+|+++++
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            48999999999999999999999999998883     3567799999999999999999999999999999999999987


Q ss_pred             CCC
Q 046223          303 GGH  305 (408)
Q Consensus       303 ~~~  305 (408)
                      +..
T Consensus        88 ~~~   90 (104)
T 1p1t_A           88 EKN   90 (104)
T ss_dssp             TTH
T ss_pred             ccc
Confidence            654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.64  E-value=2.2e-16  Score=124.09  Aligned_cols=79  Identities=19%  Similarity=0.318  Sum_probs=70.9

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ....+|||+||+.++++++|+++|+.||.|...    ..++.++|||||+|.+.++|++|++ |||..|.|+.|+|.+++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~   93 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcC
Confidence            346899999999999999999999999987662    2456789999999999999999999 99999999999999998


Q ss_pred             CCCC
Q 046223          302 PGGH  305 (408)
Q Consensus       302 ~~~~  305 (408)
                      ++..
T Consensus        94 ~~~~   97 (101)
T 1fj7_A           94 GRDG   97 (101)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.64  E-value=5.8e-16  Score=123.20  Aligned_cols=76  Identities=24%  Similarity=0.334  Sum_probs=66.3

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      .....+++|||+|||.++|+++|+++|++||.|..|.+.   +|||||+|.+.++|++|++.|||..|.  |+  .+++.
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~--g~--~l~V~   98 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFA--NQ--PLEVV   98 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEET--TE--ECEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEEC--Ce--EEEEE
Confidence            345568999999999999999999999999999999987   899999999999999999999998875  66  45555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        99 ~a~  101 (108)
T 2jvo_A           99 YSK  101 (108)
T ss_dssp             SCS
T ss_pred             Eec
Confidence            544

>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=99.64  E-value=2.8e-16  Score=126.34  Aligned_cols=77  Identities=21%  Similarity=0.493  Sum_probs=70.6

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ..++|||+||+.++++++|+++|+.||.|..|+     .++..+|||||+|.+.++|++|+ .|||..|+|+.|+|++++
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            458999999999999999999999999999984     33678999999999999999999 999999999999999997


Q ss_pred             CCC
Q 046223          302 PGG  304 (408)
Q Consensus       302 ~~~  304 (408)
                      ++.
T Consensus       103 ~~~  105 (114)
T 2cq4_A          103 AEK  105 (114)
T ss_dssp             HHH
T ss_pred             CCc
Confidence            653

>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=99.64  E-value=8.2e-16  Score=122.50  Aligned_cols=79  Identities=13%  Similarity=0.220  Sum_probs=71.0

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCC-ceeecc------CCCCccEEEEEECCHHHHHHHHHHhC--CceeCCeEEEE
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGP-VKELRE------TPLKKHQRFIEFYDVRDAAKALKEMN--GQEIYGKHVVI  297 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~-v~~v~~------~~~~~g~afV~F~~~~~A~~A~~~l~--g~~~~g~~l~v  297 (408)
                      ..++|||+|||.++++++|+++|++||. |..+..      ++.++|||||+|.+.++|++|++.||  +..++|+.|+|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V   86 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            3589999999999999999999999998 988842      34789999999999999999999996  58999999999


Q ss_pred             EEecCCCC
Q 046223          298 EFSRPGGH  305 (408)
Q Consensus       298 ~~a~~~~~  305 (408)
                      +|++++..
T Consensus        87 ~~a~~~~~   94 (109)
T 2dis_A           87 DWAEPEID   94 (109)
T ss_dssp             EESCSSCS
T ss_pred             EEcCCCCC
Confidence            99987654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.64  E-value=6.8e-16  Score=125.98  Aligned_cols=77  Identities=19%  Similarity=0.303  Sum_probs=70.9

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+||+.++++++|+++|++||.|..|+     .++.++|||||+|.+.++|++|+ .|||..|+|+.|+|+++++
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            48999999999999999999999999999883     46778999999999999999999 7999999999999999986


Q ss_pred             CCC
Q 046223          303 GGH  305 (408)
Q Consensus       303 ~~~  305 (408)
                      ...
T Consensus       115 ~~~  117 (124)
T 2jwn_A          115 NMP  117 (124)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=1.2e-15  Score=120.19  Aligned_cols=79  Identities=14%  Similarity=0.188  Sum_probs=68.5

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....+.++|||+|||.++|+++|+++|++||.|..|++..   .++|||||+|.+.++|++|++.|||..|.  |+  .|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~--~l   85 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVA--TK--PL   85 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSS--SS--BC
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeC--Cc--EE
Confidence            3445788999999999999999999999999999999886   46899999999999999999999998875  66  35


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.|+.
T Consensus        86 ~V~~a~   91 (103)
T 2d9p_A           86 YVALAQ   91 (103)
T ss_dssp             EEEECS
T ss_pred             EEEEec
Confidence            555544

>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=99.63  E-value=7.5e-16  Score=122.06  Aligned_cols=81  Identities=14%  Similarity=0.212  Sum_probs=68.3

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccc-cccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHM-QLQQQS  150 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i-~~~gr~  150 (408)
                      ....+.++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|||..+ .+.++ 
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~-   86 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNR-   86 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSS-
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCc-
Confidence            4455789999999999999999999999999999999876     3589999999999999999999999875 22356 


Q ss_pred             cceeccccC
Q 046223          151 YGLKNPYSS  159 (408)
Q Consensus       151 l~~~~~~s~  159 (408)
                       .|++.|+.
T Consensus        87 -~l~v~~a~   94 (106)
T 2dgp_A           87 -PIQVKPAD   94 (106)
T ss_dssp             -CCEEEECC
T ss_pred             -eEEEEECC
Confidence             45555544

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.63  E-value=2.8e-16  Score=116.32  Aligned_cols=70  Identities=23%  Similarity=0.261  Sum_probs=65.1

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       230 ~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      +|||+|||.++++++|+++|++||.|..++     .++.++|||||+|.+.++|++|++ |||..++|+.|+|++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            589999999999999999999999999983     367789999999999999999998 9999999999999875

>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=99.63  E-value=4.7e-16  Score=124.37  Aligned_cols=76  Identities=20%  Similarity=0.311  Sum_probs=70.7

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      .++|||+|||.++++++|+++|++||.|..|... ..+|||||+|.+.++|++|++.|||..|+|+.|.|+|++...
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            4899999999999999999999999999998643 588999999999999999999999999999999999997654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.63  E-value=6.5e-16  Score=125.24  Aligned_cols=79  Identities=23%  Similarity=0.262  Sum_probs=69.1

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccE-EEEEECCHHHHHHHHHHhCCceeCC--eEEEEEEecCCCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQ-RFIEFYDVRDAAKALKEMNGQEIYG--KHVVIEFSRPGGH  305 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~-afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~a~~~~~  305 (408)
                      ..|||+||++.+++++|+++|++||.|.+|+...+ .|| |||+|.+.++|.+|++.|||..|.|  +.|+|+||+++..
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l  104 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRL  104 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSCC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCcc
Confidence            45689999999999999999999999999854333 486 9999999999999999999999987  6999999998865


Q ss_pred             CCC
Q 046223          306 SKK  308 (408)
Q Consensus       306 ~~~  308 (408)
                      ..+
T Consensus       105 ~v~  107 (124)
T 2e5i_A          105 NVI  107 (124)
T ss_dssp             CCS
T ss_pred             eee
Confidence            433

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.63  E-value=3.7e-16  Score=124.56  Aligned_cols=74  Identities=9%  Similarity=0.060  Sum_probs=65.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccC-CeEEEEEe-ecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFG-EVRGVQME-RLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G-~V~~v~~~-~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      ...+|||+|||+++|+++|+++|++|| +|..+.+. ++++|||||+|.+.++|++|++.|||..|.  ||.  |++.++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~--Gr~--i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFR--GSV--ITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEET--TEE--EEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEEC--CeE--EEEEEC
Confidence            467999999999999999999999999 99999985 468999999999999999999999998876  774  444443

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2.9e-16  Score=123.74  Aligned_cols=75  Identities=17%  Similarity=0.263  Sum_probs=68.9

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..++|||+|||.++|+++|+++|++||.|.+|+    ..+.++|||||+|.+.++|.+|++ ++|..++|+.|.|.++..
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            358999999999999999999999999999883    237789999999999999999999 999999999999999864

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=9.6e-16  Score=123.57  Aligned_cols=79  Identities=13%  Similarity=0.224  Sum_probs=71.8

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ..++|||+||+.++++++|+++|+.||.|..|+     .++.++|||||+|.+.++|++|++. +|..|+|+.|+|++++
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            358999999999999999999999999998883     4567899999999999999999997 9999999999999998


Q ss_pred             CCCCC
Q 046223          302 PGGHS  306 (408)
Q Consensus       302 ~~~~~  306 (408)
                      ++...
T Consensus       105 ~~~~~  109 (116)
T 1x4b_A          105 AREES  109 (116)
T ss_dssp             SCCCC
T ss_pred             CCccC
Confidence            87643

>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=99.63  E-value=7.3e-16  Score=117.89  Aligned_cols=76  Identities=14%  Similarity=0.304  Sum_probs=69.8

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ..++|||+|||.++++++|+++|++| .|..++.. .++|||||+|.+.++|++|++.|||..++|++|+|+++....
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            35899999999999999999999999 89888654 789999999999999999999999999999999999986543

>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=99.63  E-value=1.2e-15  Score=125.42  Aligned_cols=79  Identities=15%  Similarity=0.183  Sum_probs=68.4

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....++++|||+|||.++|+++|+++|++||+|..|++.+     +++|||||+|.+.++|++|++.|||..|.  |+  
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~--g~--  116 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD--GR--  116 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSS--SS--
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEEC--CE--
Confidence            3455688999999999999999999999999999999875     46899999999999999999999998876  66  


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                      .|++.|+.
T Consensus       117 ~l~V~~a~  124 (129)
T 2kxn_B          117 RIRVDFSI  124 (129)
T ss_dssp             CCEESCCS
T ss_pred             EEEEEEec
Confidence            45555544

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=6.5e-16  Score=120.85  Aligned_cols=80  Identities=24%  Similarity=0.368  Sum_probs=67.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeE-EEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVR-GVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~-~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ...++++|||+|||.++|+++|+++|++||.|. .|++.+     +++|||||+|.+.++|++|++.|||..|.  |+.+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~~   82 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLP--GATP   82 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEES--SCSS
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccC--CCCc
Confidence            345689999999999999999999999999999 998875     34799999999999999999999998876  5541


Q ss_pred             --ceeccccC
Q 046223          152 --GLKNPYSS  159 (408)
Q Consensus       152 --~~~~~~s~  159 (408)
                        .+++.|+.
T Consensus        83 ~~~l~v~~a~   92 (99)
T 2div_A           83 AKRFKLNYAT   92 (99)
T ss_dssp             CEECCEEETT
T ss_pred             ceeEEEeecC
Confidence              25665544

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=6.5e-16  Score=121.68  Aligned_cols=73  Identities=21%  Similarity=0.251  Sum_probs=63.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ....++|||+|||.++|+++|+++|++||.|.+|.+.+    .++|||||+|.+.++|++|++ ++|..|.  |+.|.+.
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~--gr~l~V~   84 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYK--ETDLLIL   84 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCT--TTTCEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEEC--CEEEEEE
Confidence            44578999999999999999999999999999999886    469999999999999999998 8987765  6744433

>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=99.63  E-value=3.3e-15  Score=117.72  Aligned_cols=78  Identities=21%  Similarity=0.330  Sum_probs=70.1

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||..+++++|+++|++||.|..|+     .++.++|||||+|.+.++|++|++  ++..|+|+.|+|+++
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a   90 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLP   90 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEec
Confidence            4468999999999999999999999999999883     357789999999999999999998  578999999999999


Q ss_pred             cCCCC
Q 046223          301 RPGGH  305 (408)
Q Consensus       301 ~~~~~  305 (408)
                      +++..
T Consensus        91 ~~~~~   95 (103)
T 2cqg_A           91 NSKQS   95 (103)
T ss_dssp             CTTCC
T ss_pred             CCCCc
Confidence            87654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.63  E-value=2e-16  Score=119.01  Aligned_cols=69  Identities=23%  Similarity=0.301  Sum_probs=63.9

Q ss_pred             ceEEEcCCCCCC------cHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCe-EEEE
Q 046223          229 GTIVVFNLDSGV------SSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK-HVVI  297 (408)
Q Consensus       229 ~~l~V~nLp~~~------t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~-~l~v  297 (408)
                      ++|||+|||..+      ++++|+++|++||.|..++   .++.++|||||+|.+.++|++|++.|||..++|+ .|+|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            789999999999      7899999999999999983   4567899999999999999999999999999999 8876

>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=99.63  E-value=2.9e-16  Score=120.64  Aligned_cols=72  Identities=8%  Similarity=0.077  Sum_probs=61.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccC--CeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFG--EVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G--~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      .+|||+|||+++|+++|+++|++||  .|.+|++..     +++|||||+|.+.++|++|++.|||..|.  ||.  ++|
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~--gr~--i~V   77 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELH--GQN--PVV   77 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSS--SCC--CEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeC--CEE--EEE
Confidence            4799999999999999999999999  999998876     45899999999999999999999998876  773  455


Q ss_pred             ccc
Q 046223          156 PYS  158 (408)
Q Consensus       156 ~~s  158 (408)
                      .++
T Consensus        78 ~~~   80 (90)
T 3p5t_L           78 TPS   80 (90)
T ss_dssp             CCC
T ss_pred             EEC
Confidence            443

>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=99.63  E-value=1.6e-15  Score=121.11  Aligned_cols=79  Identities=15%  Similarity=0.208  Sum_probs=68.2

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhc------Ccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIR------EQHMQ  145 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~ln------g~~i~  145 (408)
                      ....+.++|||+|||.++|+++|+++|++||.|..|++.+     .++|||||+|.+.++|++|++.||      |..|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            4456789999999999999999999999999999999885     469999999999999999999999      87765


Q ss_pred             ccccccceeccccC
Q 046223          146 LQQQSYGLKNPYSS  159 (408)
Q Consensus       146 ~~gr~l~~~~~~s~  159 (408)
                        |+  .|++.|+.
T Consensus        90 --g~--~l~v~~a~   99 (111)
T 1x4h_A           90 --GR--QLKVDLAV   99 (111)
T ss_dssp             --SC--EEEEECCC
T ss_pred             --CE--EEEEEECC
Confidence              66  35555544

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=1e-15  Score=122.74  Aligned_cols=80  Identities=16%  Similarity=0.155  Sum_probs=68.4

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeE--------EEEEee-----cCccEEEEEECCHHHHHHHHHHhcCc
Q 046223           76 PPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVR--------GVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQ  142 (408)
Q Consensus        76 ~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~--------~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~  142 (408)
                      .......++|||+|||.++|+++|+++|++||.|.        .|++..     +++|||||+|.+.++|++|++.|||.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A            9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            35566789999999999999999999999999998        587765     34899999999999999999999998


Q ss_pred             cccccccccceeccccC
Q 046223          143 HMQLQQQSYGLKNPYSS  159 (408)
Q Consensus       143 ~i~~~gr~l~~~~~~s~  159 (408)
                      .|.  |+.  |++.++.
T Consensus        89 ~~~--g~~--l~V~~a~  101 (113)
T 2cpe_A           89 DFQ--GSK--LKVSLAR  101 (113)
T ss_dssp             EET--TEE--CEEECSS
T ss_pred             ccC--CCE--EEEEECC
Confidence            876  663  5555544

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=6.5e-16  Score=121.56  Aligned_cols=78  Identities=15%  Similarity=0.278  Sum_probs=67.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ...+.++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|||..|.  |+  .
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~--~   83 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF--GR--T   83 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEET--TE--E
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--Cc--E
Confidence            345688999999999999999999999999999999875     36999999999999999999999998876  66  4


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.|+.
T Consensus        84 l~V~~a~   90 (102)
T 2cqb_A           84 IRVNLAK   90 (102)
T ss_dssp             EEEEECC
T ss_pred             EEEEeCC
Confidence            5555544

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.3e-15  Score=119.75  Aligned_cols=78  Identities=13%  Similarity=0.212  Sum_probs=67.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ...+.++|||+|||.++|+++|+++|++||.|..|++.+     .++|||||+|.+.++|++|++.|||..|.  |+.  
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~--   83 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD--GRQ--   83 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTT--SCC--
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEEC--CeE--
Confidence            344678999999999999999999999999999999976     35899999999999999999999998876  663  


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.|+.
T Consensus        84 l~v~~a~   90 (102)
T 1x5s_A           84 IRVDQAG   90 (102)
T ss_dssp             CEEEEEE
T ss_pred             EEEEECC
Confidence            5555544

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.62  E-value=4.5e-16  Score=122.06  Aligned_cols=76  Identities=14%  Similarity=0.154  Sum_probs=66.0

Q ss_pred             CCCCCEEEEcCCCC------CCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccc
Q 046223           79 TGPTRTLVLSYVPG------DVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQ  147 (408)
Q Consensus        79 ~~~~rtlfV~nLp~------~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~  147 (408)
                      ...+++|||+|||.      ++++++|+++|++||.|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  
T Consensus         3 ~~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~--   80 (100)
T 3ns6_A            3 LGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD--   80 (100)
T ss_dssp             SCGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSS--
T ss_pred             CCcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccC--
Confidence            34578999999999      999999999999999999999875     46899999999999999999999998876  


Q ss_pred             c-cccceecccc
Q 046223          148 Q-QSYGLKNPYS  158 (408)
Q Consensus       148 g-r~l~~~~~~s  158 (408)
                      | +.  +++.++
T Consensus        81 g~r~--l~V~~a   90 (100)
T 3ns6_A           81 LKHR--LFLYTM   90 (100)
T ss_dssp             SSCB--CEEEES
T ss_pred             CCeE--EEEEEC
Confidence            5 63  455443

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.4e-16  Score=121.07  Aligned_cols=75  Identities=16%  Similarity=0.253  Sum_probs=68.4

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ..++|||+|||.++++++|+++|++||.|..+.     .++.++|||||+|.+.++|++|++.|||..+.|+.|++.+++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            358999999999999999999999999999883     456779999999999999999999999999999999877654

>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=99.62  E-value=2.7e-16  Score=123.32  Aligned_cols=77  Identities=19%  Similarity=0.317  Sum_probs=68.8

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec------cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR------ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~------~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ...++|||+||+.++++++|+++|++|| |.+++      .++.++|||||+|.+.++|.+|+ .|||..|+|+.|+|++
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEe
Confidence            4469999999999999999999999999 99883      35678999999999999999999 8999999999999999


Q ss_pred             ecCCC
Q 046223          300 SRPGG  304 (408)
Q Consensus       300 a~~~~  304 (408)
                      ++++.
T Consensus        95 a~~~~   99 (100)
T 2j76_E           95 ADQAQ   99 (100)
T ss_dssp             CCCSC
T ss_pred             ccCCC
Confidence            97653

>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=99.62  E-value=4.4e-16  Score=122.16  Aligned_cols=76  Identities=20%  Similarity=0.340  Sum_probs=62.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec------CccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL------MEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~------~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      .....++|||+|||.++|+++|+++|++|| |.+|++.+.      ++|||||+|.+.++|++|+ .|||..|.  |+. 
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~--g~~-   89 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG--NRR-   89 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBT--TBC-
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEEC--CeE-
Confidence            345679999999999999999999999999 999998753      4899999999999999999 89998876  663 


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                       +++.++.
T Consensus        90 -l~V~~a~   96 (100)
T 2j76_E           90 -IRVDVAD   96 (100)
T ss_dssp             -CCCEECC
T ss_pred             -EEEEecc
Confidence             4554443

>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=99.62  E-value=9.7e-16  Score=117.41  Aligned_cols=74  Identities=12%  Similarity=0.181  Sum_probs=61.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      ..+..+|||+|||+++||++|+++|++||.|.+|++.++++|||||+|.+.++|+    .|+|..+.+.++  .+.+.++
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~----~~~~~~~~~~g~--~v~v~~a   81 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQ----SLCGEDLIIKGI--SVHISNA   81 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHH----HHTTCEEEETTE--EEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHH----HHcCCCcccCCE--EEEEEEc
Confidence            3457899999999999999999999999999999999889999999999999998    367777766666  4444443

>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=99.62  E-value=2.1e-15  Score=121.55  Aligned_cols=77  Identities=13%  Similarity=0.230  Sum_probs=67.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ....++|||+|||.++|+++|+++|++||.|..|.+..    +++|||||+|.+.++|++|++.|||..|.  |+  .|+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~--g~--~l~   79 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLH--GK--AIK   79 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCS--SS--BCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEEC--CE--EEE
Confidence            34678999999999999999999999999999999876    35899999999999999999999998876  66  456


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.++.
T Consensus        80 V~~a~   84 (116)
T 2fy1_A           80 VEQAK   84 (116)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            65554

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=1.8e-15  Score=121.47  Aligned_cols=79  Identities=15%  Similarity=0.100  Sum_probs=67.8

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ....++++|||+|||.++|+++|+++|++||.|..|++.+    +++|||||+|.+.++|++|++.|||..|.  |+.  
T Consensus        10 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~--   85 (114)
T 2do0_A           10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLF--DRP--   85 (114)
T ss_dssp             CCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEET--TEE--
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC--CCE--
Confidence            3445688999999999999999999999999999999876    34899999999999999999999998876  664  


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.++.
T Consensus        86 l~v~~a~   92 (114)
T 2do0_A           86 MHVKMDE   92 (114)
T ss_dssp             CEEEECS
T ss_pred             EEEEEcc
Confidence            4554443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=5.9e-16  Score=120.33  Aligned_cols=76  Identities=12%  Similarity=0.299  Sum_probs=66.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEE-EEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGV-QMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v-~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      .++++|||+|||.++|+++|+++|++||.|..| ++.+     .++|||||+|.+.++|++|++.|||..|.  |+.  |
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~--l   78 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLC--NRP--I   78 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEET--TEE--C
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEEC--CEE--E
Confidence            467899999999999999999999999999998 8876     35899999999999999999999998876  664  5


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.|+.
T Consensus        79 ~v~~a~   84 (96)
T 1x5t_A           79 TVSYAF   84 (96)
T ss_dssp             EEEESC
T ss_pred             EEEEec
Confidence            555544

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.62  E-value=2e-15  Score=125.80  Aligned_cols=75  Identities=27%  Similarity=0.491  Sum_probs=69.0

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||..+++++|+++|++||.|..++     .++..+|||||+|.+.++|++|++.|||..|+|+.|+|++|
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            4569999999999999999999999999999983     45678999999999999999999999999999999999986

>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=99.62  E-value=1.4e-15  Score=120.77  Aligned_cols=72  Identities=18%  Similarity=0.205  Sum_probs=64.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ...+.++|||+|||.++|+++|+++|++||.|..|.+..    +++|||||+|.+.++|++|++.|||..|.  |+.|
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l  100 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLD--GRPM  100 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeC--CcEE
Confidence            445689999999999999999999999999999999885    35899999999999999999999998876  6643

>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=99.62  E-value=8.8e-16  Score=119.58  Aligned_cols=78  Identities=17%  Similarity=0.336  Sum_probs=67.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHH----HHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVR----RDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~----~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ...++++|||+|||.++++++|+    ++|++||.|..|.+.+  +++|||||+|.+.++|++|++.|||..|.  |+  
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~--   79 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFY--DK--   79 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEET--TE--
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEEC--Cc--
Confidence            34568999999999999999999    9999999999998875  56899999999999999999999998875  66  


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                      .+++.|+.
T Consensus        80 ~l~v~~a~   87 (97)
T 1nu4_A           80 PMRIQYAK   87 (97)
T ss_dssp             ECEEEECS
T ss_pred             EEEEEEcc
Confidence            45555554

>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=99.62  E-value=1e-15  Score=123.25  Aligned_cols=78  Identities=19%  Similarity=0.471  Sum_probs=71.6

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec--cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~--~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ..++|||+|||..+++++|+++|+.||.|..+.  ..+.++|||||+|.+.++|.+|++.|||..++|+.|+|.|+++..
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANR   86 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCh
Confidence            358999999999999999999999999999984  346678999999999999999999999999999999999998654

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

Probab=99.62  E-value=1.8e-15  Score=116.65  Aligned_cols=76  Identities=16%  Similarity=0.229  Sum_probs=66.5

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ......++|||+|||.++|+++|+++|++||.|..|.+.   ++||||+|.+.++|++|++.|||..|.  |+  .+++.
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~--g~--~l~V~   77 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQ--GK--RMHVQ   77 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEET--TE--EEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeC--Cc--EEEEE
Confidence            345578999999999999999999999999999999987   679999999999999999999998876  66  45555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        78 ~a~   80 (92)
T 2dgt_A           78 LST   80 (92)
T ss_dssp             ESS
T ss_pred             Ecc
Confidence            544

>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=99.62  E-value=1.3e-15  Score=121.55  Aligned_cols=79  Identities=11%  Similarity=0.244  Sum_probs=67.9

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....++++|||+|||.++|+++|+++|++||.|..|.+..     .++|||||+|.+.++|++|++.|||..|.  |+. 
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~-   97 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM--GQT-   97 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEET--TEE-
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEEC--CcE-
Confidence            3455679999999999999999999999999999999875     34899999999999999999999998876  663 


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                       |++.|+.
T Consensus        98 -l~V~~a~  104 (110)
T 1oo0_B           98 -IQVDWCF  104 (110)
T ss_dssp             -CEEEESE
T ss_pred             -EEEEEcc
Confidence             5555543

>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=99.62  E-value=1.6e-15  Score=115.74  Aligned_cols=73  Identities=16%  Similarity=0.297  Sum_probs=64.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee------cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ..++|||+|||.++|+++|+++|++||.|..|.+..      +++|||||+|.+.++|++|++.|||..|.  |+.  ++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~--l~   78 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQID--GQE--IT   78 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEET--TEE--CE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeEC--CeE--EE
Confidence            468999999999999999999999999999998865      26999999999999999999999998876  664  44


Q ss_pred             ccc
Q 046223          155 NPY  157 (408)
Q Consensus       155 ~~~  157 (408)
                      +.+
T Consensus        79 v~~   81 (88)
T 4a8x_A           79 ATA   81 (88)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            443

>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=99.62  E-value=1.5e-15  Score=118.13  Aligned_cols=76  Identities=13%  Similarity=0.179  Sum_probs=66.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHH----HHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           80 GPTRTLVLSYVPGDVSETIVR----RDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~----~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....+|||+|||.++++++|+    ++|++||.|.+|++..  ..+|||||+|.+.++|++|++.|||..|.  ||  .|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~--gr--~l   82 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIG--SK--KI   82 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEET--TE--EE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEEC--Ce--EE
Confidence            356799999999999999999    9999999999999985  23899999999999999999999998876  77  45


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.++.
T Consensus        83 ~V~~a~   88 (96)
T 2dgx_A           83 LVSLAT   88 (96)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            665544

>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=99.61  E-value=1.7e-15  Score=120.71  Aligned_cols=77  Identities=14%  Similarity=0.243  Sum_probs=67.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      .....++|||+|||.++|+++|+++|++||.|..|++.+. +|||||+|.+.++|++|++.|||..|.  |+  .|++.|
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~afV~f~~~~~a~~A~~~l~g~~~~--g~--~l~v~~   95 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIE--GH--VVKCYW   95 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEET--TE--ECEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHcCCCEEC--Cc--EEEEEe
Confidence            3446789999999999999999999999999999999864 999999999999999999999998876  66  455655


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus        96 a~   97 (109)
T 1x4g_A           96 GK   97 (109)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.61  E-value=1.6e-15  Score=119.86  Aligned_cols=78  Identities=22%  Similarity=0.239  Sum_probs=70.0

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCcee-e----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKE-L----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~-v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ....+|||+|||+++++++|+++|+.||.|.. |    ..+++++|||||+|.+.++|++|++. |+..++|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEEC
Confidence            44689999999999999999999999999876 5    24678899999999999999999997 999999999999998


Q ss_pred             cCCC
Q 046223          301 RPGG  304 (408)
Q Consensus       301 ~~~~  304 (408)
                      ....
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            6544

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=2.7e-15  Score=116.88  Aligned_cols=77  Identities=14%  Similarity=0.226  Sum_probs=64.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEe-ecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQME-RLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~-~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ....+++|||+|||.++|+++|+++|++||.|. +.++ .+++|||||+|.+.++|++|++.|||..|.  |+.  |++.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~--l~V~   89 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLG--TDT--LRVA   89 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSS--SSC--CEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEEC--CcE--EEEE
Confidence            345678999999999999999999999999996 4444 367999999999999999999999998876  663  5555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      ++.
T Consensus        90 ~a~   92 (97)
T 2e5j_A           90 LAR   92 (97)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=2.2e-15  Score=118.96  Aligned_cols=77  Identities=17%  Similarity=0.214  Sum_probs=66.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhc-cCCeEEEEEeec----CccEEEEEECCHHHHHHHHHHhcCcc-ccccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEV-FGEVRGVQMERL----MEGIVTVHFYDLRHAEMAFKEIREQH-MQLQQQSYG  152 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~-~G~V~~v~~~~~----~kG~afV~F~~~~~A~~Ai~~lng~~-i~~~gr~l~  152 (408)
                      ..+.++|||+|||.++|+++|+++|++ ||.|..|++.+.    ++|||||+|.+.++|++|++.|||.. |.  |+  .
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~--g~--~   81 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLG--SK--P   81 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSS--SS--C
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccC--CE--e
Confidence            346789999999999999999999999 999999998763    69999999999999999999999988 65  66  3


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.++.
T Consensus        82 l~v~~a~   88 (104)
T 2dhg_A           82 VRLSVAI   88 (104)
T ss_dssp             CCCCBCC
T ss_pred             EEEEEcc
Confidence            5555543

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.61  E-value=1.3e-15  Score=120.56  Aligned_cols=69  Identities=16%  Similarity=0.254  Sum_probs=62.7

Q ss_pred             CCCCCCCEEEEcCCCCCC------CHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           77 PSTGPTRTLVLSYVPGDV------SETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~v------te~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      .....+++|||+|||.++      |+++|+++|++||.|..|.+.+   +++|||||+|.+.++|++|++.|||..|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~   87 (105)
T 2nlw_A           10 EADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD   87 (105)
T ss_dssp             SCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECS
T ss_pred             CCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccC
Confidence            445567899999999999      7899999999999999999875   46899999999999999999999998876

>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=99.61  E-value=8.5e-16  Score=122.87  Aligned_cols=76  Identities=13%  Similarity=0.198  Sum_probs=66.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      ....++|||+|||.++|+++|+++|++||.|..|.+. .++|||||+|.+.++|++|++.|||..|.  |+  .|++.|+
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~--~l~V~~a   81 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFH--HV--PLYLEWA   81 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSS--SS--BCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEeCCHHHHHHHHHHhCCCEEC--Ce--EEEEEEC
Confidence            3456899999999999999999999999999999887 48999999999999999999999998876  66  4556565


Q ss_pred             C
Q 046223          159 S  159 (408)
Q Consensus       159 ~  159 (408)
                      .
T Consensus        82 ~   82 (111)
T 1whx_A           82 P   82 (111)
T ss_dssp             E
T ss_pred             C
Confidence            4

>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=99.61  E-value=2.1e-15  Score=120.00  Aligned_cols=76  Identities=22%  Similarity=0.338  Sum_probs=68.8

Q ss_pred             CCceEEE--cCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCcee-----CCeEEEEEE
Q 046223          227 NQGTIVV--FNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI-----YGKHVVIEF  299 (408)
Q Consensus       227 ~~~~l~V--~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~-----~g~~l~v~~  299 (408)
                      +.++|||  +||++++++++|+++|++||.|.+|... ..+|||||+|.+.++|++|++.|||+++     .|+.|.|.|
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~-~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~  102 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF  102 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEe
Confidence            3588999  7799999999999999999999998643 4689999999999999999999999998     689999999


Q ss_pred             ecCC
Q 046223          300 SRPG  303 (408)
Q Consensus       300 a~~~  303 (408)
                      ++..
T Consensus       103 a~~~  106 (114)
T 2cq2_A          103 VEKV  106 (114)
T ss_dssp             ESCC
T ss_pred             cccC
Confidence            9754

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.61  E-value=1.8e-15  Score=124.74  Aligned_cols=78  Identities=10%  Similarity=0.241  Sum_probs=66.2

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEE--EEEee-----cCccEEEEEECCHHHHHHHHHHhcCc----ccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRG--VQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQ----HMQ  145 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~--v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~----~i~  145 (408)
                      .....+++|||+|||+++||++|+++|++||.|..  |++++     +++|||||+|.+. +|.+|++.|||.    .|.
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~   96 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTID   96 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGG
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCC
Confidence            45567899999999999999999999999999976  88775     4599999999999 999999999998    654


Q ss_pred             ccccccceeccccC
Q 046223          146 LQQQSYGLKNPYSS  159 (408)
Q Consensus       146 ~~gr~l~~~~~~s~  159 (408)
                        ||.  |+|.|+.
T Consensus        97 --gr~--l~V~~a~  106 (131)
T 2m2b_A           97 --GKT--INVEFAK  106 (131)
T ss_dssp             --GCC--CCCEECC
T ss_pred             --CEE--EEEEECC
Confidence              774  4444543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.61  E-value=1.8e-15  Score=122.40  Aligned_cols=77  Identities=13%  Similarity=0.102  Sum_probs=69.1

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCC---ceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGP---VKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE  298 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~---v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  298 (408)
                      ....+|||+|||+++|+++|+++|+.||.   |..|+    ..++++|||||+|.+.++|++|++ |||..|+|+.|+|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   93 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEE
Confidence            34689999999999999999999999998   66662    347789999999999999999999 99999999999999


Q ss_pred             EecCC
Q 046223          299 FSRPG  303 (408)
Q Consensus       299 ~a~~~  303 (408)
                      ++..+
T Consensus        94 ~a~~~   98 (118)
T 2db1_A           94 KSHRT   98 (118)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            98654

>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=99.61  E-value=3.6e-15  Score=119.75  Aligned_cols=80  Identities=18%  Similarity=0.329  Sum_probs=71.5

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCcee--------CC
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEI--------YG  292 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~--------~g  292 (408)
                      ....++|||+|||.++++++|+++|+.||.|..++    .++.++|||||+|.+.++|++|++.|||..|        .+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            34568999999999999999999999999999883    3567789999999999999999999999999        57


Q ss_pred             eEEEEEEecCCC
Q 046223          293 KHVVIEFSRPGG  304 (408)
Q Consensus       293 ~~l~v~~a~~~~  304 (408)
                      +.|.|.|++++.
T Consensus       102 ~~l~v~~a~p~~  113 (114)
T 1x5o_A          102 EPLLCKFSGPSS  113 (114)
T ss_dssp             SCBEEEECCCSC
T ss_pred             CceeEEccCCCC
Confidence            889999998653

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=2.7e-15  Score=116.55  Aligned_cols=79  Identities=13%  Similarity=0.196  Sum_probs=70.4

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec--cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~--~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ...++|||+|||+++++++|+++|++||.|..++  ......+.|||+|.+.++|++|++.|||..|+|+.|+|++++++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   92 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE   92 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCC
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCcc
Confidence            3458999999999999999999999999999983  33345566999999999999999999999999999999999876


Q ss_pred             C
Q 046223          304 G  304 (408)
Q Consensus       304 ~  304 (408)
                      .
T Consensus        93 ~   93 (96)
T 2e44_A           93 M   93 (96)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.61  E-value=1.4e-15  Score=121.58  Aligned_cols=80  Identities=11%  Similarity=0.110  Sum_probs=68.8

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHH---HHhhccCCeEEEEEee--------cCccEEEEEECCHHHHHHHHHHhcCccc
Q 046223           76 PPSTGPTRTLVLSYVPGDVSETIVR---RDLEVFGEVRGVQMER--------LMEGIVTVHFYDLRHAEMAFKEIREQHM  144 (408)
Q Consensus        76 ~~~~~~~rtlfV~nLp~~vte~~L~---~~F~~~G~V~~v~~~~--------~~kG~afV~F~~~~~A~~Ai~~lng~~i  144 (408)
                      .......++|||+|||+++++++|+   ++|++||+|..|.+.+        .++|||||+|.+.++|++|++.|||..|
T Consensus         9 ~~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   88 (111)
T 2cpi_A            9 SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV   88 (111)
T ss_dssp             CCCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             cccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEE
Confidence            3445567899999999999999999   9999999999999875        2358999999999999999999999987


Q ss_pred             cccccccceeccccC
Q 046223          145 QLQQQSYGLKNPYSS  159 (408)
Q Consensus       145 ~~~gr~l~~~~~~s~  159 (408)
                      .  |+  .|++.|+.
T Consensus        89 ~--gr--~l~V~~a~   99 (111)
T 2cpi_A           89 D--GR--TLKASLGT   99 (111)
T ss_dssp             T--TE--EEEEESCC
T ss_pred             C--CE--EEEEEecc
Confidence            6  77  46666655

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=2.7e-15  Score=116.14  Aligned_cols=76  Identities=24%  Similarity=0.296  Sum_probs=66.3

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      .++|||+|||.++++++|+++|++||.|.+|........||||+|.+.++|++|++ |||..|+|+.|+|+++.++.
T Consensus         8 ~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~   83 (94)
T 2e5g_A            8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKE   83 (94)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCC
Confidence            47999999999999999999999999999983221111299999999999999999 99999999999999886554

>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=99.60  E-value=2e-16  Score=121.55  Aligned_cols=75  Identities=25%  Similarity=0.416  Sum_probs=66.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ++|||+|||.++++++|+++|++||.|..++     .++.++|||||+|.+.+ |.+|++.|||..++|+.|+|++|.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            6899999999999999999999999999883     34778999999999999 99999999999999999999999775


Q ss_pred             C
Q 046223          304 G  304 (408)
Q Consensus       304 ~  304 (408)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=4.2e-15  Score=112.40  Aligned_cols=73  Identities=16%  Similarity=0.196  Sum_probs=63.3

Q ss_pred             CCCE-EEEcCCCCCCCHHH----HHHHhhcc-CCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           81 PTRT-LVLSYVPGDVSETI----VRRDLEVF-GEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        81 ~~rt-lfV~nLp~~vte~~----L~~~F~~~-G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ++.| |||+|||+++++++    |+++|++| |+|.+|     ..|+|||+|.+.++|++|++.|||..|.  ||  .++
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-----tgG~AfV~F~~~esA~~A~~~l~G~~l~--gr--~i~   77 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-----TGCSAILRFINQDSAERAQKRMENEDVF--GN--RII   77 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-----CTTCEEEEESSHHHHHHHHHHHTTCCSS--SS--CCE
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-----ecCEEEEEECCHHHHHHHHHHhcCCccC--Cc--eEE
Confidence            4666 99999999999998    55899999 599998     2499999999999999999999999987  77  577


Q ss_pred             ccccCccc
Q 046223          155 NPYSSGLM  162 (408)
Q Consensus       155 ~~~s~~~s  162 (408)
                      +.|+...+
T Consensus        78 v~~A~~~s   85 (96)
T 2diu_A           78 VSFTPKNR   85 (96)
T ss_dssp             EESSCCSC
T ss_pred             EEecCCCc
Confidence            77877554

>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=99.60  E-value=1.4e-15  Score=122.28  Aligned_cols=78  Identities=9%  Similarity=0.155  Sum_probs=69.8

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCc-eee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPV-KEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v-~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ....+|||+|||+++|+++|+++|+.||.| ..|    ..++.++|||||+|.+.++|++|++. ||..|+|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a   91 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVV   91 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEEC
Confidence            446899999999999999999999999999 555    23577899999999999999999996 999999999999999


Q ss_pred             cCCC
Q 046223          301 RPGG  304 (408)
Q Consensus       301 ~~~~  304 (408)
                      .++.
T Consensus        92 ~~~~   95 (114)
T 2cpy_A           92 TLED   95 (114)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            7654

>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=99.60  E-value=2.6e-15  Score=118.34  Aligned_cols=75  Identities=16%  Similarity=0.345  Sum_probs=65.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ...+.++|||+|||.++|+++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|||..|.  ++  .|++.|
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~--g~--~l~v~~   79 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLE--GE--NIEIVF   79 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEET--TE--EEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccC--CC--EEEEEE
Confidence            34467899999999999999999999999999999886   789999999999999999999998876  66  455555


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus        80 a~   81 (103)
T 2dgu_A           80 AK   81 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

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

Probab=99.60  E-value=2.5e-15  Score=115.33  Aligned_cols=74  Identities=16%  Similarity=0.221  Sum_probs=65.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      ....++|||+|||.++|+++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..|.  |+  .+++.++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~--g~--~l~v~~a   78 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVK--GK--RINVELS   78 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEET--TE--ECEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEEC--Cc--EEEEEEC
Confidence            4567899999999999999999999999999999987   679999999999999999999998876  66  3555554


Q ss_pred             C
Q 046223          159 S  159 (408)
Q Consensus       159 ~  159 (408)
                      .
T Consensus        79 ~   79 (90)
T 2dnp_A           79 T   79 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.60  E-value=1.8e-15  Score=121.61  Aligned_cols=77  Identities=17%  Similarity=0.243  Sum_probs=66.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      .....++|||+|||.++|+++|+++|++||.|..|++..     .++|||||+|.+.++|++|+ .|||..|.  |+.  
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~~--   95 (114)
T 2cq4_A           21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLL--GVP--   95 (114)
T ss_dssp             THHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEET--TEE--
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeC--CeE--
Confidence            345678999999999999999999999999999999974     46899999999999999999 99998876  663  


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.++.
T Consensus        96 l~V~~a~  102 (114)
T 2cq4_A           96 IIVQASQ  102 (114)
T ss_dssp             EEEEEHH
T ss_pred             EEEEecC
Confidence            5554443

>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=99.60  E-value=3e-15  Score=126.39  Aligned_cols=79  Identities=20%  Similarity=0.245  Sum_probs=69.5

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ......++|||+|||+++|+++|+++|++||.|.+|++.+.++|||||+|.+.++|++|++.|||..|.  |+.  |++.
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~--l~v~  143 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLC--GCR--VRVE  143 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSS--SSC--CEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEEC--CeE--EEEE
Confidence            344567999999999999999999999999999999999888999999999999999999999998875  673  5555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus       144 ~a~  146 (150)
T 2i2y_A          144 LSN  146 (150)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.60  E-value=5.6e-16  Score=115.23  Aligned_cols=71  Identities=24%  Similarity=0.305  Sum_probs=65.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ++|||+|||.++++++|+++|++||.|..+.     .++.++|||||+|.+.++|++|++.++ ..++|+.|+|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            4799999999999999999999999998883     356779999999999999999999999 9999999999987

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=3e-15  Score=118.41  Aligned_cols=78  Identities=13%  Similarity=0.194  Sum_probs=66.8

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....+.++|||+|||.++|+++|+++|++||+|..|++.+     .++|||||+|.+.++|++|++. ++..|.  |+  
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~--g~--   85 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLD--GR--   85 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEET--TE--
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeEC--CE--
Confidence            4456789999999999999999999999999999999876     3479999999999999999998 987766  66  


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                      .|++.++.
T Consensus        86 ~l~V~~a~   93 (105)
T 2dh8_A           86 NIDPKPCT   93 (105)
T ss_dssp             EEBCCCSC
T ss_pred             EEEEEEcc
Confidence            45555544

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

Probab=99.60  E-value=6.7e-15  Score=115.07  Aligned_cols=75  Identities=16%  Similarity=0.252  Sum_probs=65.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcc--CCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVF--GEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~--G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ...++++|||+|||.++|+++|+++|++|  |.|..|++.   +|||||+|.+.++|++|++.|||..|.  |+  .|++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~--g~--~l~v   83 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---RDYAFVHFSNREDAVEAMKALNGKVLD--GS--PIEV   83 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC---SSEEEEEESSHHHHHHHHHHHSSEEET--TE--EEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe---CCeEEEEeCCHHHHHHHHHHhCCCEeC--Cc--EEEE
Confidence            34567899999999999999999999999  999998774   899999999999999999999999876  66  4566


Q ss_pred             cccC
Q 046223          156 PYSS  159 (408)
Q Consensus       156 ~~s~  159 (408)
                      .|+.
T Consensus        84 ~~a~   87 (99)
T 2cpd_A           84 TLAK   87 (99)
T ss_dssp             ECCC
T ss_pred             EECC
Confidence            5554

>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=99.60  E-value=2.8e-15  Score=118.34  Aligned_cols=75  Identities=20%  Similarity=0.346  Sum_probs=64.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee------cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ..+.++|||+|||.++|+++|+++|+.|| |..|.+.+      +++|||||+|.+.++|++|+ .|||..|.  |+.  
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~~--   85 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG--NKR--   85 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEET--TEE--
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeC--CcE--
Confidence            34578999999999999999999999999 99999874      34899999999999999999 89998875  663  


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.++.
T Consensus        86 l~V~~a~   92 (104)
T 1wi8_A           86 IRVDVAD   92 (104)
T ss_dssp             CEEEECC
T ss_pred             EEEEEcc
Confidence            5555544

>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=99.60  E-value=2.5e-15  Score=114.53  Aligned_cols=73  Identities=15%  Similarity=0.211  Sum_probs=62.1

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....+.++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++ +++..|.  |+.|
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~--g~~i   82 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLD--GRVI   82 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEET--TEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEEC--CEEE
Confidence            4556789999999999999999999999999999999875     348999999999999999996 4676654  6644


Q ss_pred             c
Q 046223          152 G  152 (408)
Q Consensus       152 ~  152 (408)
                      .
T Consensus        83 ~   83 (87)
T 3s7r_A           83 D   83 (87)
T ss_dssp             E
T ss_pred             E
Confidence            3

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=4e-15  Score=119.89  Aligned_cols=78  Identities=15%  Similarity=0.178  Sum_probs=66.7

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           76 PPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        76 ~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      .......++|||+|||.++||++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|++ .|.  ++.
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~--g~~   87 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IID--GRK   87 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EET--TEE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCC--CEE
Confidence            34556789999999999999999999999999999999976     3589999999999999999999998 554  674


Q ss_pred             cceecccc
Q 046223          151 YGLKNPYS  158 (408)
Q Consensus       151 l~~~~~~s  158 (408)
                        |+|.++
T Consensus        88 --l~V~~a   93 (116)
T 2cqd_A           88 --ANVNLA   93 (116)
T ss_dssp             --CEEEES
T ss_pred             --EEEEEc
Confidence              455444

>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=99.59  E-value=4.7e-15  Score=113.58  Aligned_cols=75  Identities=20%  Similarity=0.310  Sum_probs=62.8

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCce--eCCeEEEEEEecCCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE--IYGKHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~--~~g~~l~v~~a~~~~  304 (408)
                      ...+|||+|||+++|+++|+++|++||.|.+++....++|||||+|.+.++|++    |+|..  +.|+.|.|.+++++.
T Consensus        10 ~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k~   85 (89)
T 3d2w_A           10 HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPKH   85 (89)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC---
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCCC
Confidence            358999999999999999999999999999997665689999999999999983    66665  459999999998765


Q ss_pred             C
Q 046223          305 H  305 (408)
Q Consensus       305 ~  305 (408)
                      .
T Consensus        86 ~   86 (89)
T 3d2w_A           86 N   86 (89)
T ss_dssp             -
T ss_pred             c
Confidence            3

>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=99.59  E-value=8.6e-16  Score=125.42  Aligned_cols=77  Identities=13%  Similarity=0.121  Sum_probs=70.0

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ....+|||+|||+++|+++|+++|+.||.|..+     ..++.++|||||+|.+.++|++|++ |||..|+|+.|+|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            345899999999999999999999999998763     3567789999999999999999999 9999999999999999


Q ss_pred             cCC
Q 046223          301 RPG  303 (408)
Q Consensus       301 ~~~  303 (408)
                      ..+
T Consensus       102 ~~~  104 (124)
T 1wel_A          102 TKK  104 (124)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            764

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

Probab=99.59  E-value=3.6e-15  Score=115.96  Aligned_cols=75  Identities=16%  Similarity=0.199  Sum_probs=64.1

Q ss_pred             CCCCCCEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           78 STGPTRTLVLSYVPG-DVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~-~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ...++++|||+|||. ++|+++|+++|++||.|..|.+.   +|||||+|.+.++|++|++.|||..+.  |+.  +++.
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~--l~V~   78 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIECESQEMNF--GKK--LILE   78 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE---TTEEEEEESCHHHHHHHHHHHTCSSCB--TTT--BCEE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCeeC--CcE--EEEE
Confidence            345688999999998 99999999999999999999884   899999999999999999999998876  664  4554


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      ++.
T Consensus        79 ~a~   81 (96)
T 2kvi_A           79 VSS   81 (96)
T ss_dssp             EEE
T ss_pred             EcC
Confidence            443

>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=99.59  E-value=6.5e-15  Score=117.50  Aligned_cols=74  Identities=18%  Similarity=0.248  Sum_probs=65.0

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           79 TGPTRTLVLSYVPGD-VSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~-vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ...+++|||+|||.+ +|+++|+++|++||.|..|.+   ++|||||+|.+.++|++|++.|||..|.  |+.  |++.|
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~--l~V~~   96 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLA--GQT--LDINM   96 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHHHTTCEET--TEE--CCEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEEC--CeE--EEEEE
Confidence            345689999999999 999999999999999999988   6899999999999999999999998876  663  55555


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus        97 a~   98 (110)
T 1wf1_A           97 AG   98 (110)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

>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=99.59  E-value=1e-15  Score=118.70  Aligned_cols=73  Identities=14%  Similarity=0.118  Sum_probs=62.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ..++|||+|||.++|+++|+++|++||.|..+.++.     +++|||||+|.+.++|++|++.|||..|.  ||.  +++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~--gr~--l~v   89 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIG--SRK--VKL   89 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEE--CEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeEC--CcE--EEE
Confidence            468999999999999999999999999998766654     45899999999999999999999998876  674  444


Q ss_pred             cc
Q 046223          156 PY  157 (408)
Q Consensus       156 ~~  157 (408)
                      .+
T Consensus        90 ~~   91 (95)
T 2ek1_A           90 SG   91 (95)
T ss_dssp             EC
T ss_pred             Ee
Confidence            43

>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=99.59  E-value=1.6e-15  Score=118.31  Aligned_cols=77  Identities=13%  Similarity=0.114  Sum_probs=64.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      .....++|||+|||.++|+++|+++|++||.|..+.++.     +++|||||+|.+.++|++|++.|||..|.  |+.  
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~--g~~--   86 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIG--SRK--   86 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEET--TEE--
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeC--CeE--
Confidence            344568999999999999999999999999998755543     35899999999999999999999998876  674  


Q ss_pred             eecccc
Q 046223          153 LKNPYS  158 (408)
Q Consensus       153 ~~~~~s  158 (408)
                      +++.++
T Consensus        87 l~V~~a   92 (98)
T 2cqp_A           87 VKLVLG   92 (98)
T ss_dssp             CEEEES
T ss_pred             EEEEEc
Confidence            455443

>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=99.59  E-value=3.8e-15  Score=121.89  Aligned_cols=79  Identities=14%  Similarity=0.299  Sum_probs=68.0

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....++++|||+|||.++|+++|+++|++||.|..|.+..     .++|||||+|.+.++|++|++.|||..|.  |+. 
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~-   93 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM--GQP-   93 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSS--SSB-
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeC--CeE-
Confidence            3445688999999999999999999999999999999875     34999999999999999999999998875  663 


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                       |++.|+.
T Consensus        94 -l~v~~a~  100 (126)
T 3ex7_B           94 -ISVDWCF  100 (126)
T ss_dssp             -CEEEESE
T ss_pred             -EEEEEec
Confidence             5555544

>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=99.59  E-value=1.8e-15  Score=125.01  Aligned_cols=77  Identities=12%  Similarity=0.080  Sum_probs=69.0

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCC---ceee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGP---VKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE  298 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~---v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  298 (408)
                      ....+|||+|||+++|+++|+++|+.||.   |..|    ...++++|||||+|.+.++|++|++ |||..|+|+.|+|.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVF  120 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            44689999999999999999999999999   6666    2347889999999999999999999 99999999999999


Q ss_pred             EecCC
Q 046223          299 FSRPG  303 (408)
Q Consensus       299 ~a~~~  303 (408)
                      ++..+
T Consensus       121 ~a~~~  125 (136)
T 2hgl_A          121 KSHRT  125 (136)
T ss_dssp             ECCHH
T ss_pred             ECChH
Confidence            98643

>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=99.59  E-value=1.9e-15  Score=118.89  Aligned_cols=76  Identities=13%  Similarity=0.199  Sum_probs=68.0

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ...+|||+|||+++|++||+++|+.||.+ .|    ..+++++|||||+|.+.++|++|++ +|+..|+|+.|+|.++..
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~~   91 (102)
T 1wez_A           14 TGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNST   91 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCC
Confidence            35899999999999999999999999954 66    2367889999999999999999995 899999999999999876


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      ..
T Consensus        92 ~~   93 (102)
T 1wez_A           92 AG   93 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            55

>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=99.59  E-value=3.1e-15  Score=114.36  Aligned_cols=74  Identities=11%  Similarity=0.146  Sum_probs=65.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      ...++|||+|||+++++++|+++|++| +|..|++. +++|||||+|.+.++|++|++.|||..+.  |+  .+++.++.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~--g~--~l~V~~a~   76 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFR--GK--DLIVQLQP   76 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEET--TE--EEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeEC--Cc--EEEEEEcC
Confidence            457899999999999999999999999 99999886 68999999999999999999999998876  67  35555554

>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=99.58  E-value=1.8e-15  Score=116.93  Aligned_cols=75  Identities=15%  Similarity=0.138  Sum_probs=63.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCC-eEEEEEeecCccEEEEEECCHHHHHHHHHHhcC-ccccccccccceecc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGE-VRGVQMERLMEGIVTVHFYDLRHAEMAFKEIRE-QHMQLQQQSYGLKNP  156 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~-V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng-~~i~~~gr~l~~~~~  156 (408)
                      ....++|||+|||.++|+++|+++|++||. |..+.+.  ++|||||+|.+.++|++|++.||| ..|.  |+  .+++.
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~--g~--~l~v~   78 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL--KSGYAFVDYPDQNWAIRAIETLSGKVELH--GK--IMEVD   78 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE--ETTEEEECCSCHHHHHHHHHHHTTTCEET--TE--ECEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc--CCCEEEEEECCHHHHHHHHHHccCCeeEC--CE--EEEEE
Confidence            346789999999999999999999999999 6666653  699999999999999999999999 7765  66  35555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        79 ~a~   81 (93)
T 2cqh_A           79 YSV   81 (93)
T ss_dssp             ECC
T ss_pred             Ecc
Confidence            544

>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=99.58  E-value=1.1e-15  Score=120.54  Aligned_cols=77  Identities=13%  Similarity=0.223  Sum_probs=66.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....++|||+|||.++++++|+++|++||.|..|++.+     .++|||||+|.+.++|++|++.|||..|.  |+.  +
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~--l   80 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFS--GRA--L   80 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCS--SSC--B
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeC--CcE--E
Confidence            34578999999999999999999999999999999875     33899999999999999999999998875  663  5


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.|+.
T Consensus        81 ~v~~a~   86 (104)
T 1p1t_A           81 RVDNAA   86 (104)
T ss_dssp             EEEETT
T ss_pred             EEEeCC
Confidence            555543

>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=99.58  E-value=8.4e-15  Score=117.61  Aligned_cols=69  Identities=16%  Similarity=0.246  Sum_probs=62.9

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ....+.++|||+|||.++|+++|+++|++||.|..|++.+    .++|||||+|.+.++|++|++.|||..|.
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~   92 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIK   92 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEc
Confidence            3445678999999999999999999999999999999876    35899999999999999999999999875

>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=99.58  E-value=2.3e-15  Score=121.20  Aligned_cols=76  Identities=17%  Similarity=0.225  Sum_probs=65.2

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeE-----EEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH-----VVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~-----l~v~~a~  301 (408)
                      ...+|||+|||+++++++|+++|++||.|..|.....  |||||+|.+.++|++|++.|||..|+|+.     |+|..+.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~   92 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   92 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCC
Confidence            3589999999999999999999999999999864332  99999999999999999999999999988     7777776


Q ss_pred             CCC
Q 046223          302 PGG  304 (408)
Q Consensus       302 ~~~  304 (408)
                      ++.
T Consensus        93 ~~~   95 (115)
T 3beg_B           93 PRS   95 (115)
T ss_dssp             ---
T ss_pred             CCC
Confidence            644

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.58  E-value=5e-15  Score=131.67  Aligned_cols=78  Identities=18%  Similarity=0.367  Sum_probs=72.2

Q ss_pred             CCceEEEcCCC-CCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          227 NQGTIVVFNLD-SGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp-~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ++++|||+||+ ..+++++|+++|++||.|.+|+.....+|||||+|.+.++|++|++.|||..+.|+.|+|.+++...
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~   81 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA   81 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCc
Confidence            35899999999 8999999999999999999997666678999999999999999999999999999999999997544

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.58  E-value=6e-15  Score=116.22  Aligned_cols=76  Identities=16%  Similarity=0.251  Sum_probs=64.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ...+.++|||+|||.++|+++|+++|++|| |..|++.+     +++|||||+|.+.++|++|+ .|||..|.  |+  .
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~--~   84 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLG--DR--S   84 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEET--TE--E
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeEC--Ce--E
Confidence            344678999999999999999999999997 99999876     34899999999999999999 89998876  66  3


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.++.
T Consensus        85 l~V~~a~   91 (103)
T 2dng_A           85 LRVDIAE   91 (103)
T ss_dssp             CEEEECC
T ss_pred             EEEEEec
Confidence            5555544

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.58  E-value=3.2e-15  Score=119.12  Aligned_cols=75  Identities=15%  Similarity=0.201  Sum_probs=59.8

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....+.++|||+|||.++|+++|+++|++||.|..|++.+     .++|||||+|.+.++|++|++.+ |..|  .|+.|
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l--~g~~l   96 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHEL--DSKTI   96 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEE--TTEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcC--CCEEE
Confidence            4556789999999999999999999999999999999875     35899999999999999999876 4554  47744


Q ss_pred             cee
Q 046223          152 GLK  154 (408)
Q Consensus       152 ~~~  154 (408)
                      .+.
T Consensus        97 ~V~   99 (109)
T 2rs2_A           97 DPK   99 (109)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            433

>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=99.58  E-value=4.6e-15  Score=113.50  Aligned_cols=73  Identities=14%  Similarity=0.186  Sum_probs=63.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ..++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|+ .|||..|.  |+.  +++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~--g~~--l~V   79 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFR--GRQ--IKV   79 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEET--TEE--CEE
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEEC--CcE--EEE
Confidence            468999999999999999999999999999999875     34999999999999999999 89998876  664  444


Q ss_pred             ccc
Q 046223          156 PYS  158 (408)
Q Consensus       156 ~~s  158 (408)
                      .++
T Consensus        80 ~~a   82 (89)
T 3ucg_A           80 IPK   82 (89)
T ss_dssp             EET
T ss_pred             EEc
Confidence            443

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.58  E-value=5.6e-15  Score=120.55  Aligned_cols=78  Identities=17%  Similarity=0.204  Sum_probs=68.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....+++|||+|||.++++++|+++|++||.|..|++.+    +++|||||+|.+.++|++|++.|||..|.  |+  .+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~--~l  106 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLD--GR--PM  106 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESS--SC--EE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEEC--Cc--EE
Confidence            445678999999999999999999999999999999876    36899999999999999999999998875  66  35


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.|+.
T Consensus       107 ~V~~a~  112 (124)
T 2kt5_A          107 DIQLVA  112 (124)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            555544

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.57  E-value=9.4e-15  Score=121.69  Aligned_cols=72  Identities=18%  Similarity=0.310  Sum_probs=64.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ...+.++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|||..|.  |+.|
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l  135 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF--GRTI  135 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEET--TEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEEC--CEEE
Confidence            345689999999999999999999999999999999875     35999999999999999999999998876  6643

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.57  E-value=1.4e-15  Score=125.96  Aligned_cols=83  Identities=25%  Similarity=0.356  Sum_probs=70.6

Q ss_pred             CCCCCCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccc
Q 046223           73 PLPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQ  147 (408)
Q Consensus        73 ~~p~~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~  147 (408)
                      ..++....+.++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|||..|.  
T Consensus        38 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~--  115 (135)
T 2lea_A           38 GRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD--  115 (135)
T ss_dssp             CCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSS--
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC--
Confidence            34455666789999999999999999999999999999999875     45899999999999999999999998876  


Q ss_pred             ccccceeccccC
Q 046223          148 QQSYGLKNPYSS  159 (408)
Q Consensus       148 gr~l~~~~~~s~  159 (408)
                      |+  .|+|.|+.
T Consensus       116 g~--~l~V~~a~  125 (135)
T 2lea_A          116 GR--ELRVQMAR  125 (135)
T ss_dssp             SS--CCEEEECC
T ss_pred             CE--EEEEEECC
Confidence            66  35555544

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.35  E-value=1.7e-16  Score=128.07  Aligned_cols=81  Identities=25%  Similarity=0.395  Sum_probs=72.8

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCcee--------e-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKE--------L-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG  292 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~--------v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g  292 (408)
                      .+.++|||+|||.++++++|+++|++||.|..        |     +.++.++|||||+|.+.++|++|++.|||..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            34689999999999999999999999999987        5     2456779999999999999999999999999999


Q ss_pred             eEEEEEEecCCCCC
Q 046223          293 KHVVIEFSRPGGHS  306 (408)
Q Consensus       293 ~~l~v~~a~~~~~~  306 (408)
                      +.|+|++++++...
T Consensus        85 ~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           85 NPIKVSFATRRADF   98 (116)
Confidence            99999999876543

>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=99.57  E-value=1.4e-15  Score=112.49  Aligned_cols=70  Identities=20%  Similarity=0.308  Sum_probs=64.3

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       230 ~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      +|||+|||.++++++|+++|++||.|..+.     .++.++|||||+|.+.++|++|++ +++..++|+.|+|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            589999999999999999999999999883     346789999999999999999999 5999999999999875

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=7.7e-15  Score=116.58  Aligned_cols=73  Identities=12%  Similarity=0.212  Sum_probs=66.4

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..+|||+|||+++|++||+++|+.| .|..|+    ..++++|||||+|.+.++|++|+ .|||..|+||.|+|..+..
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            4799999999999999999999999 787772    34778999999999999999999 6999999999999988864

>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=99.57  E-value=3.8e-15  Score=119.91  Aligned_cols=67  Identities=16%  Similarity=0.197  Sum_probs=59.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      ....+|||+|||+++|+++|+++|++||+|..|.+...  |||||+|.+.++|++||+.|||..|.  |+.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~--gr~   80 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFR--SHE   80 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCC--CTT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEEC--CcE
Confidence            35689999999999999999999999999999999854  99999999999999999999998876  553

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.56  E-value=3.1e-15  Score=116.27  Aligned_cols=79  Identities=20%  Similarity=0.246  Sum_probs=66.3

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ....+.++|||+|||.++|+++|+++|++||.|..+.....++|||||+|.+.++|++|++.|||..|.  |+.  +++.
T Consensus        11 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~--l~v~   86 (96)
T 1fjc_A           11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEID--GRS--VSLY   86 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEET--TEE--EEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--CeE--EEEE
Confidence            344578999999999999999999999999999888333366999999999999999999999998876  663  5555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      ++.
T Consensus        87 ~a~   89 (96)
T 1fjc_A           87 YTG   89 (96)
T ss_dssp             ECS
T ss_pred             EcC
Confidence            543

>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=99.56  E-value=5.4e-15  Score=117.72  Aligned_cols=76  Identities=14%  Similarity=0.163  Sum_probs=65.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCC-eEEEEEee------cCccEEEEEECCHHHHHHHHHHhc--Cccccccccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGE-VRGVQMER------LMEGIVTVHFYDLRHAEMAFKEIR--EQHMQLQQQS  150 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~-V~~v~~~~------~~kG~afV~F~~~~~A~~Ai~~ln--g~~i~~~gr~  150 (408)
                      .+.++|||+|||.++|+++|+++|++||. |..|.+..      +++|||||+|.+.++|++|++.|+  +..|.  |+ 
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~--g~-   82 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLW--GH-   82 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBT--TB-
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceec--CC-
Confidence            46789999999999999999999999998 99998872      569999999999999999999996  45654  66 


Q ss_pred             cceeccccC
Q 046223          151 YGLKNPYSS  159 (408)
Q Consensus       151 l~~~~~~s~  159 (408)
                       .+++.|+.
T Consensus        83 -~l~V~~a~   90 (109)
T 2dis_A           83 -QIAVDWAE   90 (109)
T ss_dssp             -CCEEEESC
T ss_pred             -eEEEEEcC
Confidence             45665554

>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=99.56  E-value=5.8e-15  Score=112.42  Aligned_cols=71  Identities=20%  Similarity=0.275  Sum_probs=63.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcc----C-------CeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVF----G-------EVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQ  147 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~----G-------~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~  147 (408)
                      ..+.++|||+|||.++|+++|+++|++|    |       .|.++++.+ ++|||||+|.+.++|++|+ .|||..|.  
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~-~kg~afV~f~~~~~a~~A~-~l~g~~~~--   78 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ-DKNFAFLEFRSVDETTQAM-AFDGIIFQ--   78 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECS-SSSEEEEEESSHHHHHHHG-GGTTCEET--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecC-CCcEEEEEcCCHHHHHHHH-hcCCCEEC--
Confidence            3567999999999999999999999999    8       999998874 5999999999999999999 99998876  


Q ss_pred             ccccce
Q 046223          148 QQSYGL  153 (408)
Q Consensus       148 gr~l~~  153 (408)
                      |+.|.+
T Consensus        79 g~~l~V   84 (87)
T 2hzc_A           79 GQSLKI   84 (87)
T ss_dssp             TEECEE
T ss_pred             CeEEEE
Confidence            664443

>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=99.56  E-value=2.1e-15  Score=119.83  Aligned_cols=77  Identities=13%  Similarity=0.069  Sum_probs=69.1

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCC---ceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGP---VKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE  298 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~---v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  298 (408)
                      ....+|||+|||+++|+++|+++|+.||.   |..|+    ..+.++|||||+|.+.++|++|++ |||..++|+.|+|.
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVY   87 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEE
Confidence            45689999999999999999999999988   77662    237789999999999999999999 99999999999999


Q ss_pred             EecCC
Q 046223          299 FSRPG  303 (408)
Q Consensus       299 ~a~~~  303 (408)
                      ++.++
T Consensus        88 ~a~~~   92 (107)
T 2lmi_A           88 EINNE   92 (107)
T ss_dssp             ECCHH
T ss_pred             ECCHH
Confidence            98754

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.56  E-value=3.2e-15  Score=110.54  Aligned_cols=65  Identities=15%  Similarity=0.157  Sum_probs=58.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      +|||+|||.++|+++|+++|++||.|..|.+.+     +++|||||+|.+.++|++|++ |+|..|.  |+.|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~--g~~l   70 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEIN--NKMV   70 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSS--SCCC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEEC--CEEE
Confidence            589999999999999999999999999998875     348999999999999999998 9998876  6643

>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=99.56  E-value=9e-15  Score=124.32  Aligned_cols=78  Identities=15%  Similarity=0.213  Sum_probs=67.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ...+.++|||+|||.++|+++|+++|++||+|..|.+..     .++|||||+|.+.++|++|++.|||..|.  ++  .
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~--~  110 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLD--DR--I  110 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEET--TE--E
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEEC--Ce--E
Confidence            345679999999999999999999999999999999875     35899999999999999999999998876  66  4


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |+|.|+.
T Consensus       111 l~V~~a~  117 (156)
T 1h2v_Z          111 IRTDWDA  117 (156)
T ss_dssp             CEEEEES
T ss_pred             EEEEECC
Confidence            5555554

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=2.5e-15  Score=111.64  Aligned_cols=69  Identities=17%  Similarity=0.258  Sum_probs=59.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ++|||+|||.++|+++|+++|++||+|..|.+.+     +++|||||+|.+.++|++|++.++ ..+.  |+.+.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~--g~~l~v~   74 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELD--SKTIDPK   74 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCS--SCCCEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccC--CEEEEEE
Confidence            4799999999999999999999999999998875     348999999999999999999888 5554  6644443

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=2.3e-14  Score=111.55  Aligned_cols=75  Identities=19%  Similarity=0.274  Sum_probs=65.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ...+.++|||+||  ++|+++|+++|++||+|..|.+. +++|||||+|.+.++|++|++.|||..|.  |+  .|++.|
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~--g~--~l~v~~   83 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTYEKMESADQAVAELNGTQVE--SV--QLKVNI   83 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHTTTEEET--TE--EEEEEC
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-CCCCEEEEEECCHHHHHHHHHHhCCCeEC--Ce--EEEEEE
Confidence            3446789999996  99999999999999999999886 68999999999999999999999998875  66  456655


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus        84 a~   85 (97)
T 1x5p_A           84 AR   85 (97)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>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=99.56  E-value=5.1e-15  Score=113.07  Aligned_cols=75  Identities=21%  Similarity=0.279  Sum_probs=65.3

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCc--eeCCeEEEEEEecCCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ--EIYGKHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~--~~~g~~l~v~~a~~~~  304 (408)
                      ..++|||+|||.++++++|+++|++||.|..++....++|||||+|.+.++|++|    ++.  .+.|+.|+|.+++++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~----~~~~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSL----CGEDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHT----TTCEEEETTEEEEEECCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHH----hcCCceeCCEEEEEEecCCCC
Confidence            3589999999999999999999999999999976556899999999999999754    444  5589999999998765


Q ss_pred             C
Q 046223          305 H  305 (408)
Q Consensus       305 ~  305 (408)
                      .
T Consensus        80 ~   80 (88)
T 1wf0_A           80 N   80 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=6.5e-15  Score=115.57  Aligned_cols=78  Identities=17%  Similarity=0.241  Sum_probs=63.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEe-ecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQME-RLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~-~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ...+.++|||+|||.++|+++|+++|++||.|.-+... .+++|||||+|.+.++|++|++.|||..|.  ++  .|++.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~--~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIE--GR--AIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEET--TE--EEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeC--Ce--EEEEE
Confidence            44568999999999999999999999999988332221 146999999999999999999999998876  66  45555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        87 ~a~   89 (101)
T 2fc9_A           87 LQG   89 (101)
T ss_dssp             ECS
T ss_pred             EcC
Confidence            554

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.56  E-value=4e-15  Score=116.81  Aligned_cols=77  Identities=9%  Similarity=0.033  Sum_probs=63.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEe----ecCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQME----RLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~----~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      .....++|||+|||.++|+++|+++|++||.|..+.+.    .+++|||||+|.+.++|++|++ |||..|.  |+  .|
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~--g~--~l   87 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVF--GN--EI   87 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBT--TB--CC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEEC--Cc--EE
Confidence            34467899999999999999999999999988772111    2569999999999999999998 9998876  66  35


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.++.
T Consensus        88 ~V~~a~   93 (101)
T 1fj7_A           88 KLEKPK   93 (101)
T ss_dssp             EEECCS
T ss_pred             EEEEcC
Confidence            555544

>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=99.56  E-value=2.7e-15  Score=135.58  Aligned_cols=77  Identities=14%  Similarity=0.177  Sum_probs=70.3

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCC--Cceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFG--PVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G--~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ...+|||+||++++|+++|+++|++||  .|++|+     .+++++|||||+|.+.++|++||+.|||..|.|+.|+|++
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            457999999999999999999999999  898883     4778899999999999999999999999999999999999


Q ss_pred             ecCC
Q 046223          300 SRPG  303 (408)
Q Consensus       300 a~~~  303 (408)
                      +++.
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8753

>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=99.56  E-value=2.1e-14  Score=113.09  Aligned_cols=77  Identities=17%  Similarity=0.229  Sum_probs=63.2

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....+.++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.  +..|.  |+. 
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~--g~~-   84 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMID--GRW-   84 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEET--TEE-
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc--CCeeC--CeE-
Confidence            4455678999999999999999999999999999999876     3489999999999999999983  54443  663 


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                       +++.++.
T Consensus        85 -l~v~~a~   91 (103)
T 2cqg_A           85 -CDCKLPN   91 (103)
T ss_dssp             -EEEECCC
T ss_pred             -EEEEecC
Confidence             4554543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=9.2e-15  Score=114.88  Aligned_cols=79  Identities=15%  Similarity=0.219  Sum_probs=63.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ....+.++|||+|||.++|+++|+++|+.|+.|..+....  +++|||||+|.+.++|++|++.|||..|.  |+  .|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~--~l~   85 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEID--GN--KVT   85 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET--TE--ECE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeEC--Ce--EEE
Confidence            4456789999999999999999999999987554443221  45899999999999999999999998876  66  456


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.|+.
T Consensus        86 V~~a~   90 (102)
T 2fc8_A           86 LDWAK   90 (102)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            65554

>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=99.55  E-value=1.4e-14  Score=114.40  Aligned_cols=72  Identities=17%  Similarity=0.138  Sum_probs=61.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEE-EEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRG-VQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~-v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      .....+|||+|||+++||++|+++|+.||.|.. |.+..    +++|||||+|.+.++|++|++. ++..|.  +|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~--gr~i~v   88 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIG--HRYIEI   88 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSS--SSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhC--CcEEEE
Confidence            345789999999999999999999999999987 77754    5699999999999999999987 887765  674333

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.55  E-value=6e-15  Score=119.25  Aligned_cols=75  Identities=20%  Similarity=0.114  Sum_probs=64.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCC---eEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGE---VRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~---V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....++|||+|||+++||++|+++|+.||.   |..|++..    +++|||||+|.+.++|++|++ |||..|.  +|. 
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~--gr~-   89 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMG--HRY-   89 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEET--TEE-
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeEC--CeE-
Confidence            446789999999999999999999999999   88888875    458999999999999999999 9998765  774 


Q ss_pred             ceecccc
Q 046223          152 GLKNPYS  158 (408)
Q Consensus       152 ~~~~~~s  158 (408)
                       |++.++
T Consensus        90 -i~V~~a   95 (118)
T 2db1_A           90 -IEVFKS   95 (118)
T ss_dssp             -EEEEEE
T ss_pred             -EEEEEC
Confidence             444443

>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=99.55  E-value=5.4e-15  Score=118.77  Aligned_cols=77  Identities=12%  Similarity=0.029  Sum_probs=65.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCe-EEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEV-RGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V-~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ...+.++|||+|||+++|+++|+++|+.||.| ..|++++    +++|||||+|.+.++|++|++. |+..|.  ||.  
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~--gr~--   85 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLN--GRE--   85 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEET--TEE--
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccC--CeE--
Confidence            44567999999999999999999999999999 7788875    4699999999999999999986 887765  774  


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.++.
T Consensus        86 i~v~~a~   92 (114)
T 2cpy_A           86 AFVHVVT   92 (114)
T ss_dssp             EEEEEEC
T ss_pred             EEEEECC
Confidence            4554443

>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=99.55  E-value=9.1e-15  Score=117.55  Aligned_cols=77  Identities=18%  Similarity=0.157  Sum_probs=64.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCe----EEEEEee-cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEV----RGVQMER-LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V----~~v~~~~-~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ..++++|||+|||.++|+++|+++|++||.|    ..+++.. +++|||||+|.+.++|++|++.|||..|.  |+  .|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~--g~--~l   97 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLY--GK--IL   97 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCS--SC--BC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeC--Cc--EE
Confidence            4467899999999999999999999999998    4555443 66999999999999999999999998875  66  45


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.|+.
T Consensus        98 ~v~~a~  103 (115)
T 2cpx_A           98 VIEFGK  103 (115)
T ss_dssp             EEEECC
T ss_pred             EEEEcc
Confidence            665554

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=1.1e-14  Score=111.90  Aligned_cols=75  Identities=19%  Similarity=0.168  Sum_probs=64.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ....++|||+|||.++|+++|+++|+.| .|..|++.+    +++|||||+|.+.++|++|++ |||..|.  ||.  ++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~--gr~--i~   80 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMG--GRY--IE   80 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEET--TEE--EE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeC--CcE--EE
Confidence            3467899999999999999999999999 899999876    348999999999999999999 9998876  673  45


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.++.
T Consensus        81 v~~a~   85 (91)
T 2dgw_A           81 VFREK   85 (91)
T ss_dssp             EEEES
T ss_pred             EEECC
Confidence            54443

>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=99.55  E-value=8.7e-14  Score=129.81  Aligned_cols=79  Identities=18%  Similarity=0.268  Sum_probs=69.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ...++++|||+|||.++|+++|+++|++||.|.+|++....+|||||+|.+.++|.+|++.|||..|. .|+  .|++.|
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-~g~--~l~v~~  279 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKIT-QNN--AMKISF  279 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeC-CCC--EEEEEE
Confidence            45568999999999999999999999999999999999766799999999999999999999998876 245  466666


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      ++
T Consensus       280 ak  281 (282)
T 3pgw_A          280 AK  281 (282)
T ss_pred             ec
Confidence            43

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=7.7e-15  Score=116.56  Aligned_cols=72  Identities=17%  Similarity=0.081  Sum_probs=62.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ......+|||+|||+++||++|+++|+.| .|..|+|..    +++|||||+|.+.++|++|+ .+|+..|.  ||.|.+
T Consensus        12 ~~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~--gr~i~V   87 (109)
T 2dnn_A           12 INPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMI--QRYVEV   87 (109)
T ss_dssp             CCHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEET--TEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeEC--CeEEEE
Confidence            34456899999999999999999999999 899999875    46999999999999999999 69998875  774433

>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=99.55  E-value=6.7e-15  Score=112.43  Aligned_cols=74  Identities=15%  Similarity=0.253  Sum_probs=62.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      ..+++|||+|||.++||++|+++|++||.|..|++.++++|||||+|.+.++|++    +++..+.+.++  .+++.++.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~----~~~~~~~~~g~--~l~v~~a~   76 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQS----LCGEDLIIKGI--SVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHH----TTTCEEEETTE--EEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHH----HhcCCceeCCE--EEEEEecC
Confidence            4579999999999999999999999999999999988889999999999999975    45556655565  45555543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=2.3e-14  Score=111.22  Aligned_cols=76  Identities=17%  Similarity=0.289  Sum_probs=64.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEE-Eee-cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQ-MER-LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~-~~~-~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ..+++|||+|||+++|+++|+++|++||.|..|+ +.. ...|.|||+|.+.++|++|++.|||..|.  |+.  +++.|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~--g~~--l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLE--NFT--LKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCS--SCB--CEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEEC--CcE--EEEEE
Confidence            4568999999999999999999999999999994 665 34667999999999999999999998876  673  55555


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus        89 a~   90 (96)
T 2e44_A           89 IP   90 (96)
T ss_dssp             CC
T ss_pred             cC
Confidence            44

>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=99.54  E-value=2.8e-15  Score=115.07  Aligned_cols=72  Identities=13%  Similarity=0.185  Sum_probs=62.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ++|||+|||.++++++|+++|++||+|.+|.+.+     +++|||||+|.+.+ |++|++.|||..+.  |+.  +++.+
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~--g~~--l~V~~   76 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFM--GRT--IRVTE   76 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCS--SSS--CSEEE
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEEC--CeE--EEEEE
Confidence            6899999999999999999999999999999875     45899999999999 99999999998876  664  45544


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus        77 a~   78 (90)
T 2ki2_A           77 AN   78 (90)
T ss_dssp             C-
T ss_pred             cC
Confidence            43

>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=99.54  E-value=8.7e-15  Score=115.06  Aligned_cols=71  Identities=17%  Similarity=0.176  Sum_probs=60.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....++|||+|||+++||++|+++|+.||.| .|++.+    +++|||||+|.+.++|++||+ +|+..|.  +|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~--gr~i~V   86 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQ--HRYVEL   86 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSS--SSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeEC--CcEEEE
Confidence            4456899999999999999999999999954 888875    458999999999999999995 7987765  674433

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.54  E-value=1.2e-14  Score=126.12  Aligned_cols=78  Identities=27%  Similarity=0.414  Sum_probs=71.5

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ...++|||+||+..+++++|+++|++||.|..|.    .++.++|||||+|.+.++|++|++.|||..|+|+.|+|+|+.
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            4568999999999999999999999999999883    246788999999999999999999999999999999999997


Q ss_pred             CC
Q 046223          302 PG  303 (408)
Q Consensus       302 ~~  303 (408)
                      ..
T Consensus       166 ~~  167 (177)
T 2f3j_A          166 SQ  167 (177)
T ss_dssp             SG
T ss_pred             CC
Confidence            54

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.54  E-value=1.3e-14  Score=110.46  Aligned_cols=70  Identities=24%  Similarity=0.431  Sum_probs=64.4

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcC----C-------CceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAF----G-------PVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~----G-------~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      .++|||+|||.++++++|+++|++|    |       .|.+++.. ..+|||||+|.+.++|++|+ .|||..++|+.|+
T Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~-~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   83 (87)
T 2hzc_A            6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   83 (87)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEC-SSSSEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEec-CCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEEE
Confidence            5899999999999999999999999    8       88888533 56999999999999999999 9999999999999


Q ss_pred             EEE
Q 046223          297 IEF  299 (408)
Q Consensus       297 v~~  299 (408)
                      |+.
T Consensus        84 V~r   86 (87)
T 2hzc_A           84 IRR   86 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            873

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.54  E-value=6.1e-15  Score=115.94  Aligned_cols=76  Identities=22%  Similarity=0.387  Sum_probs=69.3

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..++|||+|||.++++++|+++|+.||.|..++    .++.++|||||+|.+.++|++|++  +|..++|+.|.|.++.+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCc
Confidence            358999999999999999999999999999883    266789999999999999999999  99999999999999976


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      +.
T Consensus        86 ~~   87 (102)
T 2xs2_A           86 KQ   87 (102)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=99.54  E-value=6.7e-15  Score=121.62  Aligned_cols=72  Identities=19%  Similarity=0.111  Sum_probs=62.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCC---eEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGE---VRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~---V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....++|||+|||+++||++|+++|+.||.   |..|++.+    +++|||||+|.+.++|++|++ |||..|.  +|.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~--gr~i  117 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMG--HRYI  117 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESS--SSEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEEC--CEEE
Confidence            446789999999999999999999999999   78888875    458999999999999999999 9998876  7743


Q ss_pred             ce
Q 046223          152 GL  153 (408)
Q Consensus       152 ~~  153 (408)
                      .+
T Consensus       118 ~V  119 (136)
T 2hgl_A          118 EV  119 (136)
T ss_dssp             EE
T ss_pred             EE
Confidence            33

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.53  E-value=1.1e-14  Score=118.84  Aligned_cols=75  Identities=11%  Similarity=0.144  Sum_probs=64.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ...++|||+|||.++|+++|+++|++||.|..|++.+     .++|||||+|.+.++|++|+ .|||..|.  |+.  |+
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~~--l~  108 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFR--GRT--IK  108 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEET--TEE--CE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeEC--CeE--EE
Confidence            3578999999999999999999999999999999875     34999999999999999999 79998876  663  55


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.++.
T Consensus       109 V~~a~  113 (124)
T 2jwn_A          109 VLPKR  113 (124)
T ss_dssp             EEESS
T ss_pred             EEECC
Confidence            55543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=3e-14  Score=110.22  Aligned_cols=71  Identities=17%  Similarity=0.218  Sum_probs=59.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ....++|||+|||.++|+++|+++|++||.|.+|.+.+....||||+|.+.++|++|++ |||..|.  |+.|.
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~--g~~l~   75 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLG--GHRLR   75 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEET--TEECC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEEC--CEEEE
Confidence            34578999999999999999999999999999984443222299999999999999999 9998876  66433

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=8.2e-15  Score=118.94  Aligned_cols=75  Identities=13%  Similarity=0.117  Sum_probs=66.8

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCc----eee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPV----KEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v----~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ..+|||+|||+++|++||+++|+.||.|    ..|    ..+++++|||||+|.+.++|++|++. |+..|+||.|+|..
T Consensus        23 ~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~  101 (123)
T 2dha_A           23 QVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFR  101 (123)
T ss_dssp             CCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEE
Confidence            5899999999999999999999999975    344    24678899999999999999999995 99999999999998


Q ss_pred             ecCC
Q 046223          300 SRPG  303 (408)
Q Consensus       300 a~~~  303 (408)
                      +.++
T Consensus       102 a~~~  105 (123)
T 2dha_A          102 STAA  105 (123)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8643

>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=99.53  E-value=2.4e-14  Score=122.88  Aligned_cols=79  Identities=11%  Similarity=0.219  Sum_probs=67.3

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec-----CccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL-----MEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~-----~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....++++|||+|||.++|+++|+++|++||.|..|.+...     ++|||||+|.+.++|++||+.|||..|.  |+. 
T Consensus        67 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~-  143 (165)
T 1rk8_A           67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM--GQT-  143 (165)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEET--TEE-
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEEC--CEE-
Confidence            34456789999999999999999999999999999998863     4899999999999999999999998875  664 


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                       |.|.|+.
T Consensus       144 -l~V~~a~  150 (165)
T 1rk8_A          144 -IQVDWCF  150 (165)
T ss_dssp             -CEEEESE
T ss_pred             -EEEEEec
Confidence             5555543

>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=99.53  E-value=3.1e-14  Score=121.90  Aligned_cols=77  Identities=27%  Similarity=0.552  Sum_probs=71.2

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+|||.++++++|+++|+.||.|.+++     .++.++|||||+|.+.++|++|++.|+|..+.|+.|+|.++++
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   82 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   82 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCC
Confidence            58999999999999999999999999999883     3566789999999999999999999999999999999999976


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      ..
T Consensus        83 ~~   84 (168)
T 1b7f_A           83 GG   84 (168)
T ss_dssp             CS
T ss_pred             Cc
Confidence            54

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=1.4e-14  Score=116.69  Aligned_cols=76  Identities=16%  Similarity=0.227  Sum_probs=65.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....++|||+|||.++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++. ++..|.  |+  .|
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~--g~--~l   98 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSID--GR--VV   98 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEET--TE--EE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEEC--CE--EE
Confidence            34568999999999999999999999999999999876     3589999999999999999987 887765  66  35


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.++.
T Consensus        99 ~V~~a~  104 (116)
T 1x4b_A           99 EPKRAV  104 (116)
T ss_dssp             EEECCS
T ss_pred             EEEECC
Confidence            555544

>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=99.53  E-value=2.6e-14  Score=121.69  Aligned_cols=77  Identities=23%  Similarity=0.299  Sum_probs=67.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....++|||+|||+++|+++|+++|+.||.|..|++.+     +++|||||+|.+.++|++|++.|||..|.  |+  .|
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~--~l  142 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD--GR--EL  142 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESS--SS--EE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEEC--Ce--EE
Confidence            34578999999999999999999999999999999875     46999999999999999999999998875  67  45


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.|+.
T Consensus       143 ~v~~a~  148 (158)
T 2kn4_A          143 RVQMAR  148 (158)
T ss_dssp             EEEEEC
T ss_pred             EEEECC
Confidence            555544

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=1.3e-14  Score=116.57  Aligned_cols=60  Identities=15%  Similarity=0.271  Sum_probs=54.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--------cCccEEEEEECCHHHHHHHHHHh
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--------LMEGIVTVHFYDLRHAEMAFKEI  139 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--------~~kG~afV~F~~~~~A~~Ai~~l  139 (408)
                      ...+++|||+|||+++|+++|+++|++||+|. +.++.        +++|||||+|.+.++|++|++.|
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~   72 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC   72 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh
Confidence            45678999999999999999999999999999 66653        45899999999999999999998

>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=99.52  E-value=4.1e-14  Score=120.92  Aligned_cols=77  Identities=21%  Similarity=0.465  Sum_probs=71.1

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+|||.++++++|+++|+.||.|.+++     .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            48999999999999999999999999999883     3677789999999999999999999999999999999999976


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            53

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.52  E-value=3.7e-14  Score=126.88  Aligned_cols=77  Identities=30%  Similarity=0.378  Sum_probs=70.8

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      +.++|||+|||.++|+++|+++|++||.|.+|+     .++.++|||||+|.+.++|.+|++.+|+..+.|+.|++.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            458999999999999999999999999999883     467889999999999999999999999999999999999986


Q ss_pred             CC
Q 046223          302 PG  303 (408)
Q Consensus       302 ~~  303 (408)
                      ..
T Consensus        94 ~~   95 (213)
T 4f02_A           94 RD   95 (213)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>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=99.52  E-value=7.2e-15  Score=108.58  Aligned_cols=67  Identities=13%  Similarity=0.268  Sum_probs=58.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      +|||+|||.++|+++|+++|++||.|..|.+.+     +++|||||+|.+.++|++|++. ++..|.  |+.+.+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~--g~~l~v   72 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVG--LSKCEI   72 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBT--TBCCCE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeEC--CEEEEE
Confidence            599999999999999999999999999998865     4589999999999999999984 776654  664443

>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=99.52  E-value=1.2e-14  Score=115.27  Aligned_cols=70  Identities=10%  Similarity=-0.009  Sum_probs=61.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCC---eEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGE---VRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~---V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      ......+|||+|||+++|+++|+++|+.||.   |..|++..    +++|||||+|.+.++|++|++ ++|..|.  ||.
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~--gr~   83 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMG--QRY   83 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSS--SSC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeC--CeE
Confidence            3456789999999999999999999999998   88888875    468999999999999999999 9997765  674

>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=99.52  E-value=1.5e-14  Score=117.97  Aligned_cols=76  Identities=13%  Similarity=0.020  Sum_probs=62.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEE-EEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGV-QMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v-~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....++|||+|||+++|+++|+++|+.||.|..+ .+..    +++|||||+|.+.++|++||+ |||..|.  ||.  |
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~--gr~--i   96 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMG--NRF--I   96 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCST--TSC--B
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeEC--CcE--E
Confidence            3456899999999999999999999999999773 3322    459999999999999999999 9998876  673  4


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      +|.++.
T Consensus        97 ~V~~a~  102 (124)
T 1wel_A           97 QVHPIT  102 (124)
T ss_dssp             EEEEEC
T ss_pred             EEEECC
Confidence            554443

>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=99.52  E-value=3.9e-15  Score=123.48  Aligned_cols=77  Identities=9%  Similarity=0.131  Sum_probs=68.7

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ...+|||+|||+++|++||+++|++|| |.+|+    ..++++|||||+|.+.++|++|+ .+|+..|+|+.|+|.++..
T Consensus        45 ~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~  122 (139)
T 2hgn_A           45 TGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNST  122 (139)
T ss_dssp             CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCC
Confidence            458999999999999999999999999 66772    34778999999999999999999 7999999999999999876


Q ss_pred             CCC
Q 046223          303 GGH  305 (408)
Q Consensus       303 ~~~  305 (408)
                      ...
T Consensus       123 ~~~  125 (139)
T 2hgn_A          123 TGA  125 (139)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            653

>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=99.51  E-value=1.7e-14  Score=130.37  Aligned_cols=75  Identities=7%  Similarity=0.060  Sum_probs=64.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccC--CeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFG--EVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G--~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ..++|||+||++++||++|+++|++||  .|.+|+|++     +++|||||+|.+.++|++||+.|||..|.  ||.  |
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~--Gr~--l  142 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELH--GQN--P  142 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBT--TBC--C
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeEC--CEE--e
Confidence            577999999999999999999999999  999999876     45899999999999999999999998876  673  5


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      +|.++.
T Consensus       143 ~V~~a~  148 (229)
T 3q2s_C          143 VVTPVN  148 (229)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            555544

>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=99.50  E-value=2.6e-14  Score=119.56  Aligned_cols=77  Identities=12%  Similarity=0.178  Sum_probs=64.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEE--------EEEee--cCccEEEEEECCHHHHHHHHHHhcCccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRG--------VQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQ  148 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~--------v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~g  148 (408)
                      ..++++|||+|||+++|+++|+++|+.||.|..        |.+..  +++|||||+|.+.++|.+|++.|||..|.  |
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~--g  119 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLF--G  119 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEET--T
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeC--C
Confidence            456789999999999999999999999999876        33332  67999999999999999999999998876  6


Q ss_pred             cccceeccccC
Q 046223          149 QSYGLKNPYSS  159 (408)
Q Consensus       149 r~l~~~~~~s~  159 (408)
                      +  .|+|.|+.
T Consensus       120 ~--~l~V~~a~  128 (143)
T 3egn_A          120 K--PMVVQFAR  128 (143)
T ss_dssp             E--ECEEEECC
T ss_pred             c--EEEEEECC
Confidence            7  45555554

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.50  E-value=1.5e-14  Score=113.61  Aligned_cols=71  Identities=15%  Similarity=0.222  Sum_probs=60.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ......++|||+|||.++|+++|+++|++||.|..|++.+    +++|||||+|.+.++|++|++  +|..|.  |+.|
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~--g~~l   78 (102)
T 2xs2_A            4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFH--GKKL   78 (102)
T ss_dssp             CCEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEET--TEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeEC--CEEE
Confidence            3445678999999999999999999999999999999876    358999999999999999998  665554  5533

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.49  E-value=1.2e-13  Score=108.99  Aligned_cols=76  Identities=22%  Similarity=0.238  Sum_probs=66.3

Q ss_pred             CceEEEcCCCC-----CCcHHHHHHHHhcCCCceeecc------CCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          228 QGTIVVFNLDS-----GVSSSTLKEIFQAFGPVKELRE------TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       228 ~~~l~V~nLp~-----~~t~~~L~~~F~~~G~v~~v~~------~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      +++|+|.||-.     +.++++|+++|++||.|.+|..      .+.++|||||+|.+.++|.+|++.|||+.++||.|.
T Consensus         8 s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~   87 (105)
T 2pe8_A            8 TKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVK   87 (105)
T ss_dssp             CSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEE
Confidence            58999999963     2368999999999999999831      246799999999999999999999999999999999


Q ss_pred             EEEecCC
Q 046223          297 IEFSRPG  303 (408)
Q Consensus       297 v~~a~~~  303 (408)
                      |.++...
T Consensus        88 v~~a~~~   94 (105)
T 2pe8_A           88 ACFYNLD   94 (105)
T ss_dssp             EEECCHH
T ss_pred             EEEcCHH
Confidence            9999753

>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=99.49  E-value=3.1e-14  Score=115.83  Aligned_cols=75  Identities=17%  Similarity=0.219  Sum_probs=65.7

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCce--ee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVK--EL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~--~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ....+|||+|||+++|+++|+++|+.| .|.  .|    ...++++|||||+|.+.++|++|++ +++..|+||.|+|..
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEE
Confidence            346899999999999999999999999 565  66    2347789999999999999999998 588999999999998


Q ss_pred             ecC
Q 046223          300 SRP  302 (408)
Q Consensus       300 a~~  302 (408)
                      +..
T Consensus       118 a~~  120 (126)
T 2hgm_A          118 SSQ  120 (126)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            854

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.49  E-value=4.9e-14  Score=112.70  Aligned_cols=75  Identities=21%  Similarity=0.421  Sum_probs=66.5

Q ss_pred             ceEEEcCC----CCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECC----HHH----HHHHHH--HhCCce
Q 046223          229 GTIVVFNL----DSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYD----VRD----AAKALK--EMNGQE  289 (408)
Q Consensus       229 ~~l~V~nL----p~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~----~~~----A~~A~~--~l~g~~  289 (408)
                      ..|||+||    ++.+++++|+++|+.||+|.++     +.++.++|||||+|.+    .++    |.+|++  .|+|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999     5788999999999996    333    888988  789999


Q ss_pred             eCCeEEEEEEecCC
Q 046223          290 IYGKHVVIEFSRPG  303 (408)
Q Consensus       290 ~~g~~l~v~~a~~~  303 (408)
                      |+|+.|+|.+-+..
T Consensus        83 I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           83 IMGFKFEVILNKHS   96 (136)
T ss_dssp             ETTEEEEEEECCTT
T ss_pred             ecCcEEEEEECccc
Confidence            99999999987643

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.49  E-value=6e-14  Score=121.61  Aligned_cols=78  Identities=17%  Similarity=0.213  Sum_probs=67.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....+++|||+|||.++++++|+++|++||.|..|.+..    .++|||||+|.+.++|++|++.|||..|.  |+.  |
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~--Gr~--l  159 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLD--GRP--M  159 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCS--SSB--C
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEEC--CEE--E
Confidence            345678999999999999999999999999999999875    45899999999999999999999998876  664  5


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      +|.|+.
T Consensus       160 ~V~~a~  165 (177)
T 2f3j_A          160 DIQLVA  165 (177)
T ss_dssp             EEEEES
T ss_pred             EEEEec
Confidence            555544

>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=99.49  E-value=1e-13  Score=136.93  Aligned_cols=77  Identities=19%  Similarity=0.328  Sum_probs=67.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ..+.++|||+||+.++|+++|+++|++||.|..|.|+.     +++|||||+|.+.++|.+||+.|||..|.  |+  .|
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~--gr--~i  174 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKID--GR--RV  174 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEEC--CE--EE
Confidence            44568999999999999999999999999999999875     35999999999999999999999998876  66  45


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      .|.|+.
T Consensus       175 ~V~~a~  180 (437)
T 3pgw_S          175 LVDVER  180 (437)
T ss_pred             EEEEeC
Confidence            565554

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.49  E-value=9.7e-14  Score=118.43  Aligned_cols=76  Identities=28%  Similarity=0.453  Sum_probs=69.2

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ++|||+|||.++|+++|+++|++||.|.+++    ..+.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++....
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            5899999999999999999999999999883    345678999999999999999999999999999999999997654

>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=99.48  E-value=1.4e-14  Score=120.11  Aligned_cols=70  Identities=16%  Similarity=0.146  Sum_probs=59.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      .....++|||+|||+++||++|+++|++|| |..|+|++    +++|||||+|.+.++|++|| .+|+..|.  +|.|
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~--gR~i  115 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQ--HRYI  115 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSS--SCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEEC--CEEE
Confidence            344578999999999999999999999999 77888875    56999999999999999999 78997765  6743

>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=99.48  E-value=7.1e-14  Score=113.68  Aligned_cols=70  Identities=14%  Similarity=0.169  Sum_probs=59.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeE--EEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVR--GVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~--~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ....++|||+|||+++||++|+++|+.| .|.  .|++.+    +++|||||+|.+.++|++|++ +++..|.  ||.|.
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~--gR~I~  114 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIG--HRYIE  114 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBT--TBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEEC--CEEEE
Confidence            3457889999999999999999999999 577  788875    569999999999999999998 4676654  77433

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.48  E-value=4.5e-14  Score=127.24  Aligned_cols=79  Identities=19%  Similarity=0.333  Sum_probs=70.1

Q ss_pred             CCCCceEEEcCCCCCC---------cHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCcee-----
Q 046223          225 GNNQGTIVVFNLDSGV---------SSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI-----  290 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~---------t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~-----  290 (408)
                      ....++|||+||+..+         ++++|+++|++||.|++|+.. .++|||||+|.+.++|+.|++.|+|..|     
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~-~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~  209 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD  209 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTS
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEE-CCCCEEEEEeCCHHHHHHHHHHhCCCEEecccc
Confidence            3457999999999998         799999999999999999644 5799999999999999999999999999     


Q ss_pred             -------CCeEEEEEEecCCC
Q 046223          291 -------YGKHVVIEFSRPGG  304 (408)
Q Consensus       291 -------~g~~l~v~~a~~~~  304 (408)
                             .|+.|.|+||+...
T Consensus       210 ~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          210 KEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             TTGGGGGGSCCCEEEECC---
T ss_pred             ccccccCCCCEEEEEEccCCC
Confidence                   89999999997653

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=2.7e-14  Score=115.89  Aligned_cols=68  Identities=12%  Similarity=0.051  Sum_probs=58.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCe----EEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEV----RGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V----~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      ....+|||+|||+++||++|+++|++||.|    ..|+|..    +++|||||+|.+.++|++|++. |+..|.  +|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~--gR~   96 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLG--KRY   96 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESS--SCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeC--CeE
Confidence            456899999999999999999999999976    5677764    4689999999999999999985 887664  663

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.22  E-value=3e-15  Score=120.67  Aligned_cols=77  Identities=16%  Similarity=0.236  Sum_probs=66.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEE--------EEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRG--------VQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~--------v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ..+.++|||+|||.++|+++|+++|++||.|..        |++..     +++|||||+|.+.++|++|++.|||..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            456789999999999999999999999999998        77764     45899999999999999999999998876


Q ss_pred             ccccccceeccccC
Q 046223          146 LQQQSYGLKNPYSS  159 (408)
Q Consensus       146 ~~gr~l~~~~~~s~  159 (408)
                        |+  .|++.++.
T Consensus        84 --g~--~l~V~~a~   93 (116)
T 2lcw_A           84 --GN--PIKVSFAT   93 (116)
Confidence              66  45555544

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=1.7e-13  Score=109.91  Aligned_cols=74  Identities=19%  Similarity=0.203  Sum_probs=62.9

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee----ccC---CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RET---PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v----~~~---~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ..++|||+|||+++++++|+++|++||.|..+    ..+   +.++|||||+|.+.++|++|++.|+  .++|+.|.+..
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~~   84 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCVS   84 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCCEECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEEC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEEEEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEecc
Confidence            35899999999999999999999999999833    122   5789999999999999999999995  37888888876


Q ss_pred             ecC
Q 046223          300 SRP  302 (408)
Q Consensus       300 a~~  302 (408)
                      +..
T Consensus        85 ~~~   87 (114)
T 2dnl_A           85 SPT   87 (114)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            543

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=3.4e-13  Score=107.84  Aligned_cols=79  Identities=13%  Similarity=0.215  Sum_probs=68.1

Q ss_pred             CCCceEEEcCCCCCCc-----------HHHHHHHHhcCCCceeec-cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCe
Q 046223          226 NNQGTIVVFNLDSGVS-----------SSTLKEIFQAFGPVKELR-ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK  293 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t-----------~~~L~~~F~~~G~v~~v~-~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~  293 (408)
                      ..+++|+|.||-....           +++|+++|++||.|..|. ....++|||||+|.+.++|++|++.|||..|+|+
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   92 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR   92 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            3469999999954432           589999999999999984 2335799999999999999999999999999999


Q ss_pred             EEEEEEecCCC
Q 046223          294 HVVIEFSRPGG  304 (408)
Q Consensus       294 ~l~v~~a~~~~  304 (408)
                      .|+|.++.++.
T Consensus        93 ~l~v~~a~~~~  103 (112)
T 2dit_A           93 QITAQAWDGTT  103 (112)
T ss_dssp             ECEEEECCSCC
T ss_pred             EEEEEEeCCCC
Confidence            99999998754

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.47  E-value=7.8e-14  Score=125.65  Aligned_cols=65  Identities=18%  Similarity=0.254  Sum_probs=61.4

Q ss_pred             CCCCCEEEEcCCCCCC---------CHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccc
Q 046223           79 TGPTRTLVLSYVPGDV---------SETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHM  144 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~v---------te~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i  144 (408)
                      ...+++|||+||+.++         +|++|+++|++||+|.+|+++. ++|||||+|.+.++|+.|+++|+|+.|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-~kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-SKNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-GGTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-CCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            5578999999999998         7999999999999999999884 799999999999999999999999998

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.46  E-value=7.9e-14  Score=132.29  Aligned_cols=82  Identities=16%  Similarity=0.129  Sum_probs=70.2

Q ss_pred             CCCCCCEEEEcC--CCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccc-ccccccee
Q 046223           78 STGPTRTLVLSY--VPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQL-QQQSYGLK  154 (408)
Q Consensus        78 ~~~~~rtlfV~n--Lp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~-~gr~l~~~  154 (408)
                      ...++++|||+|  |+.++||++|+++|++||+|.+|.+.. +||||||+|.+.++|++|++.|||+.+.. .|+.+.+.
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly   92 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   92 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEE
Confidence            356789999999  589999999999999999999998874 79999999999999999999999999842 35655566


Q ss_pred             ccccCc
Q 046223          155 NPYSSG  160 (408)
Q Consensus       155 ~~~s~~  160 (408)
                      +.|...
T Consensus        93 ~~~~~~   98 (345)
T 3tht_A           93 LNFVEK   98 (345)
T ss_dssp             EEECSS
T ss_pred             EEEeec
Confidence            677653

>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=99.44  E-value=2.3e-13  Score=117.14  Aligned_cols=76  Identities=17%  Similarity=0.245  Sum_probs=65.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeec----CccEEEEEECCHHHHHHHHHHhcCcccccc-cccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERL----MEGIVTVHFYDLRHAEMAFKEIREQHMQLQ-QQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~----~kG~afV~F~~~~~A~~Ai~~lng~~i~~~-gr~l~~~  154 (408)
                      ...++|||+|||.++|+++|+++|++||.|..|++.+.    ++|||||+|.+.++|.+|++.|||..+..+ ++  .++
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~--~l~  170 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSS--PMV  170 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSS--CCE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCC--CeE
Confidence            36789999999999999999999999999999998863    589999999999999999999999877532 35  344


Q ss_pred             ccc
Q 046223          155 NPY  157 (408)
Q Consensus       155 ~~~  157 (408)
                      +.|
T Consensus       171 V~~  173 (175)
T 3nmr_A          171 VKF  173 (175)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            444

>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=99.44  E-value=1.7e-13  Score=124.04  Aligned_cols=79  Identities=24%  Similarity=0.407  Sum_probs=72.4

Q ss_pred             CCCceEEEcCCCC-CCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          226 NNQGTIVVFNLDS-GVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       226 ~~~~~l~V~nLp~-~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ..+++|||+|||. ++++++|+++|++||.|.+|+.....+|||||+|.+.++|++|++.|||..+.|+.|+|.+++...
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  111 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN  111 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCcc
Confidence            3469999999999 999999999999999999996555558999999999999999999999999999999999998654

>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=99.44  E-value=2.7e-13  Score=119.19  Aligned_cols=78  Identities=13%  Similarity=0.241  Sum_probs=69.2

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+     .++.++|||||+|.+.++|.+|++. ++..+.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecc
Confidence            3468999999999999999999999999999883     3567899999999999999999985 999999999999998


Q ss_pred             cCCC
Q 046223          301 RPGG  304 (408)
Q Consensus       301 ~~~~  304 (408)
                      ....
T Consensus        90 ~~~~   93 (196)
T 1l3k_A           90 VSRE   93 (196)
T ss_dssp             CC--
T ss_pred             cCcc
Confidence            7543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.43  E-value=4.2e-13  Score=105.78  Aligned_cols=77  Identities=16%  Similarity=0.193  Sum_probs=64.2

Q ss_pred             CCCCCEEEEcCCCC-----CCCHHHHHHHhhccCCeEEEEEee------cCccEEEEEECCHHHHHHHHHHhcCcccccc
Q 046223           79 TGPTRTLVLSYVPG-----DVSETIVRRDLEVFGEVRGVQMER------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQ  147 (408)
Q Consensus        79 ~~~~rtlfV~nLp~-----~vte~~L~~~F~~~G~V~~v~~~~------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~  147 (408)
                      ..++++|+|.||-.     +-++++|+++|++||.|.+|.+.+      +++|||||+|.+.++|.+|++.|||..+.  
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~--   82 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFG--   82 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEET--
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEEC--
Confidence            35689999999952     237899999999999999999875      35899999999999999999999999886  


Q ss_pred             ccccceeccccC
Q 046223          148 QQSYGLKNPYSS  159 (408)
Q Consensus       148 gr~l~~~~~~s~  159 (408)
                      ||  .+++.|+.
T Consensus        83 Gr--~i~v~~a~   92 (105)
T 2pe8_A           83 GR--VVKACFYN   92 (105)
T ss_dssp             TE--ECEEEECC
T ss_pred             Cc--EEEEEEcC
Confidence            77  45555544

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.43  E-value=1.7e-13  Score=120.83  Aligned_cols=77  Identities=25%  Similarity=0.418  Sum_probs=71.4

Q ss_pred             CceEEEcCCCC-CCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          228 QGTIVVFNLDS-GVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~-~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      +++|||+|||. ++++++|+++|+.||.|.+|+.....+|||||+|.+.++|++|++.|||..+.|+.|+|.+++...
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~   80 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   80 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCS
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCC
Confidence            58999999999 999999999999999999996555558999999999999999999999999999999999998654

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.43  E-value=2.5e-13  Score=121.26  Aligned_cols=76  Identities=22%  Similarity=0.319  Sum_probs=68.3

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeecc-----CCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRE-----TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~-----~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+|||.++|+++|+++|+.||.|.+|+.     ++.++|||||+|.+.++|.+|++.|||..|+|+.|+|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            489999999999999999999999999999842     567899999999999999999999999999999999988765


Q ss_pred             C
Q 046223          303 G  303 (408)
Q Consensus       303 ~  303 (408)
                      .
T Consensus       108 ~  108 (216)
T 2qfj_A          108 I  108 (216)
T ss_dssp             C
T ss_pred             c
Confidence            4

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.41  E-value=6.2e-13  Score=122.72  Aligned_cols=77  Identities=21%  Similarity=0.321  Sum_probs=71.1

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ...++|||+|||.++|+++|+++|+.||.|..|.. ..++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.+.
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i-~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~~   96 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI-NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHG   96 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEE-eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecccC
Confidence            44589999999999999999999999999999964 467999999999999999999999999999999999999753

>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=99.41  E-value=5.1e-13  Score=117.41  Aligned_cols=75  Identities=16%  Similarity=0.210  Sum_probs=67.1

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      .++|||+|||.++++++|+++|++||.|..|+    ..+..+|||||+|.+.++|.+|++.++ ..++|+.|.|.+++.-
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHHH
Confidence            48999999999999999999999999999883    346789999999999999999998654 5999999999997654

>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=99.40  E-value=2.9e-13  Score=116.87  Aligned_cols=78  Identities=19%  Similarity=0.328  Sum_probs=69.3

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ...++|||+|||.++++++|+++|+.||.+..+    ..++.++|||||+|.+.++|.+|++ |||..+.|+.|+|.++.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~~   89 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   89 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecCC
Confidence            446999999999999999999999999876552    3567789999999999999999995 99999999999999997


Q ss_pred             CCC
Q 046223          302 PGG  304 (408)
Q Consensus       302 ~~~  304 (408)
                      +..
T Consensus        90 ~~~   92 (175)
T 1fje_B           90 GRD   92 (175)
T ss_dssp             CSS
T ss_pred             Ccc
Confidence            654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.40  E-value=2.2e-13  Score=108.91  Aligned_cols=70  Identities=10%  Similarity=0.173  Sum_probs=58.5

Q ss_pred             CEEEEcCC----CCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECC----HHH----HHHHHH--HhcCcc
Q 046223           83 RTLVLSYV----PGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYD----LRH----AEMAFK--EIREQH  143 (408)
Q Consensus        83 rtlfV~nL----p~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~----~~~----A~~Ai~--~lng~~  143 (408)
                      ..|||+||    ++.++|++|+++|+.||+|.++.++.     .++|||||+|.|    .++    |.+|++  .|+|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    99999999999999999999988875     569999999996    433    888988  789988


Q ss_pred             cccccccccee
Q 046223          144 MQLQQQSYGLK  154 (408)
Q Consensus       144 i~~~gr~l~~~  154 (408)
                      |.  ||.|.+.
T Consensus        83 I~--Gr~irV~   91 (136)
T 2j8a_A           83 IM--GFKFEVI   91 (136)
T ss_dssp             ET--TEEEEEE
T ss_pred             ec--CcEEEEE
Confidence            76  7744444

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.38  E-value=1.6e-12  Score=102.48  Aligned_cols=77  Identities=19%  Similarity=0.360  Sum_probs=65.0

Q ss_pred             CCceEEEcCCC--CCC--------cHHHHHHHHhcCCCceeeccC-------CCCccEEEEEECCHHHHHHHHHHhCCce
Q 046223          227 NQGTIVVFNLD--SGV--------SSSTLKEIFQAFGPVKELRET-------PLKKHQRFIEFYDVRDAAKALKEMNGQE  289 (408)
Q Consensus       227 ~~~~l~V~nLp--~~~--------t~~~L~~~F~~~G~v~~v~~~-------~~~~g~afV~F~~~~~A~~A~~~l~g~~  289 (408)
                      ++++|.|.|+=  ..+        .++||++.|++||.|.+|...       +.++|+|||+|.+.++|.+|++.|||+.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            35899999983  233        247999999999999999321       2568999999999999999999999999


Q ss_pred             eCCeEEEEEEecCC
Q 046223          290 IYGKHVVIEFSRPG  303 (408)
Q Consensus       290 ~~g~~l~v~~a~~~  303 (408)
                      ++||.|+|.|+...
T Consensus        84 f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           84 FANRVVVTKYCDPD   97 (105)
T ss_dssp             ETTEECEEEEECHH
T ss_pred             eCCCEEEEEEeCHH
Confidence            99999999998654

>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=99.37  E-value=1.1e-12  Score=112.76  Aligned_cols=74  Identities=23%  Similarity=0.394  Sum_probs=66.3

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcC----C-------CceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAF----G-------PVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~----G-------~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      .++|||+|||.++|+++|+++|++|    |       .|.++. .+.++|||||+|.+.++|++|+ .|||..+.|+.|+
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~-~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~   81 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ-INQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEE-EETTTTEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeE-ecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCceee
Confidence            5899999999999999999999999    6       555554 4567999999999999999999 8999999999999


Q ss_pred             EEEecCC
Q 046223          297 IEFSRPG  303 (408)
Q Consensus       297 v~~a~~~  303 (408)
                      |.+++..
T Consensus        82 v~~~~~~   88 (172)
T 2g4b_A           82 IRRPHDY   88 (172)
T ss_dssp             EECCSSC
T ss_pred             ecCCccc
Confidence            9987654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.37  E-value=1.1e-12  Score=115.32  Aligned_cols=75  Identities=21%  Similarity=0.340  Sum_probs=66.5

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCC-----------CceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFG-----------PVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G-----------~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      .++|||+|||.++|+++|+++|+.||           .|.++. .+.++|||||+|.+.++|++|+ .|||..|.|+.|+
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~-~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~   81 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ-INQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEE-EETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEE
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeE-ecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEE
Confidence            58999999999999999999999994           455543 4577999999999999999999 7999999999999


Q ss_pred             EEEecCCC
Q 046223          297 IEFSRPGG  304 (408)
Q Consensus       297 v~~a~~~~  304 (408)
                      |.+++...
T Consensus        82 v~~~~~~~   89 (198)
T 2yh0_A           82 IRRPHDYQ   89 (198)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99886543

>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=99.36  E-value=1.1e-12  Score=112.11  Aligned_cols=74  Identities=19%  Similarity=0.302  Sum_probs=66.8

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+|||.++|+++|+++|+.||.|.+++     .++.++|||||+|.+.++|++|++.  +..+.|+.|.|.++.+
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccccc
Confidence            48999999999999999999999999999983     4577899999999999999999984  6789999999998865


Q ss_pred             C
Q 046223          303 G  303 (408)
Q Consensus       303 ~  303 (408)
                      .
T Consensus        81 ~   81 (167)
T 2cjk_A           81 R   81 (167)
T ss_dssp             H
T ss_pred             h
Confidence            3

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.35  E-value=2.5e-12  Score=102.76  Aligned_cols=78  Identities=13%  Similarity=0.248  Sum_probs=63.6

Q ss_pred             CCCCCCEEEEcCCCCCCC-----------HHHHHHHhhccCCeEEEEEee-cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           78 STGPTRTLVLSYVPGDVS-----------ETIVRRDLEVFGEVRGVQMER-LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vt-----------e~~L~~~F~~~G~V~~v~~~~-~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ...++++|+|.||-...+           +++|+++|++||.|..|.|.. .++|||||+|.+.++|++|++.|||..|.
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            445789999999944332           689999999999999997642 56999999999999999999999998876


Q ss_pred             ccccccceeccccC
Q 046223          146 LQQQSYGLKNPYSS  159 (408)
Q Consensus       146 ~~gr~l~~~~~~s~  159 (408)
                        ||.  +++.|+.
T Consensus        91 --gr~--l~v~~a~  100 (112)
T 2dit_A           91 --GRQ--ITAQAWD  100 (112)
T ss_dssp             --TEE--CEEEECC
T ss_pred             --CcE--EEEEEeC
Confidence              774  5555543

>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=99.35  E-value=1.4e-12  Score=114.67  Aligned_cols=70  Identities=21%  Similarity=0.281  Sum_probs=60.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ..++|||+|||.++|+++|+++|++||.|..|++.+    .++|||||+|.+.++|++|++.++ ..|  +|+.|.+
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~--~Gr~l~V  181 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKY--KETDLLI  181 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEE--TTEECEE
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeE--CCEEEEE
Confidence            468999999999999999999999999999999885    468999999999999999998654 344  4774433

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=4.1e-12  Score=98.89  Aligned_cols=66  Identities=23%  Similarity=0.317  Sum_probs=58.9

Q ss_pred             CCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCC
Q 046223          238 SGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGH  305 (408)
Q Consensus       238 ~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  305 (408)
                      ..+++++|+++|++||.|.+|+..+.++|||||+|.+.++|++|++.+++  +.|+.|+|+|++++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            46899999999999999999977678999999999999999999998655  5799999999987653

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.34  E-value=5.1e-13  Score=105.18  Aligned_cols=68  Identities=25%  Similarity=0.373  Sum_probs=58.0

Q ss_pred             EcCCCCCCcHHHHHHHH------------hcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          233 VFNLDSGVSSSTLKEIF------------QAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       233 V~nLp~~~t~~~L~~~F------------~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      +.||+..+++++|++.|            ++||.|.+|.    ..+.++|||||+|.+.++|.+|++.|||+.++||.|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56677777777776666            9999999993    2346799999999999999999999999999999999


Q ss_pred             EEEe
Q 046223          297 IEFS  300 (408)
Q Consensus       297 v~~a  300 (408)
                      |+|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.33  E-value=4.2e-12  Score=102.03  Aligned_cols=75  Identities=23%  Similarity=0.302  Sum_probs=64.4

Q ss_pred             CceEEEcCCCC-----CCcHHHHHHHHhcCCCceeec-----c----CCCCccEEEEEECCHHHHHHHHHHhCCceeCCe
Q 046223          228 QGTIVVFNLDS-----GVSSSTLKEIFQAFGPVKELR-----E----TPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK  293 (408)
Q Consensus       228 ~~~l~V~nLp~-----~~t~~~L~~~F~~~G~v~~v~-----~----~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~  293 (408)
                      +++|+|.|+-.     +-.++||++.|++||.|.+|.     .    ++.++|++||+|.+.++|.+|++.|||+.++||
T Consensus        20 s~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR   99 (118)
T 3ue2_A           20 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR   99 (118)
T ss_dssp             CCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            48999999942     224789999999999999882     1    234579999999999999999999999999999


Q ss_pred             EEEEEEecC
Q 046223          294 HVVIEFSRP  302 (408)
Q Consensus       294 ~l~v~~a~~  302 (408)
                      .|+|.|+..
T Consensus       100 ~i~v~~~~~  108 (118)
T 3ue2_A          100 KVVAEVYDQ  108 (118)
T ss_dssp             ECEEEEECH
T ss_pred             EEEEEEcCh
Confidence            999999865

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.32  E-value=2.9e-12  Score=100.97  Aligned_cols=77  Identities=19%  Similarity=0.329  Sum_probs=63.8

Q ss_pred             CCCCCEEEEcCC--CCCCC--------HHHHHHHhhccCCeEEEEEee-------cCccEEEEEECCHHHHHHHHHHhcC
Q 046223           79 TGPTRTLVLSYV--PGDVS--------ETIVRRDLEVFGEVRGVQMER-------LMEGIVTVHFYDLRHAEMAFKEIRE  141 (408)
Q Consensus        79 ~~~~rtlfV~nL--p~~vt--------e~~L~~~F~~~G~V~~v~~~~-------~~kG~afV~F~~~~~A~~Ai~~lng  141 (408)
                      ..+++.|.|.|+  +.++.        +++|++.|++||.|.+|++.+       +++|+|||+|.+.++|++|++.|||
T Consensus         2 g~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG   81 (105)
T 3v4m_A            2 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   81 (105)
T ss_dssp             CSCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            457899999998  44443        368999999999999999875       2489999999999999999999999


Q ss_pred             ccccccccccceeccccC
Q 046223          142 QHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus       142 ~~i~~~gr~l~~~~~~s~  159 (408)
                      +.+.  ||  .|++.|..
T Consensus        82 ~~f~--GR--~i~v~~~~   95 (105)
T 3v4m_A           82 RKFA--NR--VVVTKYCD   95 (105)
T ss_dssp             CEET--TE--ECEEEEEC
T ss_pred             CEeC--CC--EEEEEEeC
Confidence            9886  77  45555543

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.31  E-value=3.9e-12  Score=120.66  Aligned_cols=75  Identities=25%  Similarity=0.434  Sum_probs=65.1

Q ss_pred             CCCceEEEcC--CCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeC---Ce--EEEEE
Q 046223          226 NNQGTIVVFN--LDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY---GK--HVVIE  298 (408)
Q Consensus       226 ~~~~~l~V~n--Lp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~---g~--~l~v~  298 (408)
                      .++++|||+|  |++.+|+++|+++|++||+|.+|... .+||||||+|.+.++|++|++.|||+.+.   |+  .|.|.
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~-~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~   94 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN   94 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECC-TTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEE
Confidence            3468999999  57899999999999999999998643 47999999999999999999999999883   45  57778


Q ss_pred             Eec
Q 046223          299 FSR  301 (408)
Q Consensus       299 ~a~  301 (408)
                      |+.
T Consensus        95 ~~~   97 (345)
T 3tht_A           95 FVE   97 (345)
T ss_dssp             ECS
T ss_pred             Eee
Confidence            874

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.29  E-value=1.5e-11  Score=98.05  Aligned_cols=77  Identities=12%  Similarity=0.119  Sum_probs=64.2

Q ss_pred             CceEEEcCCCCCC----------cHHHHHHHHhcCCCceeeccC-CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          228 QGTIVVFNLDSGV----------SSSTLKEIFQAFGPVKELRET-PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       228 ~~~l~V~nLp~~~----------t~~~L~~~F~~~G~v~~v~~~-~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      +++|.|.|+=...          .++||++.|++||.|.+|... ...+|+|||+|.+.++|.+|++.|||++++||.|+
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~   86 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMIT   86 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            5889999884321          246889999999999999432 23589999999999999999999999999999999


Q ss_pred             EEEecCCC
Q 046223          297 IEFSRPGG  304 (408)
Q Consensus       297 v~~a~~~~  304 (408)
                      |.|+....
T Consensus        87 v~~~~~~~   94 (114)
T 3s6e_A           87 AAYVPLPT   94 (114)
T ss_dssp             EEEECHHH
T ss_pred             EEEEcHHH
Confidence            99996543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.26  E-value=3e-11  Score=93.96  Aligned_cols=72  Identities=25%  Similarity=0.336  Sum_probs=58.1

Q ss_pred             CCEEEEcCCC-------CCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           82 TRTLVLSYVP-------GDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        82 ~rtlfV~nLp-------~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ...|-|.-..       .++||++|+++|++||+|..|.+.++++|||||+|.+.++|++|++.+++.    .++.  |+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~~----~g~~--l~   83 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVGL----VDNP--LK   83 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCBC----SSSB--CE
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCCC----CCCe--EE
Confidence            4566666543       468999999999999999999998889999999999999999999986652    2563  55


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.|+.
T Consensus        84 V~~a~   88 (100)
T 2d9o_A           84 ISWLE   88 (100)
T ss_dssp             EECSS
T ss_pred             EEEcc
Confidence            55544

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.21  E-value=3.7e-12  Score=100.21  Aligned_cols=62  Identities=23%  Similarity=0.295  Sum_probs=52.6

Q ss_pred             EcCCCCCCCHHHHHHHh------------hccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           87 LSYVPGDVSETIVRRDL------------EVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        87 V~nLp~~vte~~L~~~F------------~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      +.||+.++++++|++.|            ++||.|.+|.+.+    +++|||||+|.+.++|++|++.|||..+.  ||.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~--Gr~   97 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFN--GQP   97 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEET--TEE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEEC--CEE
Confidence            55677777888777666            9999999999986    35999999999999999999999999876  774

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.21  E-value=3e-11  Score=97.03  Aligned_cols=75  Identities=16%  Similarity=0.165  Sum_probs=61.6

Q ss_pred             CCCEEEEcCCC--CCC---CHHHHHHHhhccCCeEEEEEeec---------CccEEEEEECCHHHHHHHHHHhcCccccc
Q 046223           81 PTRTLVLSYVP--GDV---SETIVRRDLEVFGEVRGVQMERL---------MEGIVTVHFYDLRHAEMAFKEIREQHMQL  146 (408)
Q Consensus        81 ~~rtlfV~nLp--~~v---te~~L~~~F~~~G~V~~v~~~~~---------~kG~afV~F~~~~~A~~Ai~~lng~~i~~  146 (408)
                      ++++|+|.|+-  .++   -++||++.|++||.|.+|++.+.         ++|+|||+|.+.++|.+|++.|||+.+. 
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~-   97 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA-   97 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET-
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC-
Confidence            68999999993  222   36889999999999999998762         2599999999999999999999999876 


Q ss_pred             cccccceeccccC
Q 046223          147 QQQSYGLKNPYSS  159 (408)
Q Consensus       147 ~gr~l~~~~~~s~  159 (408)
                       ||  .|++.|..
T Consensus        98 -GR--~i~v~~~~  107 (118)
T 3ue2_A           98 -GR--KVVAEVYD  107 (118)
T ss_dssp             -TE--ECEEEEEC
T ss_pred             -Cc--EEEEEEcC
Confidence             77  45555543

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.16  E-value=8.2e-11  Score=93.83  Aligned_cols=76  Identities=16%  Similarity=0.134  Sum_probs=61.4

Q ss_pred             CCCCEEEEcCCC--CCC--------CHHHHHHHhhccCCeEEEEEeec-CccEEEEEECCHHHHHHHHHHhcCccccccc
Q 046223           80 GPTRTLVLSYVP--GDV--------SETIVRRDLEVFGEVRGVQMERL-MEGIVTVHFYDLRHAEMAFKEIREQHMQLQQ  148 (408)
Q Consensus        80 ~~~rtlfV~nLp--~~v--------te~~L~~~F~~~G~V~~v~~~~~-~kG~afV~F~~~~~A~~Ai~~lng~~i~~~g  148 (408)
                      .++++|.+.|+=  .+.        -++||++.|++||.|.+|.+.+. .+|+|||+|.+.++|++|++.|||+.+.  |
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~--G   82 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFA--G   82 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEET--T
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEEC--C
Confidence            358899999982  221        23478999999999999999874 4899999999999999999999999876  7


Q ss_pred             cccceeccccC
Q 046223          149 QSYGLKNPYSS  159 (408)
Q Consensus       149 r~l~~~~~~s~  159 (408)
                      |  .+++.|..
T Consensus        83 R--~i~v~~~~   91 (114)
T 3s6e_A           83 K--MITAAYVP   91 (114)
T ss_dssp             E--ECEEEEEC
T ss_pred             E--EEEEEEEc
Confidence            7  45555543

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.03  E-value=8.4e-10  Score=82.63  Aligned_cols=72  Identities=25%  Similarity=0.440  Sum_probs=59.4

Q ss_pred             CceEEEcCCCC----CCcH----HHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          228 QGTIVVFNLDS----GVSS----STLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       228 ~~~l~V~nLp~----~~t~----~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      ..||+|.-.+.    ++-+    .+|.+.|+.||+|..++...   +.+||+|.+.++|.+|++ |||..++||.|+|++
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~---d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~l   82 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE---DKMWVTFLEGSSALNVLS-LNGKELLNRTITIAL   82 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS---SSEEEEESSHHHHHHGGG-GTTCEETTEEEEEEE
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec---CCEEEEECChHHHHHHHh-cCCeEeCCeEEEEEe
Confidence            37788876652    3333    67899999999999997443   338999999999999999 999999999999999


Q ss_pred             ecCC
Q 046223          300 SRPG  303 (408)
Q Consensus       300 a~~~  303 (408)
                      +++.
T Consensus        83 kt~d   86 (91)
T 2dnr_A           83 KSPS   86 (91)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.00  E-value=1.3e-09  Score=87.13  Aligned_cols=70  Identities=16%  Similarity=0.094  Sum_probs=59.6

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhccCCeEEEEEeecCccEEEEEECC-HHHHHHHHHHhcCcccccccc
Q 046223           79 TGPTRTLVLSYVPGD-VSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYD-LRHAEMAFKEIREQHMQLQQQ  149 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~-vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~-~~~A~~Ai~~lng~~i~~~gr  149 (408)
                      -..+..|||+||+.+ +++++|+++|++||+|..|.+.+ ..-.|||+|.+ .++|..|++.|+...+.+++.
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~-g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~   86 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-GAKEGIILFKEKAKEALGKAKDANNGNLQLRNK   86 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT-TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEec-CCCEEEEEECCChHHHHHHHHHhhcCCcEEeCc
Confidence            345788999999999 99999999999999999999985 44479999999 899999999997554444454

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.99  E-value=1.2e-09  Score=87.21  Aligned_cols=74  Identities=16%  Similarity=0.147  Sum_probs=65.1

Q ss_pred             CCceEEEcCCCCC-CcHHHHHHHHhcCCCceeeccCCCCccEEEEEECC-HHHHHHHHHHhC--CceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSG-VSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYD-VRDAAKALKEMN--GQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~-~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~-~~~A~~A~~~l~--g~~~~g~~l~v~~a~  301 (408)
                      .+..|+|+||+.. +++++|+++|+.||.|..|... .....|||+|.+ .++|.+|++.|+  |..|.|..++++...
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~-~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~   94 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   94 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC-TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEe-cCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECC
Confidence            3689999999999 9999999999999999999643 345579999999 899999999995  788999988888764

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.81  E-value=9.6e-09  Score=77.25  Aligned_cols=71  Identities=21%  Similarity=0.306  Sum_probs=58.1

Q ss_pred             CceEEEcCCCCC-----CcH----HHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q 046223          228 QGTIVVFNLDSG-----VSS----STLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE  298 (408)
Q Consensus       228 ~~~l~V~nLp~~-----~t~----~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  298 (408)
                      ..||+|.-++..     +-+    .+|.+.|+.||+|..++...   +-+||+|.+.++|.+|++ |||..++||.|+|+
T Consensus        15 D~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~---d~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~   90 (95)
T 1ufw_A           15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQ---GQMLVTFADSHSALSVLD-VDGMKVKGRAVKIS   90 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEET---TEEEEECSCSHHHHHHHH-GGGSEETTEEEEEE
T ss_pred             CCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEec---CcEEEEEcChHHHHHHHh-cCCeeeCCeEEEEe
Confidence            488999887643     222    56899999999999886442   229999999999999999 99999999999999


Q ss_pred             EecC
Q 046223          299 FSRP  302 (408)
Q Consensus       299 ~a~~  302 (408)
                      +..+
T Consensus        91 ~k~~   94 (95)
T 1ufw_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            7543

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.79  E-value=8.3e-09  Score=77.25  Aligned_cols=68  Identities=13%  Similarity=0.204  Sum_probs=54.3

Q ss_pred             CCCEEEEcCCC----CCCCH----HHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           81 PTRTLVLSYVP----GDVSE----TIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        81 ~~rtlfV~nLp----~~vte----~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      +..||+|.-.+    .++-.    .+|.+.|.+||+|..|++..   +.+||+|.+.++|.+|++ |||..+.  ||.|+
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~---d~~fVtF~d~~sAlaAi~-mnG~~v~--Gr~Lk   79 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE---DKMWVTFLEGSSALNVLS-LNGKELL--NRTIT   79 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS---SSEEEEESSHHHHHHGGG-GTTCEET--TEEEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec---CCEEEEECChHHHHHHHh-cCCeEeC--CeEEE
Confidence            45688888776    23434    56899999999999999984   449999999999999998 9998876  77444


Q ss_pred             ee
Q 046223          153 LK  154 (408)
Q Consensus       153 ~~  154 (408)
                      ++
T Consensus        80 V~   81 (91)
T 2dnr_A           80 IA   81 (91)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.72  E-value=1.3e-08  Score=91.09  Aligned_cols=65  Identities=25%  Similarity=0.314  Sum_probs=57.2

Q ss_pred             CCcHHHHHHHHhcCCCceeec---------cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          239 GVSSSTLKEIFQAFGPVKELR---------ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       239 ~~t~~~L~~~F~~~G~v~~v~---------~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      .-.+++|++.|++||.|.++.         .++.++|++||+|.+.++|.+|++.|||+.++||.|.+.|+...
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~  213 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQE  213 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCHH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCHH
Confidence            345789999999999999883         23378899999999999999999999999999999999998643

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.63  E-value=2.3e-08  Score=75.23  Aligned_cols=68  Identities=15%  Similarity=0.169  Sum_probs=54.6

Q ss_pred             CCCEEEEcCCCCC-----CCH----HHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           81 PTRTLVLSYVPGD-----VSE----TIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        81 ~~rtlfV~nLp~~-----vte----~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      +..||+|.-++.+     +-.    .+|.+.|.+||+|..|++...   -+||+|.+.++|.+||+ |+|..+.  ||.|
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d---~~fVtF~d~~sAl~AI~-ldG~~v~--Gr~L   87 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG---QMLVTFADSHSALSVLD-VDGMKVK--GRAV   87 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT---EEEEECSCSHHHHHHHH-GGGSEET--TEEE
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC---cEEEEEcChHHHHHHHh-cCCeeeC--CeEE
Confidence            4668999988743     222    458899999999999999843   39999999999999998 9998876  7754


Q ss_pred             cee
Q 046223          152 GLK  154 (408)
Q Consensus       152 ~~~  154 (408)
                      +++
T Consensus        88 ~V~   90 (95)
T 1ufw_A           88 KIS   90 (95)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            444

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.46  E-value=2.7e-07  Score=82.56  Aligned_cols=73  Identities=16%  Similarity=0.150  Sum_probs=56.8

Q ss_pred             CCEEEEcCC-----CCCCCHHHHHHHhhccCCeEEEEEee---------cCccEEEEEECCHHHHHHHHHHhcCcccccc
Q 046223           82 TRTLVLSYV-----PGDVSETIVRRDLEVFGEVRGVQMER---------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQ  147 (408)
Q Consensus        82 ~rtlfV~nL-----p~~vte~~L~~~F~~~G~V~~v~~~~---------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~  147 (408)
                      ++.+.+.|+     ..+-.+++|++.|++||+|.+|.+.+         .++|++||+|.+.++|++|++.|||+.+.  
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~--  201 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA--  201 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSS--
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceEC--
Confidence            344555444     22345678999999999999998873         35899999999999999999999999876  


Q ss_pred             ccccceecccc
Q 046223          148 QQSYGLKNPYS  158 (408)
Q Consensus       148 gr~l~~~~~~s  158 (408)
                      ||.  +++.|.
T Consensus       202 gr~--i~~~~~  210 (222)
T 3dxb_A          202 GRK--VVAEVY  210 (222)
T ss_dssp             SSB--CEEEEC
T ss_pred             CeE--EEEEEc
Confidence            774  555454

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.45  E-value=8.2e-07  Score=68.04  Aligned_cols=71  Identities=25%  Similarity=0.275  Sum_probs=63.4

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcC-----CCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAF-----GPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~-----G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      .++|-|-|||..+++..|+.+...+     |.|..+... ..-+-|+|+|.|...|.+|.-+|+|.+|.|++|++.-
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~-pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLV-SDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEE-TTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEe-cCCCceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            4889999999999999999999999     999888432 3456699999999999999999999999999999864

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.20  E-value=4.2e-06  Score=64.13  Aligned_cols=70  Identities=13%  Similarity=0.095  Sum_probs=61.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcc-----CCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVF-----GEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~-----G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ...|+|-+-|||.++++..|+.+.+.+     |.|+.|.+..+ .+=|+|+|.|...|-+|.=+|+|.+|.  ||.|.
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-H~GAivef~d~~~AgKasLaL~G~ef~--gr~Lr   93 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-FNGAIIIFRDSKFAAKMLMILNGSQFQ--GKVIR   93 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-TTEEEEECSCHHHHHHHHHHHSSEEET--TEEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-CCceEEEEccchhhHHHHhhcCCeeec--CeEEE
Confidence            347899999999999999999999999     99999988754 455999999999999999999999887  77433

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.87  E-value=4.2e-05  Score=58.45  Aligned_cols=74  Identities=16%  Similarity=0.241  Sum_probs=61.2

Q ss_pred             ceEEEcCCCCCC-c----HHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          229 GTIVVFNLDSGV-S----SSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       229 ~~l~V~nLp~~~-t----~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ++|+|.||+.++ .    .+.++++|..|+++...... ++-.-..|.|.+.++|.+|...||+..+.|++++|-|+.+.
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~l-kSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~   84 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeec-CcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCCC
Confidence            789999998755 2    36789999999988776322 23334689999999999999999999999999999999843

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.72  E-value=0.00034  Score=53.17  Aligned_cols=57  Identities=16%  Similarity=0.084  Sum_probs=49.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhc-----cCCeEEEEEeecCccEEEEEECCHHHHHHHHHH
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEV-----FGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKE  138 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~-----~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~  138 (408)
                      ....++|.|.|||.++.++.|.-+|+.     =|+|.+|....   +-|+|+|.+.+.|++.++.
T Consensus         5 ~~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~k   66 (104)
T 2dhx_A            5 SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLAQ   66 (104)
T ss_dssp             CCCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC
T ss_pred             ccCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC
Confidence            345789999999999999999999998     25899988864   8899999999999999863

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.43  E-value=0.0016  Score=49.41  Aligned_cols=77  Identities=19%  Similarity=0.288  Sum_probs=61.4

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcC-----CCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAF-----GPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~-----G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|.|.|||..++++.|+-+|++-     |+|..+...+   +-|+|+|.+.+.|++.++. ....|.|..|.|.-.-+
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~~   83 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECCC
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCCC
Confidence            5899999999999999999999872     6788886443   7899999999999998763 34577888888877655


Q ss_pred             CCCCCC
Q 046223          303 GGHSKK  308 (408)
Q Consensus       303 ~~~~~~  308 (408)
                      ....+-
T Consensus        84 ~~~~r~   89 (104)
T 2dhx_A           84 RAPARL   89 (104)
T ss_dssp             CCCCCC
T ss_pred             CCcceE
Confidence            554433

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.32  E-value=0.00038  Score=53.12  Aligned_cols=73  Identities=15%  Similarity=0.131  Sum_probs=59.4

Q ss_pred             CCEEEEcCCCCCC-CH----HHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           82 TRTLVLSYVPGDV-SE----TIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        82 ~rtlfV~nLp~~v-te----~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ..+|+|.||+.++ +.    +.++++|..|+++......+ +-.-..|.|.+.++|.+|...|++..+.  |+  .+++.
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lk-SFRRirv~F~~~~~A~~AR~~Lh~~~f~--g~--~~r~Y   79 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-SFKRVRINFSNPLSAADARLRLHKTEFL--GK--EMKLY   79 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-TTTEEEEECSSTTHHHHHHHTSTTSEET--TE--ECEEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecC-cceEEEEEeCChHHHHHHHHHhccceec--Cc--eeEEE
Confidence            4689999998876 32    46789999999999977764 5556799999999999999999999987  44  47776


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        80 Fgq   82 (104)
T 1wey_A           80 FAQ   82 (104)
T ss_dssp             CCC
T ss_pred             ecC
Confidence            655

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.18  E-value=0.0015  Score=49.00  Aligned_cols=63  Identities=10%  Similarity=0.099  Sum_probs=53.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-------cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-------LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-------~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ..|.|++||+++||+++.+.++...++.......       ..-.-|||.|.+.+++..-.+.++|..+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            4689999999999999999999998877665543       12457999999999999999999998765

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.18  E-value=0.00072  Score=50.74  Aligned_cols=54  Identities=11%  Similarity=0.167  Sum_probs=44.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIR  140 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~ln  140 (408)
                      ..++| ++|.++...||.++|+.||.|.--.+   .-.-|||.|.+.+.|..|+..+.
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wi---dDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEE---ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCEEEEEE---cCCeEEEEecCHHHHHHHHHhcc
Confidence            44566 99999999999999999995433222   46789999999999999999874

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.02  E-value=0.00088  Score=50.45  Aligned_cols=53  Identities=13%  Similarity=0.228  Sum_probs=44.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIR  140 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~ln  140 (408)
                      .++| ++|.++...||.++|+.||   .|.|..-.-.-|||.|.+.+.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg---gv~I~WidDTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG---NIQISWIDDTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE---EEEEEEEETTEEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC---CEEEEEEcCCeEEEEecCHHHHHHHHHhcc
Confidence            3455 9999999999999999999   444444457889999999999999999875

>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=96.98  E-value=0.0026  Score=47.77  Aligned_cols=55  Identities=16%  Similarity=0.298  Sum_probs=45.0

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMN  286 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~  286 (408)
                      ...++| +.|..+...||.++|+.||.|.--.   .....|||.|.+.+.|..|++.+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~W---idDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQISW---IDDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEE---EETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEEEEE---EcCCeEEEEecCHHHHHHHHHhcc
Confidence            366777 9999999999999999998553222   235679999999999999999774

>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=96.92  E-value=0.0025  Score=50.01  Aligned_cols=70  Identities=16%  Similarity=0.152  Sum_probs=57.5

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCC-eEEEEEEe
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG-KHVVIEFS  300 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g-~~l~v~~a  300 (408)
                      ..-|.|-+.+... ...|.+.|++||+|.+... .....+-.|.|.+..+|++||. .||..++| -.|-|...
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~-~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc-CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            4788888998875 5678889999999998864 3467899999999999999998 79999985 55666654

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.75  E-value=0.00069  Score=66.33  Aligned_cols=56  Identities=18%  Similarity=0.224  Sum_probs=44.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHH
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFK  137 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~  137 (408)
                      ..|+|||. .+..+++.+|.++|++||.|.++.+.+...-||.|+|.+.+++..++.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            46889998 799999999999999999999999987667799999999999997764

>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=96.72  E-value=0.0057  Score=45.76  Aligned_cols=63  Identities=16%  Similarity=0.223  Sum_probs=51.0

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeec-------cCCCCccEEEEEECCHHHHHHHHHHhCCceeC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-------ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY  291 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-------~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~  291 (408)
                      .+|.|++||..+|++++.+.++.+..+....       .....-.-|+|.|.+.+++..-.+.++|..+-
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            5799999999999999999999887765441       11122346999999999999999999998764

>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=96.43  E-value=0.0026  Score=47.92  Aligned_cols=54  Identities=17%  Similarity=0.297  Sum_probs=44.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMN  286 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~  286 (408)
                      ..++| +.|..+...||.++|+.||.|.--+   .....|||.|.+.+.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv~I~W---idDTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISW---IDDTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEEEEEE---EETTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCEEEEE---EcCCeEEEEecCHHHHHHHHHhcc
Confidence            55666 9999999999999999999543222   235679999999999999999875

>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=96.41  E-value=0.0081  Score=47.13  Aligned_cols=65  Identities=8%  Similarity=0.056  Sum_probs=53.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      .....+.|-|-+.|... -..|...|++||+|.+.... ....+-.|.|.+..+|++|+. .||+.|.
T Consensus        20 ~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~-~~~NWihI~Y~s~~~A~rAL~-kNG~ii~   84 (119)
T 1wwh_A           20 DHLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS-NTGNWMHIRYQSKLQARKALS-KDGRIFG   84 (119)
T ss_dssp             -CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC-SSSSEEEEEESSHHHHHHHHT-TTTCEET
T ss_pred             CCCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC-CCCCeEEEEeCCHHHHHHHHH-hCCeEec
Confidence            34456789999999885 56778889999999998763 467899999999999999996 6887764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.91  E-value=0.02  Score=45.57  Aligned_cols=71  Identities=21%  Similarity=0.194  Sum_probs=54.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceee-ccCC------------------CCccEEEEEECCHHHHHHHHHHhCCce
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-RETP------------------LKKHQRFIEFYDVRDAAKALKEMNGQE  289 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-~~~~------------------~~~g~afV~F~~~~~A~~A~~~l~g~~  289 (408)
                      .-|.|-+.|...+ ..+.+.|++||.|.+- ....                  ...++..|+|++..+|.+||. .||..
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            5577778876654 5677889999999873 1110                  135678999999999999998 89999


Q ss_pred             eCCeEEEEEEec
Q 046223          290 IYGKHVVIEFSR  301 (408)
Q Consensus       290 ~~g~~l~v~~a~  301 (408)
                      |+|.-|-|....
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999988887764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.68  E-value=0.019  Score=43.22  Aligned_cols=66  Identities=6%  Similarity=0.048  Sum_probs=50.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-------cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-------LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-------~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ..+-.|.|+.||+.+||+++.+.++..=++.......       ..-.-|||.|.+.++...-.+.++|..+.
T Consensus         7 ~~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A            7 HHSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             ccceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            3466899999999999999988887765543322221       11356999999999999999999998765

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.60  E-value=0.006  Score=59.72  Aligned_cols=55  Identities=15%  Similarity=0.202  Sum_probs=42.0

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHH
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK  283 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~  283 (408)
                      .++|+|. .+..+++.+|.+.|++||.|.++........||.|+|.+.+++.+++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            3889998 688999999999999999999996555566799999999999997754

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.22  E-value=0.042  Score=41.37  Aligned_cols=73  Identities=16%  Similarity=0.245  Sum_probs=51.9

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec------cCC-CCccEEEEEECCHHHHHHHHHHhCCceeCC-----eEE
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR------ETP-LKKHQRFIEFYDVRDAAKALKEMNGQEIYG-----KHV  295 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~------~~~-~~~g~afV~F~~~~~A~~A~~~l~g~~~~g-----~~l  295 (408)
                      +-+|.|+.||+.+||+++.+.++..=++....      ..+ ..-.-|+|.|.+.++...-.+..+|..+-+     -+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            46899999999999999988877654432221      011 112348999999999999999999987642     244


Q ss_pred             EEEEe
Q 046223          296 VIEFS  300 (408)
Q Consensus       296 ~v~~a  300 (408)
                      .|++|
T Consensus        89 ~VE~A   93 (97)
T 2l08_A           89 VVEFA   93 (97)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            56665

>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=89.18  E-value=0.84  Score=45.34  Aligned_cols=56  Identities=11%  Similarity=0.226  Sum_probs=46.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcC
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIRE  141 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng  141 (408)
                      ...++|+ ++..+...+|.++|+.||.|. |  ..-+...|||.|.+.+.|..++++++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v~-V--~widdt~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNIQ-I--SWIDDTSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCCE-E--EECSSSEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCEE-E--EEEcCCeEEEEECCHHHHHHHHHHHHh
Confidence            3567777 899999999999999999543 3  333677899999999999999998854

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=89.13  E-value=0.29  Score=38.83  Aligned_cols=62  Identities=11%  Similarity=0.094  Sum_probs=45.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEE-EEEee------------------cCccEEEEEECCHHHHHHHHHHhcCc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRG-VQMER------------------LMEGIVTVHFYDLRHAEMAFKEIREQ  142 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~-v~~~~------------------~~kG~afV~F~~~~~A~~Ai~~lng~  142 (408)
                      ...|.|=+.|.+. ...+.+.|++||.|.+ +...+                  ...+...|+|.+..+|.+|+. .||+
T Consensus         7 e~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            3457777886655 4467788999999877 22110                  136778999999999999996 7888


Q ss_pred             ccc
Q 046223          143 HMQ  145 (408)
Q Consensus       143 ~i~  145 (408)
                      .|.
T Consensus        85 ii~   87 (132)
T 3p3d_A           85 VFN   87 (132)
T ss_dssp             EET
T ss_pred             EeC
Confidence            775

>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=84.37  E-value=2.7  Score=41.64  Aligned_cols=55  Identities=16%  Similarity=0.282  Sum_probs=44.9

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMN  286 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~  286 (408)
                      ...++|+ ++..+...+|.++|+.||.|.-.+   .....|||.|.+.+.|..+++.++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v~V~w---iddt~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNIQISW---IDDTSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCCEEEE---CSSSEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCEEEEE---EcCCeEEEEECCHHHHHHHHHHHH
Confidence            3566666 888999999999999999654323   345679999999999999999885

>1jgn_B PAIP2, polyadenylate-binding protein-interacting protein 2; all-helical domain, protein-peptide complex, RNA binding protein; NMR {Homo sapiens}

Probab=82.75  E-value=0.58  Score=24.75  Aligned_cols=14  Identities=50%  Similarity=0.888  Sum_probs=12.1

Q ss_pred             CCCCCCCCCCCCCC
Q 046223           11 GNLDPRAQEFRPTT   24 (408)
Q Consensus        11 ~~~~~~a~~~~p~~   24 (408)
                      .+|||.|-||+|-+
T Consensus         4 s~lnp~akef~pgv   17 (26)
T 1jgn_B            4 SNLNPNAKEFVPGV   17 (26)
T ss_dssp             CSSCTTCCCCCTTS
T ss_pred             ccCCcchhhcCCCc
Confidence            47999999999854

---

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	408
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-15
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	8e-15
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-14
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	0.004
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-14
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-14
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	5e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-13
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-13
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	4e-13
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	8e-13
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-13
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-12
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-12
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	8e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	9e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-11
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	7e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-10
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-09
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	6e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	9e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	9e-09
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-08
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-08
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	7e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	8e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-07
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-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	5e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	4e-06
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	5e-06
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	5e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	7e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	1e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	1e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-04
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	0.001
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.004

>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 = 70.0 bits (171), Expect = 1e-15
 Identities = 17/85 (20%), Positives = 38/85 (44%), Gaps = 5/85 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
           T+ V NL    +   + E+F   G +K++     K  +      F+E+Y   DA  A++ 
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 285 MNGQEIYGKHVVIEFSRPGGHSKKF 309
           +NG  +  + +  ++       +++
Sbjct: 69  INGTRLDDRIIRTDWDAGFKEGRQY 93

>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 = 66.9 bits (163), Expect = 8e-15
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKE----LRETPLKKHQRFIEFYDVRDAAKALKE 284
           G ++V NLD GVS + ++E+F  FG +K+       +        + F    DA KA+K+
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 285 MNGQEIYGKHVVIEFS 300
            NG  + G+ + I+  
Sbjct: 61  YNGVPLDGRPMNIQLV 76

>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 = 67.7 bits (165), Expect = 1e-14
 Identities = 17/89 (19%), Positives = 45/89 (50%), Gaps = 3/89 (3%)

Query: 222 VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL--RETPLKKHQRFIEFYDVRDAA 279
           +P   N+  + + NL   +++  + +IF  +GP++++    TP  +   ++ + D+ DA 
Sbjct: 2   LPPEVNR-ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 60

Query: 280 KALKEMNGQEIYGKHVVIEFSRPGGHSKK 308
            A   ++G  +  +++V+ +       +K
Sbjct: 61  NACDHLSGFNVCNRYLVVLYYNANRAFQK 89

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 0.004
 Identities = 13/67 (19%), Positives = 25/67 (37%), Gaps = 5/67 (7%)

Query: 74  LPPPSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQ--MERLMEGIVTVHFYDLRH 131
           LPP      R L +  +P  ++   +      +G +R ++        G   V + D+  
Sbjct: 2   LPPE---VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFD 58

Query: 132 AEMAFKE 138
           A+ A   
Sbjct: 59  AKNACDH 65

>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 = 66.5 bits (162), Expect = 1e-14
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKE 284
           ++ V +L   V+ + L E F   GP+  +R      T       ++ F    DA +AL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 285 MNGQEIYGKHVVIEFSR 301
           MN   I GK V I +S+
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 66.2 bits (161), Expect = 2e-14
 Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKE 284
            ++V  L   ++   L  +F+A GP+   R     +T       F++F    D+ +A+K 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 285 MNGQEIYGKHVVIEFSRPG 303
           +NG  +  K + + ++RPG
Sbjct: 64  LNGITVRNKRLKVSYARPG 82

>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 = 65.4 bits (159), Expect = 5e-14
 Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 5/86 (5%)

Query: 222 VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVR 276
           + + N   T+ V  LD  VS   L E+F   GPV          T   +   F+EF    
Sbjct: 3   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 62

Query: 277 DAAKALKEMNGQEIYGKHVVIEFSRP 302
           DA  A+K M+  ++YGK + +  +  
Sbjct: 63  DADYAIKIMDMIKLYGKPIRVNKASA 88

>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 = 65.1 bits (158), Expect = 5e-14
 Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 2/83 (2%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL--RETPLKKHQRFIEFYDVRDAAK 280
           P GNN   I V NL   + +  ++++F  +G ++++  +         F+EF D RDA  
Sbjct: 9   PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAED 68

Query: 281 ALKEMNGQEIYGKHVVIEFSRPG 303
           A+   +G +  G  + +EF R G
Sbjct: 69  AVYGRDGYDYDGYRLRVEFPRSG 91

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 1e-13
 Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQ---RFIEFYDVRDAAK 280
           D     T+ V NL   V+   + ++F   GP K  +            F+EFY+ RDAA 
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 63

Query: 281 ALKEMNGQEIYGKHVVIEFSRP 302
           AL  MNG++I GK V + ++  
Sbjct: 64  ALAAMNGRKILGKEVKVNWATT 85

>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 = 63.4 bits (154), Expect = 2e-13
 Identities = 21/88 (23%), Positives = 41/88 (46%), Gaps = 7/88 (7%)

Query: 222 VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGP------VKELRETPLKKHQRFIEFYDV 275
           VP       I+V N+    +   ++E+F  FG        K++  T   +   F++F   
Sbjct: 2   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 61

Query: 276 RDAAKALKEM-NGQEIYGKHVVIEFSRP 302
           +DA KA   + +   +YG+ +V+E++  
Sbjct: 62  QDAKKAFNALCHSTHLYGRRLVLEWADS 89

>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 = 62.8 bits (152), Expect = 4e-13
 Identities = 22/75 (29%), Positives = 38/75 (50%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           T++  NL   ++   LKE+F+    ++ + +    K   +IEF    DA K L+E  G E
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77

Query: 290 IYGKHVVIEFSRPGG 304
           I G+ V + ++   G
Sbjct: 78  IDGRSVSLYYTGEKG 92

>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 = 62.4 bits (151), Expect = 5e-13
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            + V  L   V    L   F  FG + ++      ET   +   F+EF    DAA A+  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 285 MNGQEIYGKHVVIEFSRP 302
           MN  E++G+ + +  ++P
Sbjct: 67  MNESELFGRTIRVNLAKP 84

>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 = 61.6 bits (149), Expect = 8e-13
 Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 8/81 (9%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPV--------KELRETPLKKHQRFIEFYDVRDAAKAL 282
           + + NL+   +  TLK +F   G +        K      L     F+E+     A KAL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 283 KEMNGQEIYGKHVVIEFSRPG 303
           K++ G  + G  + +  S   
Sbjct: 61  KQLQGHTVDGHKLEVRISERA 81

>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 = 61.8 bits (150), Expect = 9e-13
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 4/74 (5%)

Query: 230 TIVVFNLDS-GVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
            + + NL++  V  S ++ IF  +G +       + K   F+++ + R+A  A+   +G+
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS---VHKGFAFVQYVNERNARAAVAGEDGR 73

Query: 289 EIYGKHVVIEFSRP 302
            I G+ + I  +  
Sbjct: 74  MIAGQVLDINLAAE 87

>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 = 61.5 bits (149), Expect = 1e-12
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           T+    + SG++   +++ F  FG + E+R    +K   F+ F     AA A+  +NG  
Sbjct: 20  TVYCGGIASGLTDQLMRQTFSPFGQIMEIR-VFPEKGYSFVRFSTHESAAHAIVSVNGTT 78

Query: 290 IYGKHVVIEFSRP 302
           I G  V   + + 
Sbjct: 79  IEGHVVKCYWGKE 91

>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 = 60.8 bits (147), Expect = 2e-12
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 1/78 (1%)

Query: 226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEM 285
             +  + V NL   ++   ++++F+ +G   E+      K   FI       A  A  E+
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-DKGFGFIRLETRTLAEIAKVEL 64

Query: 286 NGQEIYGKHVVIEFSRPG 303
           +   + GK + + F+   
Sbjct: 65  DNMPLRGKQLRVRFACHS 82

>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 = 60.8 bits (147), Expect = 2e-12
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 3/80 (3%)

Query: 226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGP---VKELRETPLKKHQRFIEFYDVRDAAKAL 282
           +  G I + NLD  + +  L + F AFG     K + +    K   F+ F     A +A+
Sbjct: 6   SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 65

Query: 283 KEMNGQEIYGKHVVIEFSRP 302
           ++MNG  +  + V +   + 
Sbjct: 66  EKMNGMLLNDRKVFVGRFKS 85

>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 = 60.4 bits (146), Expect = 2e-12
 Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 5/82 (6%)

Query: 226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKE-----LRETPLKKHQRFIEFYDVRDAAK 280
           ++  TI V NL      + L+E+F+ FG +        + T   K   FI F+   DAA+
Sbjct: 6   DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 65

Query: 281 ALKEMNGQEIYGKHVVIEFSRP 302
           A+  ++G       + +E+++P
Sbjct: 66  AIAGVSGFGYDHLILNVEWAKP 87

>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 = 60.0 bits (145), Expect = 3e-12
 Identities = 18/79 (22%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRE-----TPLKKHQRFIEFYDVRDAAKALKEM 285
           + +  L + ++   +KE+  +FGP+K         T L K   F E+ D+    +A+  +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 286 NGQEIYGKHVVIEFSRPGG 304
           NG ++  K ++++ +  G 
Sbjct: 64  NGMQLGDKKLLVQRASVGA 82

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.7 bits (144), Expect = 3e-12
 Identities = 16/78 (20%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKE 284
            ++V  L   ++    + +F + G ++  +      T       F+ + D +DA KA+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NG  +  K + + ++RP
Sbjct: 64  LNGLRLQTKTIKVSYARP 81

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 59.2 bits (143), Expect = 5e-12
 Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 5/74 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKE 284
            + V NL   ++   L  IF  +G + +        T   +   F+ +    +A +A+  
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 285 MNGQEIYGKHVVIE 298
           +N     G    + 
Sbjct: 68  LNNVIPEGGSQPLS 81

>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 = 59.6 bits (144), Expect = 6e-12
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLK-KHQRFIEFYDVRDAAKALKEMNGQE 289
           I+V NL   V+   L +IF  FG V ++       + Q  +++ D   A  A   ++GQ 
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 69

Query: 290 IY--GKHVVIEFSRPGGHSKKF 309
           IY     + I+FS+    + K+
Sbjct: 70  IYNACCTLRIDFSKLTSLNVKY 91

>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 = 58.5 bits (141), Expect = 8e-12
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            + V NL    S   +++ F    P    R     +   F+ F +  DA +A+K +NG+ 
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVER-VKKIRDYAFVHFSNREDAVEAMKALNGKV 68

Query: 290 IYGKHVVIEFSRP 302
           + G  + +  ++P
Sbjct: 69  LDGSPIEVTLAKP 81

>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 = 58.7 bits (141), Expect = 9e-12
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
           T+ + N     +   ++++ Q    V      P  +        +I+     DA   +++
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NG +I G  +V + S P
Sbjct: 63  LNGLKIEGYTLVTKVSNP 80

>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 = 58.6 bits (141), Expect = 9e-12
 Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 6/88 (6%)

Query: 223 PDGNNQGTIV-VFNLDSGVSSSTLKEIFQAFGPVK-----ELRETPLKKHQRFIEFYDVR 276
           P  + +G I+ V ++        ++E F  +G +K       R T   K    +E+   +
Sbjct: 1   PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 60

Query: 277 DAAKALKEMNGQEIYGKHVVIEFSRPGG 304
            A  A + +NG EI G+ + +++    G
Sbjct: 61  QALAAKEALNGAEIMGQTIQVDWCFVKG 88

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 2e-11
 Identities = 14/76 (18%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMN 286
            + V N+        L+++F  FG + ++         K   F+ F +  DA +A ++++
Sbjct: 13  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 72

Query: 287 GQEIYGKHVVIEFSRP 302
           G  + G+ + +  +  
Sbjct: 73  GTVVEGRKIEVNNATA 88

>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 = 57.4 bits (138), Expect = 2e-11
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 7/80 (8%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRD 277
           PD N    + VF L    +   L+E+F  +GP+ ++     +++   +   F+ F +V D
Sbjct: 6   PDPNC--CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 63

Query: 278 AAKALKEMNGQEIYGKHVVI 297
           A +A +  NG E+ G+ + +
Sbjct: 64  AKEAKERANGMELDGRRIRV 83

>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 = 57.7 bits (139), Expect = 2e-11
 Identities = 19/91 (20%), Positives = 43/91 (47%), Gaps = 6/91 (6%)

Query: 217 PTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIE 271
           P  N  P+  +  T+    L + +    L++ F A G V+++R      +   K   ++E
Sbjct: 7   PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 66

Query: 272 FYDVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
           F +++    A+  + GQ + G  ++++ S+ 
Sbjct: 67  FCEIQSVPLAIG-LTGQRLLGVPIIVQASQA 96

>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 = 57.4 bits (138), Expect = 2e-11
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 6/79 (7%)

Query: 230 TIVVFNLDSGVSSSTLK----EIFQAFGPVKE--LRETPLKKHQRFIEFYDVRDAAKALK 283
           TI + NL+  +    LK     IF  FG + +  +  +   + Q F+ F +V  A  AL+
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 284 EMNGQEIYGKHVVIEFSRP 302
            M G   Y K + I++++ 
Sbjct: 65  SMQGFPFYDKPMRIQYAKT 83

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.1 bits (137), Expect = 3e-11
 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR------ETPLKKHQRFIEFYDVRDAAKALKE 284
           I + NLD  +    L + F AFG + +        +T   K   FI F     +  A++ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 285 MNGQEIYGKHVVIEFSRP 302
           MNGQ +  + + + ++  
Sbjct: 61  MNGQYLCNRPITVSYAFK 78

>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 = 56.6 bits (136), Expect = 5e-11
 Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            + V      ++   L+E F  +G V ++      +   F+ F D + A           
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLC--GEDLI 64

Query: 290 IYGKHVVIEFSRP 302
           I G  V I  + P
Sbjct: 65  IKGISVHISNAEP 77

>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 = 56.7 bits (136), Expect = 6e-11
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 14/94 (14%)

Query: 223 PDGNNQG-TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-------------RETPLKKHQR 268
           PD ++    I V  L+  V+   L + F+  G VK               +ET   K   
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 269 FIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP 302
            + + D   A  A++  +G++  G  + +  +R 
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>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 = 56.2 bits (135), Expect = 7e-11
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQ-----RFIEFYDVRDAAKALKE 284
            + V  L   ++   L+++F  +G +   R    +         FI F    +A +A+K 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 285 MNGQEIYGKHVVIE 298
           +NGQ+  G    I 
Sbjct: 68  LNGQKPSGATEPIT 81

>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 = 56.6 bits (136), Expect = 7e-11
 Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 8/90 (8%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRD 277
           P+G N   + +++L        L ++F  FG V   +    K+        F+ + +   
Sbjct: 16  PEGAN---LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVS 72

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPGGHSK 307
           A  A++ MNG +I  K + ++  R    SK
Sbjct: 73  AQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 55.9 bits (134), Expect = 1e-10
 Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 5/79 (6%)

Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQ-----RFIEFYDVRDAAKALK 283
           G + V NL    S   L+++F A+GP+ EL        +      F+ F     A KA  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 284 EMNGQEIYGKHVVIEFSRP 302
           E++GQ   G+ + +  S  
Sbjct: 69  EVDGQVFQGRMLHVLPSTI 87

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.3 bits (125), Expect = 1e-09
 Identities = 17/74 (22%), Positives = 27/74 (36%), Gaps = 6/74 (8%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKEM 285
           + +  L    +   L+E F  FG VKE         +R     F+ F D     K L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 286 NGQEIYGKHVVIEF 299
           +  E+  K +  + 
Sbjct: 62  SRHELDSKTIDPKV 75

>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 = 52.7 bits (126), Expect = 1e-09
 Identities = 15/78 (19%), Positives = 27/78 (34%), Gaps = 7/78 (8%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
            ++V  L    +   LKE F  FG V  ++     K        F+ F +     K + +
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 285 MNGQEIYGKHVVIEFSRP 302
            +   I G+    +    
Sbjct: 70  RH--MIDGRWCDCKLPNS 85

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 2e-09
 Identities = 9/78 (11%), Positives = 27/78 (34%), Gaps = 6/78 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPV-----KELRETPLKKHQRFIEFYDVRDAAKALKE 284
            + +  L    +  +L+  ++ +G +          +   +   F+ F  + +   A+  
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 80

Query: 285 MNGQEIYGKHVVIEFSRP 302
                I G+ V  + +  
Sbjct: 81  ARPHSIDGRVVEPKRAVA 98

>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 = 50.5 bits (120), Expect = 6e-09
 Identities = 17/74 (22%), Positives = 26/74 (35%), Gaps = 6/74 (8%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEM 285
           I V  L    +   +K  F+ FG V +        T   +   F+ F       K   E+
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 286 NGQEIYGKHVVIEF 299
           +  EI  K V  + 
Sbjct: 61  HFHEINNKMVECKK 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 = 50.1 bits (119), Expect = 9e-09
 Identities = 16/74 (21%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ- 288
            + + NL   V++  L+++F          +  LK    F+++ D   A +A++ ++G+ 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLA-GQVLLKSGYAFVDYPDQNWAIRAIETLSGKV 61

Query: 289 EIYGKHVVIEFSRP 302
           E++GK + +++S  
Sbjct: 62  ELHGKIMEVDYSVS 75

>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 = 50.5 bits (120), Expect = 9e-09
 Identities = 9/82 (10%), Positives = 28/82 (34%), Gaps = 9/82 (10%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-------RETPLKKHQRFIEFYDVRDAAKAL 282
            + +  +        + E                   +    +   F+E+   R AA A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 283 KEMNGQ--EIYGKHVVIEFSRP 302
           +++     +++G  + ++++ P
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEP 84

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.7 bits (118), Expect = 1e-08
 Identities = 10/73 (13%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            I+V NL    +   + ++ + +            K   F+   +   A  A++  +   
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLKY--CYVDRNKRTAFVTLLNGEQAQNAIQMFHQYS 64

Query: 290 IYGKHVVIEFSRP 302
             GK ++++    
Sbjct: 65  FRGKDLIVQLQPT 77

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 2e-08
 Identities = 15/73 (20%), Positives = 36/73 (49%), Gaps = 3/73 (4%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
           T+ V+  D  ++ + L+  F  FG + +L      ++  F+ +  +  A +A+ E+NG +
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLS-MDPPRNCAFVTYEKMESADQAVAELNGTQ 63

Query: 290 IYGKHVVIEFSRP 302
           +    + +  +R 
Sbjct: 64  VESVQLKVNIARK 76

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 4/74 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            +    L +GVS + L  + +  G V  L   P  K   F  +    ++ +A   +NG+E
Sbjct: 22  VVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKE 80

Query: 290 I---YGKHVVIEFS 300
           +    G+ + +  +
Sbjct: 81  VVDDLGQKITLYLN 94

>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 = 48.4 bits (115), Expect = 3e-08
 Identities = 15/73 (20%), Positives = 24/73 (32%), Gaps = 6/73 (8%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKEM 285
           I V  L        ++E F  FG V+ +      K  +     FI F +     K + E 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60

Query: 286 NGQEIYGKHVVIE 298
               +      I+
Sbjct: 61  KYHNVGLSKCEIK 73

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 3e-08
 Identities = 17/81 (20%), Positives = 40/81 (49%), Gaps = 5/81 (6%)

Query: 227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRE-----TPLKKHQRFIEFYDVRDAAKA 281
           ++G + V  L    +  +L+++F  +G + E+       T   +   F+ F ++ DA  A
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 282 LKEMNGQEIYGKHVVIEFSRP 302
           +  MNG+ + G+ + ++ +  
Sbjct: 64  MMAMNGKSVDGRQIRVDQAGK 84

>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 = 49.9 bits (118), Expect = 4e-08
 Identities = 17/93 (18%), Positives = 44/93 (47%), Gaps = 5/93 (5%)

Query: 216 VPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQ-----RFI 270
           +P     P+ +    ++V  + + V    L+++F+ +GP++ ++    ++ +      F+
Sbjct: 30  IPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFV 89

Query: 271 EFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG 303
           +F     A +A+  +NG  I  K + +  +  G
Sbjct: 90  KFQSGSSAQQAIAGLNGFNILNKRLKVALAASG 122

>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 = 47.7 bits (113), Expect = 5e-08
 Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 6/70 (8%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEM 285
           + +  L    +   LK+ F  FG V +        T   +   F+ F +     K + + 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 286 NGQEIYGKHV 295
              ++ GK +
Sbjct: 61  KEHKLNGKVI 70

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 6e-08
 Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 225 GNNQGTIVVFNLD-SGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK 283
           GN+   ++V NL+   V+  +L  +F  +G V+ ++    KK    ++  D   A  A+ 
Sbjct: 1   GNS--VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMS 58

Query: 284 EMNGQEIYGKHVVIEFSRP 302
            +NG +++GK + I  S+ 
Sbjct: 59  HLNGHKLHGKPIRITLSKH 77

>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 = 47.4 bits (112), Expect = 7e-08
 Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRE-TPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
           T+ + N+   VS   LK +F + G V +  +     +    I+   V +A +AL +++  
Sbjct: 12  TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 71

Query: 289 EIY-GKHVVIEFSRP 302
           ++    H+ + FS+ 
Sbjct: 72  DLGENHHLRVSFSKS 86

>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 = 47.1 bits (111), Expect = 8e-08
 Identities = 12/70 (17%), Positives = 26/70 (37%), Gaps = 5/70 (7%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKE-----LRETPLKKHQRFIEFYDVRDAAKALKEM 285
           + +  L  G +   L ++ Q +G +        + T   K   F++F     A KA+  +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 286 NGQEIYGKHV 295
               +  +  
Sbjct: 61  KASGVQAQMA 70

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.2 bits (112), Expect = 1e-07
 Identities = 10/61 (16%), Positives = 25/61 (40%), Gaps = 5/61 (8%)

Query: 245 LKEIFQAFGPVKELRETPLKKHQR---FIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR 301
           L+     FG +++L      +H      + F D  +A   ++ ++G+   G+ +  +   
Sbjct: 36  LRVECSKFGQIRKLL--LFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWD 93

Query: 302 P 302
            
Sbjct: 94  G 94

>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 = 47.1 bits (111), Expect = 1e-07
 Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 5/84 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQ-----RFIEFYDVRDAAKALKE 284
           ++ V N+    +   LK+IF   GPV   R    ++        F E+ D   A  A++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 285 MNGQEIYGKHVVIEFSRPGGHSKK 308
           +NG+E  G+ + ++ +    + ++
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEE 93

>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 = 47.1 bits (111), Expect = 2e-07
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            + + NL   V+   L  +F  F   K         T   + Q FI F +   A +AL  
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +NG ++YGK +VIEF + 
Sbjct: 80  VNGYKLYGKILVIEFGKN 97

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.6 bits (110), Expect = 2e-07
 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 3/76 (3%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            + V  L    S + L   F  FG ++ +          +I++  +  A  A  +M G  
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-GDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 290 IYG--KHVVIEFSRPG 303
           + G  + + ++F++ G
Sbjct: 78  LGGPDRRLRVDFAKSG 93

>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 = 46.6 bits (110), Expect = 2e-07
 Identities = 13/60 (21%), Positives = 27/60 (45%), Gaps = 4/60 (6%)

Query: 245 LKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS 300
             E+ + +G V+E+              +++F    DA KA+ ++N +   G+ +  E S
Sbjct: 44  FTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 3e-07
 Identities = 11/77 (14%), Positives = 22/77 (28%), Gaps = 4/77 (5%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGP----VKELRETPLKKHQRFIEFYDVRDAAKALKEM 285
            + + NL   +    L+ + + FG           +   +   F            +   
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 286 NGQEIYGKHVVIEFSRP 302
           NG+ I     V   + P
Sbjct: 80  NGKFIKTPPGVSAPTEP 96

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.5 bits (110), Expect = 3e-07
 Identities = 14/70 (20%), Positives = 29/70 (41%)

Query: 242 SSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR 301
            S    +     P            + F+EF  V D  KA++ + G++   + VV ++  
Sbjct: 35  CSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD 94

Query: 302 PGGHSKKFFY 311
           P  + ++ F+
Sbjct: 95  PDSYHRRDFW 104

>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 = 46.3 bits (109), Expect = 3e-07
 Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 12/93 (12%)

Query: 222 VPDGNNQG-TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDV 275
           +P    +G T+ + NL        L E+ Q FG +K +      +T   K   F +F   
Sbjct: 1   LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 60

Query: 276 RDAAKALKEMN------GQEIYGKHVVIEFSRP 302
             A K L   +      G ++ G+ + ++ +  
Sbjct: 61  EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 93

>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 = 45.4 bits (107), Expect = 3e-07
 Identities = 10/74 (13%), Positives = 28/74 (37%), Gaps = 6/74 (8%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            + +  L    +  +L+  F+ +G + +        T   +   F+ +  V +   A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-N 66

Query: 285 MNGQEIYGKHVVIE 298
               ++ G+ V  +
Sbjct: 67  ARPHKVDGRVVEPK 80

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.1 bits (106), Expect = 5e-07
 Identities = 16/80 (20%), Positives = 37/80 (46%), Gaps = 8/80 (10%)

Query: 230 TIVVFNLDSGVSS-STLKEIFQAFGPVKEL------RETPLKKHQRFIEFYDVRDAAKAL 282
            I++ NL + +   + L+E F+ FG ++++      +E        F+ F +   A +AL
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 283 KEMNGQEIYGKHVVIEFSRP 302
            +MN   +  + + +  +  
Sbjct: 66  -QMNRSLLGNREISVSLADK 84

>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 = 44.3 bits (104), Expect = 2e-06
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGP-----VKELRETPLKKHQRFIEFYDVRDAAKALKE 284
           T  + NL   V+  ++KE F+          +E       K   + EF D+     AL  
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 75

Query: 285 MNGQEIYGKHVVIEFSRP 302
           +N + +  K + ++ +  
Sbjct: 76  LNEESLGNKRIRVDVADQ 93

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.2 bits (103), Expect = 2e-06
 Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
            I+  NL +G  ++ ++E F  FG +  +   P       +EF +  +A KA + +   +
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVL-LPEGGITAIVEFLEPLEARKAFRHLAYSK 70

Query: 290 IYGKHVVIEFSRPGGHSKK 308
            +   + +E++  G     
Sbjct: 71  FHHVPLYLEWAPIGVFGAA 89

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.3 bits (101), Expect = 4e-06
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 229 GTIVVF--NLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAK-ALKEM 285
           G ++ F  +LD       L  +F   G +K +        +  I F +    A    K+ 
Sbjct: 10  GCLLKFSGDLDDQTCREDLHILFSNHGEIKWID-FVRGAKEGIILFKEKAKEALGKAKDA 68

Query: 286 NGQEIYGKHVVIEFSRPGGHSKK 308
           N   +  ++  + +    G  +K
Sbjct: 69  NNGNLQLRNKEVTWEVLEGEVEK 91

>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 = 42.8 bits (100), Expect = 4e-06
 Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 6/84 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKE 284
            I V  L    + ++L++ F+ FG ++E      ++  +     F+   D   A +A K+
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 285 MNGQEIYGKHVVIEFSRPGGHSKK 308
            N   I G+   +  +  G   + 
Sbjct: 72  PNP-IIDGRKANVNLAYLGAKPRS 94

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 42.6 bits (99), Expect = 5e-06
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 5/77 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEM 285
            + + NL+   S + LK          +L      T   +   +++F    D  KAL+ +
Sbjct: 15  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73

Query: 286 NGQEIYGKHVVIEFSRP 302
            G +++G  + +E  + 
Sbjct: 74  TGLKVFGNEIKLEKPKG 90

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.4 bits (99), Expect = 5e-06
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 4/76 (5%)

Query: 230 TIVVFNLDSG-VSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK--EMN 286
            + + +   G      L ++ + FG +        K ++ FIE     DA  A+      
Sbjct: 10  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN-KINEAFIEMATTEDAQAAVDYYTTT 68

Query: 287 GQEIYGKHVVIEFSRP 302
              ++GK V +  S+ 
Sbjct: 69  PALVFGKPVRVHLSQK 84

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.5 bits (99), Expect = 7e-06
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 230 TIVVFNLDSGVSSST-----LKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKE 284
            ++    +  V S +      + +F+ +      +     K +  I F +   AA A   
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK-RVRINFSNPLSAADARLR 65

Query: 285 MNGQEIYGKHVVIEFSRP 302
           ++  E  GK + + F++ 
Sbjct: 66  LHKTEFLGKEMKLYFAQT 83

>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 = 41.2 bits (96), Expect = 1e-05
 Identities = 12/76 (15%), Positives = 29/76 (38%), Gaps = 6/76 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
            I V  +        L++ F+ +G ++ +     R +  K+   F+ F D  D+   +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVI 62

Query: 285 MNGQEIYGKHVVIEFS 300
                + G +  +  +
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.7 bits (97), Expect = 1e-05
 Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 2/80 (2%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKAL 282
           P   +   ++V  L    S   LK+  +  G V        K     +E+    D   AL
Sbjct: 10  PTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVC--YADVQKDGMGMVEYLRKEDMEYAL 67

Query: 283 KEMNGQEIYGKHVVIEFSRP 302
           ++++  +         + R 
Sbjct: 68  RKLDDTKFRSHEGETSYIRV 87

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (95), Expect = 1e-05
 Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 2/72 (2%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           +VV  L    S   LK+  +  G V        +     +EF    D   A+++++  + 
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVC--YADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF 60

Query: 291 YGKHVVIEFSRP 302
                   + R 
Sbjct: 61  RSHEGETAYIRV 72

>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 = 41.3 bits (96), Expect = 2e-05
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 3/75 (4%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ- 288
            + V  L   V  + L E  + FG +  +      K Q  +EF ++  A + +       
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVM-MMPFKRQALVEFENIDSAKECVTFAADVP 75

Query: 289 -EIYGKHVVIEFSRP 302
             I G+     +S  
Sbjct: 76  VYIAGQQAFFNYSTS 90

>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 = 40.9 bits (95), Expect = 2e-05
 Identities = 17/83 (20%), Positives = 33/83 (39%), Gaps = 13/83 (15%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR----------ETPLKKHQRFIEFYDVRDAA 279
            + V N+  G++   + + F A   +  L           +    K+  F+EF  V +  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 280 KALKEMNGQEIYGKHVVIEFSRP 302
           +A+   +G    G+ + I   RP
Sbjct: 63  QAMA-FDGIIFQGQSLKI--RRP 82

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (97), Expect = 4e-05
 Identities = 8/70 (11%), Positives = 23/70 (32%), Gaps = 5/70 (7%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKE 284
            + +  L    +  +L+  F+ +G + +        T   +   F+ +  V +   A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 285 MNGQEIYGKH 294
              +      
Sbjct: 68  RPHKVDGRVV 77

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (89), Expect = 1e-04
 Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 3/75 (4%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEM--NG 287
            + +  L   V+ + +  +   FG V  +      K+Q F+E      A   +       
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-GKNQAFLELATEEAAITMVNYYSAVT 68

Query: 288 QEIYGKHVVIEFSRP 302
             +  + + I++S  
Sbjct: 69  PHLRNQPIYIQYSNH 83

>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 = 37.7 bits (87), Expect = 2e-04
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 5/75 (6%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKE-----LRETPLKKHQRFIEFYDVRDAAKALKE 284
            I V N+   VS   + + F  +  +         E  +   +  + F    +A  A+ +
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 285 MNGQEIYGKHVVIEF 299
           +N + I  + V +  
Sbjct: 71  LNDRPIGSRKVKLVL 85

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (85), Expect = 4e-04
 Identities = 19/85 (22%), Positives = 31/85 (36%), Gaps = 6/85 (7%)

Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRD 277
           PD  N G + +  L  G S   + + F     V                + F++F     
Sbjct: 10  PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEI 69

Query: 278 AAKALKEMNGQEIYGKHVVIEFSRP 302
           A KALK  + + I  +++ I  S  
Sbjct: 70  AEKALK-KHKERIGHRYIEIFKSSR 93

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.6 bits (81), Expect = 0.001
 Identities = 12/77 (15%), Positives = 27/77 (35%), Gaps = 11/77 (14%)

Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGP------VKELRETPLKKHQRF-----IEFYDVRDA 278
            + V  L   ++   + +  + FG       V     T     Q       + +    DA
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 279 AKALKEMNGQEIYGKHV 295
            +A++ +N   + G+ +
Sbjct: 70  LRAIQCVNNVVVDGRTL 86

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.7 bits (76), Expect = 0.004
 Identities = 7/71 (9%), Positives = 24/71 (33%), Gaps = 2/71 (2%)

Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
           I++  L   V++  + ++   +            K   F+   +   A  A+   +   +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKY--CFVDKYKGTAFVTLLNGEQAEAAINTFHQSRL 58

Query: 291 YGKHVVIEFSR 301
             + + ++   
Sbjct: 59  RERELSVQLQP 69

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	408
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.96
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.79
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.78
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.78
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.77
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.77
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.77
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.77
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.77
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.76
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.76
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.76
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.75
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.75
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.75
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.75
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.75
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.75
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.74
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.74
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.74
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.73
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.73
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.73
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.73
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.73
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.73
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.73
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.73
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.73
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.73
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.73
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.73
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.72
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.72
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.72
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.72
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.72
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.72
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.72
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.72
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.72
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.71
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.71
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.71
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.71
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.71
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.71
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.71
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.71
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.71
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.71
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.71
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.71
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.71
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.71
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.71
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.7
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.7
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.7
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.7
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.7
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.7
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.7
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.7
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.69
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.69
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.69
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.69
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.69
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.69
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.69
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.69
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.69
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.68
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.68
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.68
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.68
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.68
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.68
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.68
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.67
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.67
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.67
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.67
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.67
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.67
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.67
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.67
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.67
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.66
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.66
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.66
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.66
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.66
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.66
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.66
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.66
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.66
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.66
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.66
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.65
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.65
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.65
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.65
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.65
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.65
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.65
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.64
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.64
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.64
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.64
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.64
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.63
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.63
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.63
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.63
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.63
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.63
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.62
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.62
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.62
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.62
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.62
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.61
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.61
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.61
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.61
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.61
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.61
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.6
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.6
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.56
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.56
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.53
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.53
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.52
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.52
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.52
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.51
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.49
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.46
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.44
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.44
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.44
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.42
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.37
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.35
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.32
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.32
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.31
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.27
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.27
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.18
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.61
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.4
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.1
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.05
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.62
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.81
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.03
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.32

>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=99.96  E-value=1.3e-28  Score=213.93  Aligned_cols=162  Identities=14%  Similarity=0.215  Sum_probs=128.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ..|+|||+|||+++||++|+++|++||+|.++.+.+     .++|||||+|.+.++|++|++.+++ .+.  .+.+....
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~-~~~--~~~~~~~~   81 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPH-KVD--GRVVEPKR   81 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSC-EET--TEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCC-ccc--ccchhhhh
Confidence            348999999999999999999999999999998875     5589999999999999999985543 332  22111111


Q ss_pred             cccCccccccCCCCCCCcccCCCChhHHHHHHhhhhccCCCCCCCcCCCCCCCCccccccCCcCCCCCCCCCCceEEEcC
Q 046223          156 PYSSGLMLMNNDNNNNNLATGCYDNQVVAESLMIMNSYAPVLPPPARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFN  235 (408)
Q Consensus       156 ~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~l~V~n  235 (408)
                      ....                                                         ............++|||+|
T Consensus        82 ~~~~---------------------------------------------------------~~~~~~~~~~~~~~i~V~~  104 (183)
T d1u1qa_          82 AVSR---------------------------------------------------------EDSQRPGAHLTVKKIFVGG  104 (183)
T ss_dssp             CCCT---------------------------------------------------------TGGGSTTTTCCCSEEEEEC
T ss_pred             hhhc---------------------------------------------------------ccccccccccccceeEEcc
Confidence            0000                                                         0000011123358999999


Q ss_pred             CCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          236 LDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       236 Lp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ||..+|+++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|++ +++..++|+.|+|.+|.++
T Consensus       105 lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         105 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             CCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCH
T ss_pred             CCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCc
Confidence            99999999999999999999988     2457889999999999999999997 7999999999999998764

>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=99.79  E-value=2e-19  Score=134.09  Aligned_cols=76  Identities=26%  Similarity=0.531  Sum_probs=70.7

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      +++|||+|||.++|+++|+++|++||.|.+++     .++.++|||||+|.+.++|++|++.|||..++|+.|+|+||+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            47899999999999999999999999999882     4667899999999999999999999999999999999999986


Q ss_pred             C
Q 046223          303 G  303 (408)
Q Consensus       303 ~  303 (408)
                      .
T Consensus        82 g   82 (82)
T d1b7fa1          82 G   82 (82)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.78  E-value=2.9e-19  Score=135.32  Aligned_cols=78  Identities=27%  Similarity=0.469  Sum_probs=72.5

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+|||.++++++|+++|++||.|.++     +.++.++|||||+|.+.++|++|++.|||..++|+.|+|+||++
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p   84 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP   84 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            5899999999999999999999999999988     34678899999999999999999999999999999999999987


Q ss_pred             CCC
Q 046223          303 GGH  305 (408)
Q Consensus       303 ~~~  305 (408)
                      +..
T Consensus        85 ~~~   87 (89)
T d2cqba1          85 MRI   87 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.78  E-value=4.2e-19  Score=134.07  Aligned_cols=78  Identities=21%  Similarity=0.400  Sum_probs=71.8

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      +..+|||+|||.++|+++|+++|++||.|.+++     .++.++|||||+|.+.++|++|++.|||..++|+.|+|+||.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            458999999999999999999999999999882     457789999999999999999999999999999999999998


Q ss_pred             CCC
Q 046223          302 PGG  304 (408)
Q Consensus       302 ~~~  304 (408)
                      +++
T Consensus        86 ~kG   88 (88)
T d1rk8a_          86 VKG   88 (88)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            764

>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=99.77  E-value=7.7e-19  Score=134.00  Aligned_cols=80  Identities=20%  Similarity=0.283  Sum_probs=72.8

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      .+++|||+|||.++|+++|+++|++||.|.+|+     .++.++|||||+|.+.++|++|++.|||..++|+.|+|+|+.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            358999999999999999999999999999983     467788999999999999999999999999999999999997


Q ss_pred             CCCCC
Q 046223          302 PGGHS  306 (408)
Q Consensus       302 ~~~~~  306 (408)
                      .....
T Consensus        86 ~~~~g   90 (93)
T d1h2vz_          86 GFKEG   90 (93)
T ss_dssp             CCCTT
T ss_pred             CCCCC
Confidence            65433

>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=99.77  E-value=6.3e-19  Score=131.40  Aligned_cols=75  Identities=21%  Similarity=0.474  Sum_probs=69.9

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..+|||+|||.++++++|+++|++||.|.+++     ..+..+|||||+|.+.++|++|++.|||..++|+.|+|+||+|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            36799999999999999999999999999883     4567889999999999999999999999999999999999986

>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=99.77  E-value=1.2e-18  Score=132.17  Aligned_cols=81  Identities=33%  Similarity=0.546  Sum_probs=72.3

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ....++|||+|||.++|+++|+++|+.||.|..++   .....+|||||+|.+.++|.+|++.|||..|.|+.|+|.||+
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            34468999999999999999999999999999883   234468999999999999999999999999999999999998


Q ss_pred             CCCC
Q 046223          302 PGGH  305 (408)
Q Consensus       302 ~~~~  305 (408)
                      ++..
T Consensus        85 ~~~~   88 (90)
T d2cqia1          85 TPSS   88 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            7654

>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=99.77  E-value=5e-19  Score=135.06  Aligned_cols=79  Identities=33%  Similarity=0.426  Sum_probs=73.0

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||..+|+++|+++|++||.|.++     +.++.++|||||+|.+.++|++|++.|||..|+|+.|+|++|
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            345899999999999999999999999999988     246788999999999999999999999999999999999999


Q ss_pred             cCCC
Q 046223          301 RPGG  304 (408)
Q Consensus       301 ~~~~  304 (408)
                      +++.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8765

>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=99.77  E-value=4.7e-19  Score=134.41  Aligned_cols=79  Identities=28%  Similarity=0.448  Sum_probs=72.8

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      .+..+|||+|||.++++++|+++|++||.|..++     .++.++|||||+|.+.++|++|++.|||..++|+.|+|+||
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            3458999999999999999999999999999883     46778999999999999999999999999999999999999


Q ss_pred             cCCC
Q 046223          301 RPGG  304 (408)
Q Consensus       301 ~~~~  304 (408)
                      +++.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            8764

>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=99.77  E-value=9.9e-19  Score=135.79  Aligned_cols=80  Identities=24%  Similarity=0.416  Sum_probs=73.2

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ...+|||+|||+++++++|+++|+.||.|..+     ..++.++|||||+|.+.++|++|++.|||..|+|+.|+|+|++
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            35789999999999999999999999999887     3567789999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 046223          302 PGGHS  306 (408)
Q Consensus       302 ~~~~~  306 (408)
                      ++..+
T Consensus        97 ~k~~~  101 (102)
T d2cpza1          97 SKNDS  101 (102)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87643

>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=99.76  E-value=3.7e-18  Score=130.20  Aligned_cols=79  Identities=18%  Similarity=0.333  Sum_probs=71.8

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ....+|||+|||+.+++++|+++|++||.|..|+   ..+.++|||||+|.+.++|.+|++.|||..|+|++|+|++|++
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~   88 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA   88 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCc
Confidence            3458899999999999999999999999999883   3445689999999999999999999999999999999999987


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      +.
T Consensus        89 r~   90 (93)
T d2cq3a1          89 RV   90 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.76  E-value=1e-18  Score=129.88  Aligned_cols=74  Identities=19%  Similarity=0.302  Sum_probs=65.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ++|||+|||.++|+++|+++|++||.|..+     ...+.++|||||+|.+.++|++|++.|||..++|++|+|++++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            799999999999999999999999999765     34678899999999999999999999999999999999999986

>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=99.76  E-value=9.3e-19  Score=134.43  Aligned_cols=81  Identities=27%  Similarity=0.405  Sum_probs=75.8

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGH  305 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  305 (408)
                      ...++|||+|||.++|+++|+++|++||.|..++..+.+++||||+|.+.++|++|++.|||..|+|+.|+|.|+.+++.
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            34689999999999999999999999999998887888999999999999999999999999999999999999998765


Q ss_pred             C
Q 046223          306 S  306 (408)
Q Consensus       306 ~  306 (408)
                      +
T Consensus        94 ~   94 (96)
T d1fjca_          94 T   94 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.76  E-value=1e-18  Score=132.66  Aligned_cols=79  Identities=24%  Similarity=0.517  Sum_probs=72.6

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      +..+|||+|||+++++++|+++|++||.|..+     ...+.++|||||+|.+.++|++|++.|||..|+|+.|+|++|.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            35889999999999999999999999999987     3567789999999999999999999999999999999999998


Q ss_pred             CCCC
Q 046223          302 PGGH  305 (408)
Q Consensus       302 ~~~~  305 (408)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.76  E-value=2.7e-18  Score=132.61  Aligned_cols=77  Identities=31%  Similarity=0.410  Sum_probs=71.8

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+|||+++++++|+++|++||.|.+++     .++.++|||||+|.+.++|++|++.|||..|+|+.|+|++++.
T Consensus         8 ~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~   87 (99)
T d1whwa_           8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTI   87 (99)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCC
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            57899999999999999999999999999883     4677899999999999999999999999999999999999987


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      +.
T Consensus        88 ~~   89 (99)
T d1whwa_          88 KK   89 (99)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>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=99.75  E-value=1.9e-18  Score=132.08  Aligned_cols=79  Identities=25%  Similarity=0.523  Sum_probs=72.2

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec------cCCCCccEEEEEECCHHHHHHHHHHh-CCceeCCeEEEEE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR------ETPLKKHQRFIEFYDVRDAAKALKEM-NGQEIYGKHVVIE  298 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~------~~~~~~g~afV~F~~~~~A~~A~~~l-~g~~~~g~~l~v~  298 (408)
                      ....+|||+|||.++++++|+++|++||.|..++      .++.++|||||+|.+.++|.+|++.| ||..|+|++|+|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            3458899999999999999999999999999883      25678999999999999999999998 8999999999999


Q ss_pred             EecCCC
Q 046223          299 FSRPGG  304 (408)
Q Consensus       299 ~a~~~~  304 (408)
                      ||+...
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998765

>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=99.75  E-value=2.7e-18  Score=131.55  Aligned_cols=79  Identities=28%  Similarity=0.488  Sum_probs=71.6

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec--cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~--~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ...++|||+|||.++|+++|+++|++||.|..+.  .....++||||+|.+.++|++|++.|||..|.|++|+|+||++.
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            4457899999999999999999999999998883  34567899999999999999999999999999999999999764


Q ss_pred             C
Q 046223          304 G  304 (408)
Q Consensus       304 ~  304 (408)
                      +
T Consensus        92 r   92 (95)
T d1x4aa1          92 R   92 (95)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.75  E-value=1.9e-18  Score=128.99  Aligned_cols=77  Identities=16%  Similarity=0.268  Sum_probs=68.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      .++++|||+|||.++|+++|+++|++||+|..|++.+..+|||||+|.+.++|.+|++.|||..|. +++  .+++.|++
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-~~~--~i~v~~ak   82 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKIT-PTH--AMKITFAK   82 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSS-TTC--BCEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeC-CCc--EEEEEEec
Confidence            457899999999999999999999999999999999888999999999999999999999998875 344  36776654

>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=99.75  E-value=2.3e-18  Score=126.83  Aligned_cols=73  Identities=30%  Similarity=0.463  Sum_probs=68.4

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       230 ~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      +|||+|||+++++++|+++|++||.|.+++    .+++++|||||+|.+.++|++|++.|||..++|+.|+|+++.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            699999999999999999999999999882    5677899999999999999999999999999999999999863

>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=99.75  E-value=1.1e-18  Score=132.01  Aligned_cols=78  Identities=24%  Similarity=0.411  Sum_probs=70.6

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ..+|||+|||.++++++|+++|+.||.|..++   ..+.++|||||+|.+.++|++|++.|||..|+|+.|+|++++++.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            36899999999999999999999999998883   334568999999999999999999999999999999999998765


Q ss_pred             C
Q 046223          305 H  305 (408)
Q Consensus       305 ~  305 (408)
                      .
T Consensus        88 ~   88 (89)
T d1cvja2          88 E   88 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.75  E-value=1.9e-18  Score=129.06  Aligned_cols=75  Identities=25%  Similarity=0.414  Sum_probs=68.6

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCceee------ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL------RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       231 l~V~nLp~~~t~~~L~~~F~~~G~v~~v------~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      |||+|||.++|+++|+++|++||.|..+      ..++.++|||||+|.+.++|++|++.|||..++|++|+|+||.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998654      2457789999999999999999999999999999999999998765


Q ss_pred             C
Q 046223          305 H  305 (408)
Q Consensus       305 ~  305 (408)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.75  E-value=1.5e-18  Score=128.47  Aligned_cols=72  Identities=32%  Similarity=0.415  Sum_probs=67.9

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       230 ~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      +|||+|||..+|+++|+++|++||.|.+++     .++.++|||||+|.+.++|.+|++.|||..++|+.|+|+||+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            699999999999999999999999999883     457789999999999999999999999999999999999985

>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=99.75  E-value=8.1e-18  Score=138.35  Aligned_cols=80  Identities=21%  Similarity=0.462  Sum_probs=72.9

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ...++|||+|||.++|+++|+++|++||.|.+|+     .++.++|||||+|.+.++|.+|++.|||..|+|+.|+|++|
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3457899999999999999999999999999883     45778999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 046223          301 RPGGH  305 (408)
Q Consensus       301 ~~~~~  305 (408)
                      +++..
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.74  E-value=2.4e-18  Score=128.96  Aligned_cols=75  Identities=15%  Similarity=0.208  Sum_probs=65.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ..++|||+|||.++||++|+++|++||+|.+|++++     .++|||||+|.+.++|++|++.|||..+.  |+..+++|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~--G~~~~i~V   82 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPS--GATEPITV   82 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCT--TCSSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeC--CCCEEEEE
Confidence            356899999999999999999999999999999875     45899999999999999999999999887  44445665


Q ss_pred             cc
Q 046223          156 PY  157 (408)
Q Consensus       156 ~~  157 (408)
                      .|
T Consensus        83 ~~   84 (85)
T d1fxla2          83 KF   84 (85)
T ss_dssp             EE
T ss_pred             Ee
Confidence            54

>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=99.74  E-value=5.5e-18  Score=131.45  Aligned_cols=80  Identities=23%  Similarity=0.353  Sum_probs=71.6

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-------------ccCCCCccEEEEEECCHHHHHHHHHHhCCceeC
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-------------RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY  291 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-------------~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~  291 (408)
                      .....+|||+|||..+|+++|+++|+.||.|..+             +.++..+|||||+|.+.++|.+|++.|||..|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            3456899999999999999999999999988644             234678899999999999999999999999999


Q ss_pred             CeEEEEEEecCCC
Q 046223          292 GKHVVIEFSRPGG  304 (408)
Q Consensus       292 g~~l~v~~a~~~~  304 (408)
                      |+.|+|++|+++.
T Consensus        85 gr~i~V~~a~~~~   97 (101)
T d2cpea1          85 GSKLKVSLARKKP   97 (101)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999998754

>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=99.74  E-value=5.5e-18  Score=127.31  Aligned_cols=77  Identities=22%  Similarity=0.347  Sum_probs=70.9

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGH  305 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  305 (408)
                      .++|||+|||.++++++|+++|++||.|..+. .+..+|||||+|.+.++|.+|++.|||..|+|+.|+|+||+|+..
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~-~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVER-VKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEE-EEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEE-EccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCC
Confidence            47999999999999999999999999987764 356899999999999999999999999999999999999987653

>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=99.73  E-value=2.1e-18  Score=127.71  Aligned_cols=77  Identities=21%  Similarity=0.325  Sum_probs=69.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCc-eeCCeEEEEEEecCCCCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ-EIYGKHVVIEFSRPGGHS  306 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~-~~~g~~l~v~~a~~~~~~  306 (408)
                      ++|||+|||.++|+++|+++|++||.|..++ ....+|||||+|.+.++|++|++.|||. .++|+.|+|+||.++..+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~-~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQ-VLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSC-EEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeE-EecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            4799999999999999999999999988764 3357899999999999999999999996 699999999999986643

>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=99.73  E-value=1.8e-18  Score=129.65  Aligned_cols=76  Identities=24%  Similarity=0.454  Sum_probs=71.0

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      .+|||+|||..+|+++|+++|++||.|.++     +.++.++|||||+|.+.++|.+|++.|||..|+|+.|+|++|++.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            579999999999999999999999999988     356788999999999999999999999999999999999999865


Q ss_pred             C
Q 046223          304 G  304 (408)
Q Consensus       304 ~  304 (408)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.73  E-value=4.7e-18  Score=129.54  Aligned_cols=79  Identities=18%  Similarity=0.186  Sum_probs=68.1

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ......++|||+|||.++|+++|+++|++||.|.+|++.+     .++|||||+|.+.++|++|++.|||..|.  |+. 
T Consensus         4 ~~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~--g~~-   80 (93)
T d1x5ua1           4 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLY--GKP-   80 (93)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCS--SCB-
T ss_pred             CcCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEEC--CEE-
Confidence            3445568999999999999999999999999999999875     46899999999999999999999998876  664 


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                       |++.|+.
T Consensus        81 -l~V~~A~   87 (93)
T d1x5ua1          81 -IRVNKAS   87 (93)
T ss_dssp             -CEEEETT
T ss_pred             -EEEEEcC
Confidence             5555544

>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=99.73  E-value=4.7e-18  Score=126.72  Aligned_cols=76  Identities=22%  Similarity=0.350  Sum_probs=70.1

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeC-CeEEEEEEec
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY-GKHVVIEFSR  301 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~-g~~l~v~~a~  301 (408)
                      .++++|||+|||.++++++|+++|+.||.|..++.....+|||||+|.+.++|.+|++.|||..+. |+.|+|+||+
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            346899999999999999999999999999999766667899999999999999999999999885 6899999996

>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=99.73  E-value=8.4e-18  Score=130.70  Aligned_cols=77  Identities=23%  Similarity=0.333  Sum_probs=69.8

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ..++|||+|||+.+++++|+++|++||.|.+|+     .++.++|||||+|.+.++|++|++.+|+ .|+|++|+|+++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            457899999999999999999999999999883     4578899999999999999999998876 7999999999997


Q ss_pred             CCC
Q 046223          302 PGG  304 (408)
Q Consensus       302 ~~~  304 (408)
                      .+.
T Consensus        88 ~~~   90 (103)
T d2cqda1          88 LGA   90 (103)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            654

>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=99.73  E-value=5.2e-18  Score=127.97  Aligned_cols=78  Identities=12%  Similarity=0.237  Sum_probs=67.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ...++++|||+|||.++|+++|+++|++||+|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  |+  .
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~--g~--~   78 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM--GQ--T   78 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEET--TE--E
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEEC--CE--E
Confidence            344678999999999999999999999999999999875     35899999999999999999999998875  67  4


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.|+.
T Consensus        79 l~V~~a~   85 (88)
T d1rk8a_          79 IQVDWCF   85 (88)
T ss_dssp             CEEEESE
T ss_pred             EEEEEec
Confidence            5666653

>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=99.73  E-value=4.7e-18  Score=126.52  Aligned_cols=74  Identities=19%  Similarity=0.351  Sum_probs=65.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      +++|||+|||.++|+++|+++|++||.|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  |+  .+++.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~--g~--~l~v~   77 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVR--NK--RLKVS   77 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEET--TE--ECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEEC--CE--EEEEE
Confidence            46899999999999999999999999999999875     44899999999999999999999998875  66  45555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        78 ~a~   80 (82)
T d1b7fa1          78 YAR   80 (82)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            543

>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=99.73  E-value=7.1e-18  Score=126.39  Aligned_cols=72  Identities=13%  Similarity=0.185  Sum_probs=64.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ...++|||+|||.++||++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++.|||..+.+.+++|
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l   80 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPL   80 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEE
Confidence            3567899999999999999999999999999999875     45899999999999999999999999887655643

>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=99.73  E-value=4.4e-18  Score=128.95  Aligned_cols=79  Identities=14%  Similarity=0.209  Sum_probs=68.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....+..+|||+|||.++|+++|+++|++||+|.+|++.+     .++|||||+|.+.++|++|++.|||..|.  |+  
T Consensus         3 ~~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~--g~--   78 (90)
T d2cq0a1           3 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYD--HL--   78 (90)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEET--TE--
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEEC--CE--
Confidence            3445678999999999999999999999999999999875     35899999999999999999999998875  66  


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                      .|++.|+.
T Consensus        79 ~i~v~~ak   86 (90)
T d2cq0a1          79 ILNVEWAK   86 (90)
T ss_dssp             ECEEEESS
T ss_pred             EEEEEeee
Confidence            46666655

>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=99.73  E-value=9.7e-18  Score=133.01  Aligned_cols=76  Identities=20%  Similarity=0.489  Sum_probs=70.6

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec--cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~--~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      +++|||+|||.++++++|+++|++||.|.+|+  .++..+|||||+|.+.++|.+|++.|||..|+|+.|+|.++...
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            58999999999999999999999999999994  45677999999999999999999999999999999999998653

>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=99.73  E-value=7.8e-18  Score=129.01  Aligned_cols=75  Identities=25%  Similarity=0.418  Sum_probs=70.0

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      .++|||+||+..+++++|+++|++||.|.+|+.. ..+|||||+|.+.++|++|++.|||..|+|+.|+|+|++++
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~-~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF-PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEE-ecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            4789999999999999999999999999999644 56999999999999999999999999999999999999764

>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=99.73  E-value=8.1e-18  Score=125.49  Aligned_cols=71  Identities=25%  Similarity=0.496  Sum_probs=65.9

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVI  297 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v  297 (408)
                      +.++|||+|||..+|+++|+++|++||.|.+++     .++.++|||||+|.+.++|++|++.|||..|+|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            358999999999999999999999999999882     45778999999999999999999999999999999987

>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=99.72  E-value=6.9e-18  Score=129.76  Aligned_cols=76  Identities=21%  Similarity=0.339  Sum_probs=68.7

Q ss_pred             CCCceEEEcCCC-CCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          226 NNQGTIVVFNLD-SGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       226 ~~~~~l~V~nLp-~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ....+|||+||+ ..+++++|+++|++||.|..++.   .+|||||+|++.++|++|++.|||+.|.|+.|+|+|++++.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            345789999997 57889999999999999999874   68999999999999999999999999999999999997643

>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=99.72  E-value=9e-18  Score=127.23  Aligned_cols=78  Identities=21%  Similarity=0.363  Sum_probs=68.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ...+.++|||+|||.++||++|+++|++||.|..|++.+   ..+|||||+|.+.++|++|++.|||..|.  |+  .++
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~--g~--~i~   79 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKIL--GK--EVK   79 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEET--TE--EEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEEC--CE--EEE
Confidence            345678999999999999999999999999999999875   34899999999999999999999999876  66  466


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.|+.
T Consensus        80 v~~a~   84 (90)
T d2cqia1          80 VNWAT   84 (90)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            66654

>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=99.72  E-value=5.8e-18  Score=127.09  Aligned_cols=75  Identities=21%  Similarity=0.419  Sum_probs=65.9

Q ss_pred             CceEEEcCCCCCCc-HHHHHHHHhcCCCceeec------cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          228 QGTIVVFNLDSGVS-SSTLKEIFQAFGPVKELR------ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       228 ~~~l~V~nLp~~~t-~~~L~~~F~~~G~v~~v~------~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      .++|||+|||.+++ +++|+++|++||.|.+++      .++.++|||||+|.+.++|++|++ |||..|+|+.|+|++|
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEEC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEc
Confidence            58999999999876 556999999999999883      356779999999999999999996 9999999999999999


Q ss_pred             cCC
Q 046223          301 RPG  303 (408)
Q Consensus       301 ~~~  303 (408)
                      +++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.72  E-value=5.7e-18  Score=126.35  Aligned_cols=69  Identities=16%  Similarity=0.168  Sum_probs=62.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      .++++|||+|||.++||++|+++|++||.|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  ||.
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--gr~   80 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD--GRR   80 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEET--TEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEEC--CEE
Confidence            3578999999999999999999999999999998875     45899999999999999999999998876  663

>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=99.72  E-value=6.4e-18  Score=126.69  Aligned_cols=73  Identities=26%  Similarity=0.451  Sum_probs=65.7

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCceeec-----cC---CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ET---PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       231 l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~---~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      |||+|||.++|+++|+++|++||.|.++.     .+   +.++|||||+|.+.++|++|++.|||..++|+.|+|+|++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            79999999999999999999999998882     11   13589999999999999999999999999999999999864


Q ss_pred             C
Q 046223          303 G  303 (408)
Q Consensus       303 ~  303 (408)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.72  E-value=9.6e-18  Score=124.83  Aligned_cols=73  Identities=22%  Similarity=0.418  Sum_probs=64.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ++|||+|||.++||++|+++|++||+|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  |+  .+++.|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~--g~--~l~v~~   78 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQ--TK--TIKVSY   78 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TE--ECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEEC--CE--EEEEEE
Confidence            5799999999999999999999999999999875     45899999999999999999999998876  66  455555


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      ++
T Consensus        79 Ak   80 (82)
T d1fxla1          79 AR   80 (82)
T ss_dssp             CC
T ss_pred             ee
Confidence            43

>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=99.72  E-value=5.4e-18  Score=131.76  Aligned_cols=80  Identities=30%  Similarity=0.384  Sum_probs=73.3

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      .++++|||+|||.++++++|+++|++||.|..+     ..++..+|||||+|.+.++|.+|++.|||..|.|+.|+|+||
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            446899999999999999999999999998877     246788999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 046223          301 RPGGH  305 (408)
Q Consensus       301 ~~~~~  305 (408)
                      +++..
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87654

>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=99.72  E-value=7.2e-18  Score=126.30  Aligned_cols=73  Identities=25%  Similarity=0.464  Sum_probs=67.0

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEEe
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG--KHVVIEFS  300 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~a  300 (408)
                      +.+|||+|||..+|+++|+++|++||.|.+++     .++.++|||||+|.+.++|.+|++.|||..+.|  ++|+|+||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            47899999999999999999999999999883     457789999999999999999999999999998  55999986

>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=99.72  E-value=1.1e-17  Score=132.74  Aligned_cols=75  Identities=16%  Similarity=0.231  Sum_probs=66.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      .+++|||+|||.++|+++|+++|++||.|.+|++..  .++|||||+|.+.++|..|++.|||..|.  |+.  |++.|+
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~--gr~--l~V~~a   81 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVC--NRY--LVVLYY   81 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEET--TEE--CEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEEC--CEE--EEEEEc
Confidence            478999999999999999999999999999999875  56999999999999999999999999876  774  555554


Q ss_pred             C
Q 046223          159 S  159 (408)
Q Consensus       159 ~  159 (408)
                      .
T Consensus        82 ~   82 (114)
T d2f9da1          82 N   82 (114)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.72  E-value=8.6e-18  Score=126.82  Aligned_cols=76  Identities=22%  Similarity=0.361  Sum_probs=69.2

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceee-ccCCCCccEEEEEECCHHHHHHHHHHhCCcee-CCeEEEEEEecCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-RETPLKKHQRFIEFYDVRDAAKALKEMNGQEI-YGKHVVIEFSRPG  303 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~-~g~~l~v~~a~~~  303 (408)
                      +++|||+|||.++++++|+++|++||.|..+ ...+..++||||+|.+.++|.+|+..|||..+ +|+.|+|+|+++.
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            5899999999999999999999999999877 34566789999999999999999999999988 5899999999763

>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=99.71  E-value=1e-17  Score=131.47  Aligned_cols=81  Identities=14%  Similarity=0.076  Sum_probs=70.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ..+..+|||+||++++||++|+++|++||.|..|.+.+ +++|||||+|.+.++|++|++.|||..|...++  .+++.|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~--~l~v~~   81 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACC--TLRIDF   81 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCC--CCEEEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCc--EEEEEe
Confidence            45678899999999999999999999999999988876 568999999999999999999999999875555  577777


Q ss_pred             cCcc
Q 046223          158 SSGL  161 (408)
Q Consensus       158 s~~~  161 (408)
                      +...
T Consensus        82 s~~~   85 (108)
T d2adba1          82 SKLT   85 (108)
T ss_dssp             CSSC
T ss_pred             cCCc
Confidence            7643

>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=99.71  E-value=1e-17  Score=125.51  Aligned_cols=74  Identities=18%  Similarity=0.333  Sum_probs=68.0

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG--KHVVIEF  299 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~  299 (408)
                      ...+|||+|||.++++++|+++|++||.|.+++     .++.++|||||+|.+.++|.+|++.|||..+.|  ++|+|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            347899999999999999999999999999883     567889999999999999999999999999976  8899998


Q ss_pred             e
Q 046223          300 S  300 (408)
Q Consensus       300 a  300 (408)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.71  E-value=6.4e-18  Score=127.45  Aligned_cols=76  Identities=20%  Similarity=0.228  Sum_probs=70.4

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ..++|||+|||.++|+++|+++|++||.|.+|+....+++||||+|.+.++|++|+.  ++..|+|++|+|++++++.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~   79 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCC
Confidence            358999999999999999999999999999998777889999999999999999985  7889999999999997755

>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=99.71  E-value=1.1e-17  Score=127.44  Aligned_cols=75  Identities=16%  Similarity=0.231  Sum_probs=66.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ..++||||+|||.++||++|+++|++||+|.+|.+.+     .++|||||+|.+.++|++|++.|||..|.  |+  .++
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~--gr--~i~   80 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLD--DR--IIR   80 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEET--TE--ECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEEC--CE--EEE
Confidence            4678999999999999999999999999999999876     35899999999999999999999999876  67  455


Q ss_pred             cccc
Q 046223          155 NPYS  158 (408)
Q Consensus       155 ~~~s  158 (408)
                      +.|+
T Consensus        81 V~~a   84 (93)
T d1h2vz_          81 TDWD   84 (93)
T ss_dssp             EEEE
T ss_pred             EEEc
Confidence            5554

>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=99.71  E-value=1.4e-17  Score=127.06  Aligned_cols=77  Identities=19%  Similarity=0.376  Sum_probs=66.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee------cCccEEEEEECCHHHHHHHHHHh-cCcccccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER------LMEGIVTVHFYDLRHAEMAFKEI-REQHMQLQQQSY  151 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~------~~kG~afV~F~~~~~A~~Ai~~l-ng~~i~~~gr~l  151 (408)
                      ...+++|||+|||.+++|++|+++|++||.|..|++.+      +++|||||+|.+.++|++|++.| ||..|.  ||  
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~--Gr--   80 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY--GR--   80 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSS--SC--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEEC--CE--
Confidence            45678899999999999999999999999999999864      35899999999999999999998 787765  67  


Q ss_pred             ceeccccC
Q 046223          152 GLKNPYSS  159 (408)
Q Consensus       152 ~~~~~~s~  159 (408)
                      .|++.|+.
T Consensus        81 ~l~V~~A~   88 (94)
T d2cpha1          81 RLVLEWAD   88 (94)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEcC
Confidence            46666655

>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=99.71  E-value=4.5e-18  Score=129.01  Aligned_cols=76  Identities=20%  Similarity=0.334  Sum_probs=69.5

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ...+|||+|||+++|+++|+++|+.||.|..+    ..++.++|||||+|.+.++|++|++ |||..++|+.|+|++|+.
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            35799999999999999999999999998776    3567889999999999999999996 999999999999999976


Q ss_pred             C
Q 046223          303 G  303 (408)
Q Consensus       303 ~  303 (408)
                      +
T Consensus        91 k   91 (91)
T d1fjeb1          91 R   91 (91)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.71  E-value=1.7e-17  Score=125.43  Aligned_cols=77  Identities=21%  Similarity=0.319  Sum_probs=69.1

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ...+|||+|||+++|+++|+++|++||.|.++     +.++.++|||||+|.+.++|++|++.  +..|+|+.|.|+++.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCC
Confidence            35889999999999999999999999999998     35688999999999999999999985  458999999999998


Q ss_pred             CCCC
Q 046223          302 PGGH  305 (408)
Q Consensus       302 ~~~~  305 (408)
                      ++..
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            7653

>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=99.71  E-value=2e-17  Score=124.59  Aligned_cols=75  Identities=15%  Similarity=0.311  Sum_probs=66.6

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ..+|||+|||.+++++||+++|++|| +..+ ..+..++||||+|.+.++|++|++.|||..|.|++|+|+|++.+.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~-~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYC-YVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCE-EEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceee-eeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            47899999999999999999999999 2222 234679999999999999999999999999999999999996554

>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=99.71  E-value=2.7e-17  Score=126.77  Aligned_cols=79  Identities=23%  Similarity=0.375  Sum_probs=70.6

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhC------CceeCCeE
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMN------GQEIYGKH  294 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~------g~~~~g~~  294 (408)
                      ...++|||+|||+++|+++|+++|++||.|..+     ...+.++|||||+|.+.++|.+|++.||      |..+.|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            345899999999999999999999999999887     2456689999999999999999999987      67899999


Q ss_pred             EEEEEecCCC
Q 046223          295 VVIEFSRPGG  304 (408)
Q Consensus       295 l~v~~a~~~~  304 (408)
                      |+|++|+++.
T Consensus        86 l~v~~a~~k~   95 (98)
T d1x4ha1          86 LKVDLAVTRD   95 (98)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999998754

>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=99.71  E-value=1.9e-17  Score=130.28  Aligned_cols=77  Identities=25%  Similarity=0.418  Sum_probs=70.5

Q ss_pred             CceEEEcCCCC-CCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          228 QGTIVVFNLDS-GVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~-~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      +.+|||+||++ .+|+++|+++|+.||.|+.|......+|||||+|++.++|.+|++.|||..|.|+.|+|+|++...
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            48999999965 699999999999999999997666678999999999999999999999999999999999987554

>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=99.71  E-value=6e-18  Score=127.91  Aligned_cols=75  Identities=16%  Similarity=0.298  Sum_probs=66.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ..++|||+|||+++|+++|+++|++||+|.+|++.+     .++|||||+|.+.++|++|++.|||..|.  |+  .+++
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~--g~--~l~v   79 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF--GR--TIRV   79 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEET--TE--EEEE
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEEC--CE--EEEE
Confidence            568999999999999999999999999999999875     56999999999999999999999998875  67  4566


Q ss_pred             cccC
Q 046223          156 PYSS  159 (408)
Q Consensus       156 ~~s~  159 (408)
                      .|+.
T Consensus        80 ~~a~   83 (89)
T d2cqba1          80 NLAK   83 (89)
T ss_dssp             EECC
T ss_pred             EEeC
Confidence            5554

>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=99.71  E-value=1.3e-17  Score=125.08  Aligned_cols=76  Identities=20%  Similarity=0.312  Sum_probs=70.5

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      .++|||+|||.++++++|+++|++||.|.+++.. ..++||||+|.+.++|.+|++.|||..|+|+.|+|+||....
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~-~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeee-cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            4789999999999999999999999999999643 568999999999999999999999999999999999997654

>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=99.71  E-value=2.1e-17  Score=124.70  Aligned_cols=76  Identities=20%  Similarity=0.213  Sum_probs=66.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      ++++|||+|||.++||++|+++|++||.|..+.+.. +++|||||+|.+.++|.+|+..|||..|. +|+  .|++.|++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~-~g~--~l~v~~sk   85 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLG-ENH--HLRVSFSK   85 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSS-SSC--BCEEEECS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEec-CCC--EEEEEeCC
Confidence            578999999999999999999999999998866554 67999999999999999999999998874 456  46777765

>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=99.71  E-value=6.7e-18  Score=130.54  Aligned_cols=75  Identities=21%  Similarity=0.500  Sum_probs=69.1

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+||++++++++|+++|+.||.|.+|     ..++.++|||||+|.+.++|++|++ |||..|+|+.|+|+++++
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            4789999999999999999999999999988     2467899999999999999999995 999999999999999865


Q ss_pred             C
Q 046223          303 G  303 (408)
Q Consensus       303 ~  303 (408)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.71  E-value=2e-17  Score=127.06  Aligned_cols=77  Identities=17%  Similarity=0.295  Sum_probs=68.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      .++++|||+|||.++|+++|+++|++||+|..|++.+ .++||||+|.+.++|++|++.|||..|.+.+  +.+++.|++
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~-~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~--~~l~v~~ak   91 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-GDSFAYIQYESLDAAQAACAKMRGFPLGGPD--RRLRVDFAK   91 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-SSCCEEEEESSHHHHHHHHHHHTTCBCSSSS--CBCEEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeec-cccEEEeccCCHHHHHHHHHHhCCCEeCCCc--eEEEEEeCC
Confidence            4578999999999999999999999999999999874 6899999999999999999999999887444  467877765

>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=99.71  E-value=9.2e-18  Score=124.20  Aligned_cols=72  Identities=18%  Similarity=0.257  Sum_probs=64.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      +|||+|||+++||++|+++|++||+|.+|++.+     +++|||||+|.+.++|++|++.|||..+.  ||  .+++.|+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~--gr--~i~v~~a   77 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIK--GK--PVRIMWS   77 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEET--TE--ECEEEEC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEEC--CE--EEEEEEe
Confidence            699999999999999999999999999999986     34899999999999999999999998876  67  4666665


Q ss_pred             C
Q 046223          159 S  159 (408)
Q Consensus       159 ~  159 (408)
                      .
T Consensus        78 ~   78 (80)
T d1cvja1          78 Q   78 (80)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.70  E-value=7.1e-18  Score=131.48  Aligned_cols=77  Identities=29%  Similarity=0.453  Sum_probs=71.1

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+|||.++++++|+++|++||.|.+|+     .++.++|||||+|.+.++|++|++.|||..|.|+.|+|+++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            37899999999999999999999999999883     4677899999999999999999999999999999999999876


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      ..
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.70  E-value=2.1e-17  Score=128.10  Aligned_cols=77  Identities=12%  Similarity=0.214  Sum_probs=70.4

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      .++|||+|||+++++++|+++|++||.|..+.     .++.++|||||+|.+.++|++|++ ++|..|+|+.|.|++|++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            37899999999999999999999999999983     456789999999999999999996 899999999999999987


Q ss_pred             CCC
Q 046223          303 GGH  305 (408)
Q Consensus       303 ~~~  305 (408)
                      +..
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>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=99.70  E-value=2.6e-17  Score=122.85  Aligned_cols=73  Identities=14%  Similarity=0.258  Sum_probs=67.7

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      .++|||+|||+++|+++|+++|++||.|..+     +.++.++|||||+|.+.++|++|++ +++..|.|+.|+|+.|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            4799999999999999999999999999888     3568889999999999999999997 79999999999999875

>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=99.70  E-value=1.4e-17  Score=122.94  Aligned_cols=73  Identities=21%  Similarity=0.444  Sum_probs=67.5

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      .++|||+||+  +|+++|+++|++||.|.+++. .+.++||||+|.+.++|.+|++.|||..++|+.|+|+|++++
T Consensus         5 ~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~-~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCEEEEECSS--CCHHHHHHHHSTTCCCSCEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCEEEEECCC--CCHHHHHHHHhccCccceeee-ccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            5899999995  899999999999999999964 367899999999999999999999999999999999999764

>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=99.70  E-value=3.1e-17  Score=129.01  Aligned_cols=74  Identities=16%  Similarity=0.218  Sum_probs=66.5

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           82 TRTLVLSYVPG-DVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        82 ~rtlfV~nLp~-~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      +++|||+||++ .+||++|+++|+.||+|..|.+.++.+|||||+|.+.++|++|++.|||..|.  |+  .|++.|+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~--g~--~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLH--GK--PIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCS--SS--BCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEEC--CE--EEEEEECC
Confidence            67999999965 59999999999999999999999888999999999999999999999999876  67  45666665

>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=99.70  E-value=2.5e-17  Score=127.70  Aligned_cols=75  Identities=15%  Similarity=0.164  Sum_probs=65.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ++++|||+|||+++||++|+++|+.||.|.++.+..     .++|||||+|.+.++|++|++.|||..|.  |+  .|+|
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~--g~--~i~V   92 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIG--MK--RLKV   92 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET--TE--ECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEEC--CE--EEEE
Confidence            467899999999999999999999999999988775     45899999999999999999999998876  67  4555


Q ss_pred             cccC
Q 046223          156 PYSS  159 (408)
Q Consensus       156 ~~s~  159 (408)
                      .|+.
T Consensus        93 ~~a~   96 (102)
T d2cpza1          93 QLKR   96 (102)
T ss_dssp             ECCC
T ss_pred             EEeC
Confidence            5544

>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=99.70  E-value=2.5e-17  Score=120.06  Aligned_cols=72  Identities=11%  Similarity=0.266  Sum_probs=65.4

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       231 l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      |||+|||.++++++|+++|++|| +..+. .+..+|||||+|.+.++|++|++.|||..+.|++|+|+|++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~-~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCF-VDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEE-EETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-cccee-ecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 44443 45789999999999999999999999999999999999996543

>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=99.70  E-value=4.2e-17  Score=124.22  Aligned_cols=78  Identities=17%  Similarity=0.222  Sum_probs=67.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .....++|||+|||+++|+++|+++|++||+|..|++..   .++|||||+|.+.++|++|++.|||..|.  |+  .|+
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~--g~--~l~   82 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVE--GR--KIE   82 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEET--TE--ECE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEEC--CE--EEE
Confidence            344567899999999999999999999999999999876   35899999999999999999999998876  66  466


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.|+.
T Consensus        83 V~~A~   87 (93)
T d2cq3a1          83 VNNAT   87 (93)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            65654

>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=99.70  E-value=1e-16  Score=131.59  Aligned_cols=77  Identities=22%  Similarity=0.340  Sum_probs=67.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....++|||+|||+++||++|+++|++||+|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  ||  .|
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~--gr--~l  114 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNIL--NK--RL  114 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECS--SC--EE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEEC--CE--EE
Confidence            34567999999999999999999999999999999875     35899999999999999999999998876  77  45


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      +|.|+.
T Consensus       115 ~V~~a~  120 (139)
T d1u6fa1         115 KVALAA  120 (139)
T ss_dssp             EEEESS
T ss_pred             EEEEcC
Confidence            665554

>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=99.70  E-value=6.3e-18  Score=123.92  Aligned_cols=71  Identities=24%  Similarity=0.303  Sum_probs=65.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ++|||+|||+++|+++|+++|++||.|.++     +.++.++|||||+|.+.++|++|++ +++..++|+.|+|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999887     3567899999999999999999997 7999999999999886

>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=99.69  E-value=3.3e-17  Score=125.43  Aligned_cols=74  Identities=14%  Similarity=0.247  Sum_probs=66.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      ..++|||+|||.+++|++|+++|++||+|.+|++.+ .+|||||+|.+.++|++|++.|||..|.  |+  .+++.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~-~kg~afV~f~~~~~A~~Ai~~l~~~~i~--g~--~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-EKGYSFVRFSTHESAAHAIVSVNGTTIE--GH--VVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTCEET--TE--ECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEe-cceEEEEEECCHHHHHHHHHHhCCCEEC--CE--EEEEEEcC
Confidence            457899999999999999999999999999999985 6999999999999999999999998876  67  46666654

>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=99.69  E-value=1.5e-17  Score=128.56  Aligned_cols=74  Identities=16%  Similarity=0.249  Sum_probs=64.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      .+...++|||+|||.++||++|+++|+.||+|.+|++.+     +++|||||+|.+.++|++|++ |||..|.  |+.|.
T Consensus        14 ~~~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~--G~~l~   90 (101)
T d2cq4a1          14 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLL--GVPII   90 (101)
T ss_dssp             THHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEET--TEEEE
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEEC--CEEEE
Confidence            334568999999999999999999999999999999986     469999999999999999995 9998876  67444


Q ss_pred             ee
Q 046223          153 LK  154 (408)
Q Consensus       153 ~~  154 (408)
                      ++
T Consensus        91 V~   92 (101)
T d2cq4a1          91 VQ   92 (101)
T ss_dssp             EE
T ss_pred             EE
Confidence            33

>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=99.69  E-value=3.2e-17  Score=123.59  Aligned_cols=79  Identities=23%  Similarity=0.219  Sum_probs=68.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ...++++|||+|||.++|+++|+++|++||.|.+|++. +++|||||+|.+.++|++|++.+++..+.+.|+  .+++.|
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~-~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~--~l~v~~   80 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML-KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQ--PIYIQY   80 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTE--ECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccc-ccceEEEEEeCCHHHHHHHHHHHccCCCccCCC--EEEEEE
Confidence            45689999999999999999999999999999999887 478999999999999999999887665555677  466666


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      ++
T Consensus        81 sk   82 (88)
T d2cq1a1          81 SN   82 (88)
T ss_dssp             CS
T ss_pred             CC
Confidence            65

>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=99.69  E-value=2.3e-17  Score=130.23  Aligned_cols=76  Identities=21%  Similarity=0.344  Sum_probs=70.7

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      +++|||+|||..+++++|+++|+.||.|..|.. ...+|||||+|.+.++|++|++.|||..|.|+.|.|+|+....
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l-~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEe-eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            479999999999999999999999999999964 4678999999999999999999999999999999999997653

>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=99.69  E-value=1.8e-17  Score=121.05  Aligned_cols=70  Identities=23%  Similarity=0.282  Sum_probs=65.2

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       230 ~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      +|||+|||.++|+++|+++|++||.|..+     ..++..++||||+|.+.++|++|++ |||..|+|+.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            59999999999999999999999999888     3467789999999999999999997 9999999999999986

>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=99.69  E-value=3.6e-17  Score=126.15  Aligned_cols=76  Identities=20%  Similarity=0.203  Sum_probs=66.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ..+.+|||+|||+++|+++|+++|++||.|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  ||.  |+
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~--gr~--i~   81 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQ--GRM--LH   81 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESS--SCE--EE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEEC--CEE--EE
Confidence            4567899999999999999999999999999999875     45999999999999999999999998876  774  55


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.++.
T Consensus        82 V~~a~   86 (99)
T d1whwa_          82 VLPST   86 (99)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            55544

>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=99.69  E-value=4e-17  Score=120.49  Aligned_cols=72  Identities=17%  Similarity=0.305  Sum_probs=66.2

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      .++|||+|||+++|+++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|++ +||..|+|+.|+|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            3789999999999999999999999999888     3567789999999999999999986 8999999999999876

>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=99.69  E-value=3.3e-17  Score=120.48  Aligned_cols=69  Identities=19%  Similarity=0.248  Sum_probs=61.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .|||+|||+++||++|+++|++||.|.+|++..    +++|||||+|.+.++|++|++.|||..+.  ||.|.++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~--g~~l~V~   74 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLD--GRPMNIQ   74 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEE
Confidence            599999999999999999999999999999875    55899999999999999999999998876  7744433

>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=99.69  E-value=2.3e-17  Score=125.14  Aligned_cols=77  Identities=29%  Similarity=0.519  Sum_probs=69.0

Q ss_pred             CceEEEcCCCCCCcHHHHHH----HHhcCCCceeec--cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          228 QGTIVVFNLDSGVSSSTLKE----IFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~----~F~~~G~v~~v~--~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      +++|||+|||..++++||++    +|++||.|.+|+  .++.++|||||+|.+.++|.+|++.|||..++|+.|+|.||+
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak   82 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK   82 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            58999999999999999864    689999999984  334568999999999999999999999999999999999998


Q ss_pred             CCC
Q 046223          302 PGG  304 (408)
Q Consensus       302 ~~~  304 (408)
                      ++.
T Consensus        83 ~~~   85 (91)
T d1nu4a_          83 TDS   85 (91)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            764

>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=99.69  E-value=5.5e-17  Score=124.12  Aligned_cols=77  Identities=16%  Similarity=0.194  Sum_probs=67.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ....++|||+|||.++|+++|+++|++||.|..+.+.+  .++|||||+|.+.++|++||+.|||..|.  |+  .|++.
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~--g~--~l~V~   86 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYD--GY--RLRVE   86 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEET--TE--ECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEEC--CE--EEEEE
Confidence            44567899999999999999999999999999998875  56999999999999999999999998876  67  45666


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        87 ~a~   89 (95)
T d1x4aa1          87 FPR   89 (95)
T ss_dssp             CCC
T ss_pred             ecc
Confidence            654

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=6.8e-18  Score=127.63  Aligned_cols=75  Identities=12%  Similarity=0.158  Sum_probs=65.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ...+|||+|||.++|+++|+++|++||.|..+++..   .++|||||+|.+.++|++|++.|||..|.  |+  .|++.+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~--g~--~i~V~~   82 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN--DR--KVFVGR   82 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEET--TE--EEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEEC--CE--EEEEEE
Confidence            346899999999999999999999999999999876   35899999999999999999999998876  66  455555


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus        83 a~   84 (89)
T d1cvja2          83 FK   84 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.68  E-value=3.2e-17  Score=122.76  Aligned_cols=71  Identities=15%  Similarity=0.268  Sum_probs=62.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEEEee--------cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           85 LVLSYVPGDVSETIVRRDLEVFGEVRGVQMER--------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        85 lfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~--------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      |||+|||+++|+++|+++|++||.|.+|++.+        .++|||||+|.+.++|++|++.|||..|.  |+  .+++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~--g~--~i~V~   76 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVD--GH--KLEVR   76 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEET--TE--ECEEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEEC--CE--EEEEE
Confidence            89999999999999999999999999998875        24899999999999999999999998876  67  45555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        77 ~a~   79 (85)
T d2cpfa1          77 ISE   79 (85)
T ss_dssp             CSS
T ss_pred             ECC
Confidence            543

>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=99.68  E-value=8.1e-17  Score=124.58  Aligned_cols=71  Identities=15%  Similarity=0.241  Sum_probs=63.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQS  150 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~  150 (408)
                      .....++|||+|||.++|+++|+++|++||.|..+.+..    .++|||||+|.+.++|++|++.|||..|.  ||.
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~--gr~   88 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIK--TPP   88 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCC--CCT
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEEC--CcC
Confidence            344568999999999999999999999999999988765    45899999999999999999999999876  663

>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=99.68  E-value=3.9e-17  Score=123.73  Aligned_cols=75  Identities=13%  Similarity=0.222  Sum_probs=65.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .+.++|||+|||+++|+++|+++|++||.|..+.+.+     .++|||||+|.+.++|++|++.|||..|.  |+.  |+
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~--g~~--l~   78 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD--GRQ--IR   78 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTT--SCC--CE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEEC--CEE--EE
Confidence            3578899999999999999999999999999988765     46999999999999999999999998875  774  44


Q ss_pred             cccc
Q 046223          155 NPYS  158 (408)
Q Consensus       155 ~~~s  158 (408)
                      +.++
T Consensus        79 V~~a   82 (90)
T d1x5sa1          79 VDQA   82 (90)
T ss_dssp             EEEE
T ss_pred             EEEc
Confidence            4443

>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=99.68  E-value=2.5e-17  Score=120.19  Aligned_cols=70  Identities=19%  Similarity=0.275  Sum_probs=64.3

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       230 ~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      +|||+|||+++|+++|+++|++||.|..+     ..+++++|||||+|.+.++|++|++ +++..|+|+.|+|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            48999999999999999999999999988     2567889999999999999999997 8999999999998654

>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=99.68  E-value=7.1e-18  Score=126.90  Aligned_cols=74  Identities=18%  Similarity=0.192  Sum_probs=67.2

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ++|||+|||+++++++|+++|++||.|..++.  ..+|||||+|.+.++|++|++.|||..|.|+.|+|.+++.+.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i--~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADV--YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEE--CTTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccc--cccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            36999999999999999999999999999864  346999999999999999999999999999999998876543

>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=99.68  E-value=1.1e-17  Score=130.37  Aligned_cols=76  Identities=13%  Similarity=0.221  Sum_probs=66.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....|+|||+|||.++|+++|+++|++||+|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  |+.  |
T Consensus         5 ~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~--g~~--i   80 (104)
T d1p1ta_           5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFS--GRA--L   80 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCS--SSC--B
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEEC--CEE--E
Confidence            34568999999999999999999999999999999875     35899999999999999999999998876  674  4


Q ss_pred             ecccc
Q 046223          154 KNPYS  158 (408)
Q Consensus       154 ~~~~s  158 (408)
                      ++.++
T Consensus        81 ~V~~a   85 (104)
T d1p1ta_          81 RVDNA   85 (104)
T ss_dssp             EEEET
T ss_pred             EEEEC
Confidence            55444

>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=99.68  E-value=5.3e-17  Score=121.09  Aligned_cols=71  Identities=15%  Similarity=0.258  Sum_probs=62.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ..++|||+|||+++|+++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++ +++..|.  ||.|.++
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~--Gr~i~V~   80 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVD--GRVVEPK   80 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEET--TEECEEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEEC--CEEEEEE
Confidence            458999999999999999999999999999999875     459999999999999999997 6888765  7755554

>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=99.68  E-value=3.4e-17  Score=121.45  Aligned_cols=73  Identities=12%  Similarity=0.069  Sum_probs=62.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      .||||+|||+++|+++|+++|++||.|..+.+..     +++|||||+|.+.++|++|++.|||..|.  |+  .+++.|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~--g~--~i~V~~   77 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIE--GY--TLVTKV   77 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEET--TE--ECEEEE
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEEC--CE--EEEEEE
Confidence            5899999999999999999999999998876653     56999999999999999999999999876  67  455555


Q ss_pred             cC
Q 046223          158 SS  159 (408)
Q Consensus       158 s~  159 (408)
                      +.
T Consensus        78 a~   79 (81)
T d2ghpa1          78 SN   79 (81)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>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=99.67  E-value=1.5e-16  Score=123.69  Aligned_cols=80  Identities=18%  Similarity=0.133  Sum_probs=69.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      ...++++|||+|||.++||++|+++|++||.|..|++. +.+|+|||+|.+.++|++|++.|++..+.+.|+  .+++.|
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~-~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~--~l~v~~   87 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM-PFKRQALVEFENIDSAKECVTFAADVPVYIAGQ--QAFFNY   87 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSS--BCEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEE-ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeE--EEEEEE
Confidence            44578999999999999999999999999999999887 479999999999999999999998776666677  466667


Q ss_pred             cCc
Q 046223          158 SSG  160 (408)
Q Consensus       158 s~~  160 (408)
                      ++.
T Consensus        88 s~~   90 (104)
T d1wexa_          88 STS   90 (104)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            653

>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=99.67  E-value=6.9e-17  Score=119.06  Aligned_cols=74  Identities=18%  Similarity=0.248  Sum_probs=64.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      +..+++|||+||+  +||++|+++|++||+|.+|++. +.+|||||+|.+.++|.+|++.|||..|.  |+  .+++.|+
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~-~~~~~afV~f~~~~~A~~Ai~~lng~~~~--g~--~l~V~~a   74 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTYEKMESADQAVAELNGTQVE--SV--QLKVNIA   74 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCBCS--SC--BCEEEEC
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeec-cCCCEEEEEEcccHHHHHHHHHhCCCEEC--CE--EEEEEEe
Confidence            3467899999985  9999999999999999999987 47899999999999999999999998876  66  4566665


Q ss_pred             C
Q 046223          159 S  159 (408)
Q Consensus       159 ~  159 (408)
                      .
T Consensus        75 ~   75 (79)
T d2bz2a1          75 R   75 (79)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.67  E-value=2.6e-17  Score=126.24  Aligned_cols=79  Identities=19%  Similarity=0.238  Sum_probs=69.2

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ....++++|||+|||.++|+++|+++|++||.|..+....+++|||||+|.+.++|++|++.|||..|.  ||  .|++.
T Consensus        11 ~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~--gr--~i~V~   86 (96)
T d1fjca_          11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEID--GR--SVSLY   86 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEET--TE--EEEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEEC--CE--EEEEE
Confidence            345568999999999999999999999999999888776678999999999999999999999998876  77  46666


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        87 ~a~   89 (96)
T d1fjca_          87 YTG   89 (96)
T ss_dssp             ECS
T ss_pred             EeC
Confidence            655

>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=99.67  E-value=6.6e-17  Score=121.15  Aligned_cols=74  Identities=19%  Similarity=0.304  Sum_probs=65.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      ...+|||+|||.++++++|+++|++||+|.+|++. +.+|||||+|.+.++|++|++.|||..|.  |+  .+++.|+.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~-~~k~~afV~f~~~~~A~~A~~~l~g~~i~--g~--~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLR--GK--QLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBT--TB--CCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeee-cccceEEEEECCHHHHHHHHHHhCCCEEC--CE--EEEEEECC
Confidence            34579999999999999999999999999999987 46999999999999999999999999876  66  45555554

>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=99.67  E-value=1.9e-17  Score=128.25  Aligned_cols=76  Identities=16%  Similarity=0.250  Sum_probs=68.7

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      +.++|||+|||.++++++|+++|+.||.|..+    ...+.++|||||+|.+.++|++|++.|||..|.|+.+.|.+++|
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            35789999999999999999999999999877    34567789999999999999999999999999999988877654

>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=99.67  E-value=4.1e-17  Score=122.04  Aligned_cols=72  Identities=17%  Similarity=0.329  Sum_probs=63.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      +|||+|||.++||++|+++|++||+|.+|++.+     +++|||||+|.+.++|++|++.|||..|.  |+  .+++.|+
T Consensus         3 rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~--g~--~l~V~~A   78 (85)
T d2u2fa_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG--DK--KLLVQRA   78 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCS--SS--CCEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEEC--CE--EEEEEEC
Confidence            699999999999999999999999999999875     45899999999999999999999998876  66  3555554


Q ss_pred             C
Q 046223          159 S  159 (408)
Q Consensus       159 ~  159 (408)
                      .
T Consensus        79 ~   79 (85)
T d2u2fa_          79 S   79 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.67  E-value=4.5e-17  Score=128.45  Aligned_cols=76  Identities=13%  Similarity=0.207  Sum_probs=66.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      .+..++|||+|||+++++++|+++|++||+|..|.|. +++|||||+|.+.++|++|++.|||..|.  |+.  |.+.|+
T Consensus         7 ~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~-~~kg~afV~f~~~~~A~~A~~~lng~~~~--gr~--l~v~~a   81 (111)
T d1whxa_           7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFH--HVP--LYLEWA   81 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSS--SSB--CEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee-ccCceEEEEEcCHHHHHHHHHHHcCCccC--CCe--EEEEEC
Confidence            3456799999999999999999999999999999886 57999999999999999999999999876  674  455454


Q ss_pred             C
Q 046223          159 S  159 (408)
Q Consensus       159 ~  159 (408)
                      .
T Consensus        82 ~   82 (111)
T d1whxa_          82 P   82 (111)
T ss_dssp             E
T ss_pred             C
Confidence            3

>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=99.67  E-value=1.2e-16  Score=123.05  Aligned_cols=80  Identities=16%  Similarity=0.226  Sum_probs=65.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcc----ccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQH----MQLQQ  148 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~----i~~~g  148 (408)
                      ...+.++|||+|||+++||++|+++|++||.|..+.+..     .++|||||+|.+.++|++|++.||+..    ..+.|
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            445678999999999999999999999999999988765     468999999999999999999998532    22346


Q ss_pred             cccceeccccC
Q 046223          149 QSYGLKNPYSS  159 (408)
Q Consensus       149 r~l~~~~~~s~  159 (408)
                      |  .+++.|+.
T Consensus        84 r--~l~v~~a~   92 (98)
T d1x4ha1          84 R--QLKVDLAV   92 (98)
T ss_dssp             C--EEEEECCC
T ss_pred             E--EEEEEECC
Confidence            6  45555554

>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=99.67  E-value=2.2e-16  Score=122.93  Aligned_cols=76  Identities=20%  Similarity=0.298  Sum_probs=66.4

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee------ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL------RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v------~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      +..+|||+|||+++|+++|+++|+.|| |.++      ...+.++|||||+|.+.++|++|+ .|||..|+|+.|+|++|
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEEC
Confidence            358999999999999999999999999 4444      235677899999999999998776 49999999999999999


Q ss_pred             cCCC
Q 046223          301 RPGG  304 (408)
Q Consensus       301 ~~~~  304 (408)
                      +++.
T Consensus        92 ~~~~   95 (104)
T d1wi8a_          92 DQAQ   95 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>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=99.67  E-value=6.2e-17  Score=122.75  Aligned_cols=76  Identities=16%  Similarity=0.333  Sum_probs=65.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHH----HHhhccCCeEEEEEee--cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           80 GPTRTLVLSYVPGDVSETIVR----RDLEVFGEVRGVQMER--LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~----~~F~~~G~V~~v~~~~--~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      +|+++|||+|||.++|++||+    ++|++||+|.+|++.+  +++|||||+|.+.++|.+|++.|||..+.  |+  .+
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~--g~--~l   76 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFY--DK--PM   76 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEET--TE--EC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEEC--CE--EE
Confidence            368999999999999999986    4689999999998875  46999999999999999999999998876  66  46


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.|+.
T Consensus        77 ~v~~ak   82 (91)
T d1nu4a_          77 RIQYAK   82 (91)
T ss_dssp             EEEECS
T ss_pred             EEEEeC
Confidence            666655

>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=99.67  E-value=2.2e-16  Score=121.19  Aligned_cols=69  Identities=13%  Similarity=0.215  Sum_probs=62.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ....++|||+|||+++++++|+++|++||+|..+.+.  .+|||||+|.+.++|++||+.|||..|.  |+.|
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~lng~~~~--g~~i   80 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ--KDGMGMVEYLRKEDMEYALRKLDDTKFR--SHEG   80 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE--TTTEEEEEESSHHHHHHHHHHHSSEEEE--CTTS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhccccccccc--ccceEEEEECCHHHHHHHHHHhCCCEeC--CeEE
Confidence            3456789999999999999999999999999999886  5799999999999999999999999876  6643

>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=99.66  E-value=2.8e-17  Score=120.41  Aligned_cols=69  Identities=16%  Similarity=0.228  Sum_probs=61.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      +|||+|||+++||++|+++|++||.|.+|++.+     +++|||||+|.+.++|++|++ +++..|.  ||.|.++.
T Consensus         2 klfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~--Gr~i~V~~   75 (77)
T d1uawa_           2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELD--SKTIDPKV   75 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCS--SCCCEEEE
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEEC--CeEEEEEE
Confidence            699999999999999999999999999998875     569999999999999999997 7888775  77665554

>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=99.66  E-value=1.2e-16  Score=119.89  Aligned_cols=73  Identities=18%  Similarity=0.265  Sum_probs=66.9

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ..+|||+|||++++++||+++|+.||.|...     ..++.++|+|||+|.+.++|++|++.|||..++||+|+|+++
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4679999999999999999999999988653     356788999999999999999999999999999999999875

>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=99.66  E-value=2.8e-17  Score=119.69  Aligned_cols=70  Identities=20%  Similarity=0.308  Sum_probs=64.2

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       230 ~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      +|||+|||+++|+++|+++|++||.|.++     +.++.++|||||+|.+.++|++|++ +++..++|+.|+|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999988     3567889999999999999999997 5778899999999875

>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=99.66  E-value=2.7e-16  Score=118.41  Aligned_cols=80  Identities=16%  Similarity=0.213  Sum_probs=70.9

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHh--CCceeCCeEEEEEEecC
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEM--NGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l--~g~~~~g~~l~v~~a~~  302 (408)
                      ..++++|||+|||.++++++|+++|++||.|.+++.. ..+++|||+|.+.++|++|++.+  ++..++|+.|+|.|++.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~-~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~   83 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML-KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   83 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccc-ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCC
Confidence            3456999999999999999999999999999999643 56899999999999999999866  57799999999999976


Q ss_pred             CCC
Q 046223          303 GGH  305 (408)
Q Consensus       303 ~~~  305 (408)
                      +..
T Consensus        84 ~~l   86 (88)
T d2cq1a1          84 KEL   86 (88)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            653

>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=99.66  E-value=1.4e-16  Score=122.31  Aligned_cols=77  Identities=19%  Similarity=0.371  Sum_probs=69.8

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEEecCCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYG--KHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g--~~l~v~~a~~~~  304 (408)
                      +.++|||+||+.++++++|+++|++||.|..++.. ..++||||+|.+.++|++|++.|||..|.|  ++|+|+|+++..
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~-~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~   94 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEEC-SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeee-ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCC
Confidence            35899999999999999999999999999999643 568999999999999999999999999986  589999998643

>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=99.66  E-value=1.4e-16  Score=119.12  Aligned_cols=73  Identities=18%  Similarity=0.270  Sum_probs=67.3

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      .++|||+|||.++|+++|+++|+.||.|..++    .++.++|||||+|.+.++|++|++ ++|..+.|+.|+|.|++
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            48999999999999999999999999999982    456788999999999999999996 79999999999999864

>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=99.66  E-value=6.5e-17  Score=117.04  Aligned_cols=63  Identities=14%  Similarity=0.158  Sum_probs=58.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccc
Q 046223           85 LVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQ  149 (408)
Q Consensus        85 lfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr  149 (408)
                      |||+|||.++||++|+++|++||.|..+++.+     .++|||||+|.+.++|++|++.|||..|.  ||
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~--Gr   68 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQ--AQ   68 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCC--EE
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEEC--CE
Confidence            79999999999999999999999999988865     46999999999999999999999998876  55

>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=99.66  E-value=1.2e-16  Score=116.50  Aligned_cols=66  Identities=14%  Similarity=0.228  Sum_probs=58.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      .|||+|||+++||++|+++|++||+|..|.+.+     +++|||||+|.+.++|++|++ +++..|.  ||.|.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~--Gr~i~   71 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLN--GKVID   71 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBT--TBCCE
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEEC--CCEEE
Confidence            489999999999999999999999999999875     569999999999999999997 7887765  67443

>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=99.66  E-value=7.4e-17  Score=126.43  Aligned_cols=79  Identities=28%  Similarity=0.317  Sum_probs=69.6

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeec-cCCCCccEEEEEECCHHHHHHHHHHhCCcee--CCeEEEEEEecCCC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-ETPLKKHQRFIEFYDVRDAAKALKEMNGQEI--YGKHVVIEFSRPGG  304 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~-~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~~~  304 (408)
                      ..+|||+||++.+|+++|+++|++||.|..+. ...+.+|+|||+|.+.++|++|++.|||..|  .|++|+|.|+++..
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~   86 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS   86 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCcc
Confidence            47899999999999999999999999998873 2335689999999999999999999999988  57899999998765


Q ss_pred             CC
Q 046223          305 HS  306 (408)
Q Consensus       305 ~~  306 (408)
                      ..
T Consensus        87 ~~   88 (108)
T d2adba1          87 LN   88 (108)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>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=99.66  E-value=5.5e-17  Score=121.65  Aligned_cols=74  Identities=14%  Similarity=0.302  Sum_probs=62.7

Q ss_pred             CCCEEEEcCCCCCCC-HHHHHHHhhccCCeEEEEEee------cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           81 PTRTLVLSYVPGDVS-ETIVRRDLEVFGEVRGVQMER------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        81 ~~rtlfV~nLp~~vt-e~~L~~~F~~~G~V~~v~~~~------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ..++|||+|||.++| |++|+++|++||+|.+|++..      +++|||||+|.+.++|++|++ |||..|.  ||  .+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~--gr--~l   77 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLG--NR--EI   77 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEET--TE--EE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEEC--CE--EE
Confidence            578999999999986 566999999999999998754      458999999999999999996 9998876  77  45


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      ++.++.
T Consensus        78 ~V~~a~   83 (86)
T d2ghpa3          78 SVSLAD   83 (86)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            555544

>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=99.66  E-value=1.5e-16  Score=119.26  Aligned_cols=74  Identities=12%  Similarity=0.177  Sum_probs=65.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      ..++|||+|||.++|+++|+++|++||.|..+.+. +++|||||+|.+.++|.+|++.|||..|.  |+  .|++.|+.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~-~~rg~afV~f~~~~~A~~Ai~~l~~~~i~--g~--~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-KIRDYAFVHFSNREDAVEAMKALNGKVLD--GS--PIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE-ECSSEEEEEESSHHHHHHHHHHHSSEEET--TE--EEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc-cccEEEEEEeCCHHHHHHHHHHcCCCEEC--CE--EEEEEecc
Confidence            45899999999999999999999999999887765 57999999999999999999999998876  67  46666654

>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=99.65  E-value=3.7e-17  Score=123.19  Aligned_cols=75  Identities=16%  Similarity=0.233  Sum_probs=64.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      ...+++|||+|||+++||++|+++|++||+|.+|++...++|||||+|.+.++|++|+.  ++..|.  |+.  |++.++
T Consensus         2 s~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~--g~~--l~v~~a   75 (88)
T d1wf0a_           2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIK--GIS--VHISNA   75 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEET--TEE--EEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEEC--CEE--eEEEeC
Confidence            34678999999999999999999999999999999988889999999999999999985  665544  774  555554


Q ss_pred             C
Q 046223          159 S  159 (408)
Q Consensus       159 ~  159 (408)
                      .
T Consensus        76 ~   76 (88)
T d1wf0a_          76 E   76 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.65  E-value=1.6e-16  Score=123.37  Aligned_cols=74  Identities=16%  Similarity=0.187  Sum_probs=63.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ....++|||+|||+++||++|+++|++||+|.+|++.+     +++|||||+|.+.++|++|++.+|+ .|  .||.|.+
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l--~Gr~l~V   83 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-II--DGRKANV   83 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EE--TTEECEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cC--CCEEEEE
Confidence            33457899999999999999999999999999999875     4699999999999999999998876 44  4775544


Q ss_pred             ec
Q 046223          154 KN  155 (408)
Q Consensus       154 ~~  155 (408)
                      ..
T Consensus        84 ~~   85 (103)
T d2cqda1          84 NL   85 (103)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

>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=99.65  E-value=8.2e-17  Score=121.16  Aligned_cols=74  Identities=11%  Similarity=0.134  Sum_probs=62.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      ..+++|||+|||++++++||+++|++|| +..+.+. .++|||||+|.+.++|++|++.|||..|.  ||  .|+|.|+.
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~-~~kg~afV~f~~~~~A~~Ai~~ln~~~~~--G~--~l~V~~a~   76 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFR--GK--DLIVQLQP   76 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEET--TE--EEEEEECC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee-ccCCceEEEECCHHHHHHHHHHhCCCEEC--CE--EEEEEEcC
Confidence            3568999999999999999999999999 4444443 57999999999999999999999998876  77  46666654

>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=99.65  E-value=3.4e-17  Score=124.06  Aligned_cols=78  Identities=9%  Similarity=0.037  Sum_probs=65.1

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           77 PSTGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        77 ~~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      ......++|||+|||+++|+++|+++|++||.|..+++..    +++|||||+|.+.++|++|++ |||..|.  |+  .
T Consensus         8 ~~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~--g~--~   82 (91)
T d1fjeb1           8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVF--GN--E   82 (91)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEET--TE--E
T ss_pred             CCCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEEC--CE--E
Confidence            3444577999999999999999999999999988876643    679999999999999999996 9998876  67  4


Q ss_pred             eeccccC
Q 046223          153 LKNPYSS  159 (408)
Q Consensus       153 ~~~~~s~  159 (408)
                      |++.+++
T Consensus        83 i~V~~ak   89 (91)
T d1fjeb1          83 IKLEKPK   89 (91)
T ss_dssp             EEEECCC
T ss_pred             EEEEecC
Confidence            5554443

>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=99.65  E-value=9.4e-17  Score=123.30  Aligned_cols=76  Identities=17%  Similarity=0.159  Sum_probs=69.7

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecCCC
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGG  304 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  304 (408)
                      ...+|||+|||++++++||+++|++||.|..++.  ..+|||||+|.+.++|++|++.|||..|.|+.|+|.+++.+.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i--~~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADV--QKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEE--ETTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccc--cccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            3578999999999999999999999999999864  357999999999999999999999999999999999997654

>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=99.65  E-value=1.7e-16  Score=116.97  Aligned_cols=70  Identities=13%  Similarity=0.256  Sum_probs=61.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .|+|||+|||+++||++|+++|++||.|..+.+..     .++|||||+|.+.++|++|++ ++|..|.  ||.|.++
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~--Gr~i~V~   76 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVN--GHNCEVR   76 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEET--TEECEEE
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEEC--CEEEEEE
Confidence            47999999999999999999999999999988875     458999999999999999995 8998876  7755554

>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=99.65  E-value=1.6e-16  Score=121.71  Aligned_cols=78  Identities=13%  Similarity=0.238  Sum_probs=67.8

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCC-ceeec------cCCCCccEEEEEECCHHHHHHHHHHhCC--ceeCCeEEEEE
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGP-VKELR------ETPLKKHQRFIEFYDVRDAAKALKEMNG--QEIYGKHVVIE  298 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~-v~~v~------~~~~~~g~afV~F~~~~~A~~A~~~l~g--~~~~g~~l~v~  298 (408)
                      +++|||+|||.++++++|+++|+.||. |..++      ..+.++|||||+|.+.++|.+|++.|++  ..++|+.|+|+
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999996 77772      2467889999999999999999999975  45679999999


Q ss_pred             EecCCCC
Q 046223          299 FSRPGGH  305 (408)
Q Consensus       299 ~a~~~~~  305 (408)
                      ||+++..
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9987653

>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=99.64  E-value=1.5e-16  Score=119.44  Aligned_cols=68  Identities=16%  Similarity=0.224  Sum_probs=60.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      +|||+|||+++|+++|+++|++||+|..+++.  .+|||||+|.+.++|++||+.|||..|.  |+.  +++.+
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~l~g~~~~--g~~--i~v~~   69 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVY--RDGTGVVEFVRKEDMTYAVRKLDNTKFR--SHE--GETAY   69 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEEC--TTSEEEEEESSHHHHHHHHHHHTTCBCC--CTT--SCCCB
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccc--ccceeeEEeCCHHHHHHHHHHhCCCEEC--CcE--eEEeE
Confidence            59999999999999999999999999999986  4699999999999999999999999976  663  44444

>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=99.64  E-value=3.5e-16  Score=118.01  Aligned_cols=72  Identities=19%  Similarity=0.243  Sum_probs=60.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ...+++|||+|||+++||++|+++|++||.|.+|++.+     .++|||||+|.+.++|++|++.++  .|  +||.|.+
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~--~l--~Gr~i~v   80 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MI--DGRWCDC   80 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCE--EE--TTEEEEE
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCC--cc--CCEEeEE
Confidence            34567899999999999999999999999999999875     459999999999999999998533  33  4774444


Q ss_pred             e
Q 046223          154 K  154 (408)
Q Consensus       154 ~  154 (408)
                      +
T Consensus        81 ~   81 (90)
T d2cqga1          81 K   81 (90)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=99.64  E-value=6.4e-17  Score=119.50  Aligned_cols=71  Identities=15%  Similarity=0.090  Sum_probs=61.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcc-ccccccccceeccccC
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQH-MQLQQQSYGLKNPYSS  159 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~-i~~~gr~l~~~~~~s~  159 (408)
                      +|||+|||.++||++|+++|++||.|..+.+.+ ++|||||+|.+.++|++|++.|||.. |.  |+  .|++.|+.
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~-~rg~aFV~f~~~~~A~~Ai~~lng~~~~~--G~--~i~V~~a~   74 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-KSGYAFVDYPDQNWAIRAIETLSGKVELH--GK--IMEVDYSV   74 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-ETTEEEECCSCHHHHHHHHHHHTTTCEET--TE--ECEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-ccceEEEEECCHHHHHHHHHHhCCCeEEC--CE--EEEEEEcC
Confidence            699999999999999999999999998866663 69999999999999999999999963 54  67  46665654

>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=99.64  E-value=3.1e-16  Score=114.17  Aligned_cols=71  Identities=17%  Similarity=0.227  Sum_probs=63.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeec---cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~---~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      .+|||+|||+++++++|+++|+.||.|..++   ..+..++||||+|++.++|++|+. +|+..|+|+.|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            4799999999999999999999999998882   344557899999999999999985 8999999999999865

>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=99.64  E-value=9.4e-16  Score=119.13  Aligned_cols=79  Identities=19%  Similarity=0.211  Sum_probs=70.3

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHh--CCceeCCeEEEEEEecCC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEM--NGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l--~g~~~~g~~l~v~~a~~~  303 (408)
                      ..+++|||+|||..+|++||+++|++||.|..++.. +.+++|||+|.+.++|++|++.|  ++..++|++|+|.|++.+
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~-~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~   91 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM-PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEE-ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCC
Confidence            346899999999999999999999999999999643 67899999999999999999988  466789999999999765


Q ss_pred             CC
Q 046223          304 GH  305 (408)
Q Consensus       304 ~~  305 (408)
                      ..
T Consensus        92 ~~   93 (104)
T d1wexa_          92 RI   93 (104)
T ss_dssp             SC
T ss_pred             cc
Confidence            43

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=4.4e-16  Score=113.32  Aligned_cols=69  Identities=17%  Similarity=0.312  Sum_probs=60.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceeccccC
Q 046223           85 LVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYSS  159 (408)
Q Consensus        85 lfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s~  159 (408)
                      |||+|||.++++++|+++|++|| +..+++. +++|||||+|.+.++|++|++.|||..+.  |+  .+++.|+.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~-~~~g~afv~f~~~~~A~~Ai~~ln~~~~~--g~--~l~V~~a~   69 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-KYKGTAFVTLLNGEQAEAAINTFHQSRLR--ER--ELSVQLQP   69 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTEESS--SC--EEEEEECC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-ccceeEEEEECCHHHHHHHHHHhCCccCC--CC--EEEEEEeC
Confidence            79999999999999999999999 6666654 58999999999999999999999998876  77  46665654

>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=99.63  E-value=1.2e-16  Score=119.10  Aligned_cols=71  Identities=13%  Similarity=0.324  Sum_probs=60.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeEEE-EEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           85 LVLSYVPGDVSETIVRRDLEVFGEVRGV-QMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        85 lfV~nLp~~vte~~L~~~F~~~G~V~~v-~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      |||+|||.++||++|+++|++||.|.++ ++.+     +++|||||+|.+.++|++|++.|+|..|.  ||.  +++.++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~--gr~--l~v~~a   76 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLC--NRP--ITVSYA   76 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEET--TEE--CEEEES
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEEC--CEE--EEEEEe
Confidence            8999999999999999999999998764 5553     45899999999999999999999998875  774  455444


Q ss_pred             C
Q 046223          159 S  159 (408)
Q Consensus       159 ~  159 (408)
                      .
T Consensus        77 ~   77 (83)
T d1x5ta1          77 F   77 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.63  E-value=2.3e-16  Score=121.14  Aligned_cols=73  Identities=15%  Similarity=0.208  Sum_probs=62.6

Q ss_pred             CCCCEEEEcCCC-CCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecccc
Q 046223           80 GPTRTLVLSYVP-GDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPYS  158 (408)
Q Consensus        80 ~~~rtlfV~nLp-~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~s  158 (408)
                      ....+|||+||+ ..+++++|+++|++||.|.+|++   ++|||||+|.+.++|++||+.|||..|.  |+.  |+|.|+
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---~rg~aFV~f~~~~~A~~Ai~~lng~~~~--g~~--l~V~~a   85 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAGEDGRMIA--GQV--LDINLA   85 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---ETEEEEEEESSHHHHHHHHHTTTTCEET--TEE--CEEEET
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---eCCeEEEEECCHHHHHHHHHHcCCCEEC--CEE--EEEEEC
Confidence            345679999996 57889999999999999999988   4899999999999999999999999876  674  555554


Q ss_pred             C
Q 046223          159 S  159 (408)
Q Consensus       159 ~  159 (408)
                      .
T Consensus        86 ~   86 (98)
T d1wf2a_          86 A   86 (98)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.63  E-value=1.5e-16  Score=120.05  Aligned_cols=71  Identities=15%  Similarity=0.328  Sum_probs=62.9

Q ss_pred             CceEEEcCCCCCCcHHHH---HHHHhcCCCceeec-----cC---CCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          228 QGTIVVFNLDSGVSSSTL---KEIFQAFGPVKELR-----ET---PLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L---~~~F~~~G~v~~v~-----~~---~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      .++|||+|||++++++||   +++|++||.|..|.     .+   +..+|||||+|.+.++|.+|++.|||..++|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            478999999999999999   77899999999992     12   22358999999999999999999999999999999


Q ss_pred             EE
Q 046223          297 IE  298 (408)
Q Consensus       297 v~  298 (408)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=99.63  E-value=2.7e-16  Score=121.72  Aligned_cols=70  Identities=17%  Similarity=0.238  Sum_probs=61.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ..++|||+|||+++|+++|+++|++||+|..|.+.+     .++|||||+|.+.++|++|++ ++|..|.  |+.|.+
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~--G~~i~V   93 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSID--GRVVEP   93 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEET--TEEEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeEC--CEEEEE
Confidence            348999999999999999999999999999999875     469999999999999999996 7888764  774443

>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=99.63  E-value=3.8e-16  Score=116.66  Aligned_cols=71  Identities=21%  Similarity=0.273  Sum_probs=61.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ..++|||+|||.++|+++|+++|+.||.|..|++.+    +++|||||+|.+.++|++|++ ++|..+.  |+.|.++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~--g~~l~v~   79 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYK--ETDLLIL   79 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEET--TEECEEE
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEEC--CEEEEEE
Confidence            468999999999999999999999999999999875    458999999999999999996 7887765  6744443

>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=99.62  E-value=3.7e-16  Score=119.64  Aligned_cols=75  Identities=17%  Similarity=0.194  Sum_probs=65.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCC-eEEEEEee------cCccEEEEEECCHHHHHHHHHHhcCccccccccccceec
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGE-VRGVQMER------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKN  155 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~-V~~v~~~~------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~  155 (408)
                      ..|||+|||.++|+++|+++|++||+ |..|++.+      +++|||||+|.+.++|.+|++.|++..+.+.|+  .+++
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~--~i~V   79 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGH--QIAV   79 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTB--CCEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCE--EEEE
Confidence            47999999999999999999999996 89998864      468999999999999999999998877776777  4666


Q ss_pred             cccC
Q 046223          156 PYSS  159 (408)
Q Consensus       156 ~~s~  159 (408)
                      .|+.
T Consensus        80 ~~A~   83 (96)
T d2disa1          80 DWAE   83 (96)
T ss_dssp             EESC
T ss_pred             EEcC
Confidence            6665

>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=99.62  E-value=1.6e-16  Score=115.59  Aligned_cols=68  Identities=15%  Similarity=0.264  Sum_probs=58.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .|||+|||+++||++|+++|++||.|..|++.+     +++|||||+|.+.++|++|++ +++..|.  |+.+.++
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~--g~~i~vk   73 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVG--LSKCEIK   73 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBT--TBCCEEE
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEEC--CEEeEEE
Confidence            489999999999999999999999999999875     569999999999999999997 4555554  6644443

>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=99.62  E-value=1.6e-16  Score=119.83  Aligned_cols=69  Identities=10%  Similarity=0.136  Sum_probs=60.7

Q ss_pred             CCCEEEEcCCCCCCCHHHH---HHHhhccCCeEEEEEeec--------CccEEEEEECCHHHHHHHHHHhcCcccccccc
Q 046223           81 PTRTLVLSYVPGDVSETIV---RRDLEVFGEVRGVQMERL--------MEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQ  149 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L---~~~F~~~G~V~~v~~~~~--------~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr  149 (408)
                      ..++|||+|||+++++++|   +++|++||+|..|.+.+.        .+|||||+|.+.++|++|++.|||..|.  ||
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~--gr   84 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD--GR   84 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET--TE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEEC--CE
Confidence            4568999999999999999   778999999999998751        2589999999999999999999998876  77


Q ss_pred             cc
Q 046223          150 SY  151 (408)
Q Consensus       150 ~l  151 (408)
                      .|
T Consensus        85 ~l   86 (89)
T d2cpia1          85 TL   86 (89)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

>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=99.62  E-value=7.7e-16  Score=119.67  Aligned_cols=79  Identities=22%  Similarity=0.190  Sum_probs=70.0

Q ss_pred             CCCCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEE
Q 046223          225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF  299 (408)
Q Consensus       225 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~  299 (408)
                      .....+|||+|||+++|++||+++|+.+|.|..+     ..++..+|||||+|.+.++|++|++ +|+..|+||.|+|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            3445789999999999999999999999988764     3567789999999999999999996 999999999999999


Q ss_pred             ecCCC
Q 046223          300 SRPGG  304 (408)
Q Consensus       300 a~~~~  304 (408)
                      +.+..
T Consensus        91 ~~~~~   95 (104)
T d1wg5a_          91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            97654

>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=99.62  E-value=4e-16  Score=120.82  Aligned_cols=78  Identities=13%  Similarity=0.182  Sum_probs=68.0

Q ss_pred             CCCceEEEcCCCCCCcHHHHHHHHhcCCCceee---ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 046223          226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL---RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       226 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v---~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~  302 (408)
                      ....+|||+|||+++|++||+++|+.||.+...   ...+..+|||||+|.+.++|++|++ ||+..|+||.|+|.++..
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~   91 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNST   91 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCcceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCC
Confidence            345899999999999999999999999854322   3567789999999999999999986 899999999999999876


Q ss_pred             CC
Q 046223          303 GG  304 (408)
Q Consensus       303 ~~  304 (408)
                      ..
T Consensus        92 ~~   93 (102)
T d1weza_          92 AG   93 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.61  E-value=5.2e-16  Score=112.94  Aligned_cols=68  Identities=13%  Similarity=0.133  Sum_probs=59.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee---cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER---LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~---~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      .+|||+|||+++++++|+++|+.||.|..|++.+   ..+|||||+|.+.++|++|++ ++++.|.  |+.|.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~--g~~i~V   71 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVG--QNEIIV   71 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEET--TEECEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEEC--CEEEEE
Confidence            4899999999999999999999999999999876   347899999999999999995 8998765  664443

>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=99.61  E-value=3.8e-16  Score=117.61  Aligned_cols=79  Identities=9%  Similarity=0.004  Sum_probs=68.2

Q ss_pred             CCCCCCEEEEcCCCCC-CCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           78 STGPTRTLVLSYVPGD-VSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~-vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ...++|+|||+|||.. +|++||.++|+.||.|.+|.+.+ .+++|||+|.+.++|..|++.|++..+.+.||  .+++.
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~-~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr--~l~V~   80 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN-KINEAFIEMATTEDAQAAVDYYTTTPALVFGK--PVRVH   80 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS-SSSCEEEEESSHHHHHHHHHHHHHSCCEETTE--ECEEE
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeec-cceEEEEEEcchhhHHHHHHHHhhCCCccCCc--eEEEE
Confidence            4567999999999986 88999999999999999999874 68999999999999999999887666666688  46666


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        81 ~s~   83 (89)
T d1x4da1          81 LSQ   83 (89)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            654

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=4.7e-16  Score=120.54  Aligned_cols=78  Identities=14%  Similarity=0.195  Sum_probs=68.8

Q ss_pred             CCceEEEcCCCCCCc-----HHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVS-----SSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t-----~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ...+|||+||+.++.     +++|+++|+.||.|.++... +++++|||+|.+.++|.+|++.|||..|+|+.|+|.|++
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~-k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   82 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEe-cCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecc
Confidence            358999999998753     36799999999999999644 679999999999999999999999999999999999997


Q ss_pred             CCCC
Q 046223          302 PGGH  305 (408)
Q Consensus       302 ~~~~  305 (408)
                      +...
T Consensus        83 ~~~~   86 (104)
T d1weya_          83 TLHI   86 (104)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            6543

>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=99.61  E-value=3.8e-16  Score=120.83  Aligned_cols=78  Identities=15%  Similarity=0.129  Sum_probs=63.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEE--------EEEee-----cCccEEEEEECCHHHHHHHHHHhcCccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRG--------VQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHM  144 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~--------v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i  144 (408)
                      .....++|||+|||.++||++|+++|+.||.|..        +.+.+     +++|||||+|.+.++|.+|++.|||..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            4456789999999999999999999999998854        33322     4589999999999999999999999887


Q ss_pred             cccccccceeccccC
Q 046223          145 QLQQQSYGLKNPYSS  159 (408)
Q Consensus       145 ~~~gr~l~~~~~~s~  159 (408)
                      .  ||.  |++.++.
T Consensus        84 ~--gr~--i~V~~a~   94 (101)
T d2cpea1          84 Q--GSK--LKVSLAR   94 (101)
T ss_dssp             T--TEE--CEEECSS
T ss_pred             C--CEE--EEEEEcC
Confidence            5  774  5555544

>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=99.61  E-value=1.4e-16  Score=123.59  Aligned_cols=76  Identities=18%  Similarity=0.198  Sum_probs=66.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .++++|||+|||.++|+++|+++|++||.|..+.+..     +++|||||+|.+.++|++|++.|||..|.  |+  .|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~--g~--~l~   91 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLY--GK--ILV   91 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCS--SC--BCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEEC--CE--EEE
Confidence            3578999999999999999999999999998866553     56999999999999999999999998875  67  466


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.|+.
T Consensus        92 V~~ak   96 (102)
T d2cpxa1          92 IEFGK   96 (102)
T ss_dssp             EEECC
T ss_pred             EEeCC
Confidence            66655

>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=99.61  E-value=1e-16  Score=116.00  Aligned_cols=66  Identities=18%  Similarity=0.321  Sum_probs=61.2

Q ss_pred             EEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q 046223          231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVV  296 (408)
Q Consensus       231 l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~  296 (408)
                      |||+|||.++|+++|+++|++||.|..+     ..++..+|+|||+|.+.++|++|++.|||..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            7999999999999999999999999888     25677899999999999999999999999999998764

>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=99.61  E-value=4.3e-16  Score=113.60  Aligned_cols=68  Identities=16%  Similarity=0.155  Sum_probs=59.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           84 TLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        84 tlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      .|||+|||.++||++|+++|++||.|..+.+..     .++|||||+|.+.++|++|++ |||..|.  ||.|.++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~--gr~i~V~   73 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEIN--NKMVECK   73 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBT--TBCCEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEEC--CeEEEEE
Confidence            489999999999999999999999999988765     459999999999999999996 9998876  7755443

>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=99.60  E-value=1.4e-15  Score=114.47  Aligned_cols=77  Identities=19%  Similarity=0.309  Sum_probs=68.6

Q ss_pred             CCCceEEEcCCCCC-CcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHh--CCceeCCeEEEEEEecC
Q 046223          226 NNQGTIVVFNLDSG-VSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEM--NGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       226 ~~~~~l~V~nLp~~-~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l--~g~~~~g~~l~v~~a~~  302 (408)
                      ..+++|||+||+.. +|++||.++|+.||.|..+... ..+++|||+|++.++|.+|++.|  ++..++|++|+|+||+.
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~-~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~   84 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEee-ccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCC
Confidence            44689999999986 8999999999999999999643 56789999999999999999966  68899999999999975


Q ss_pred             C
Q 046223          303 G  303 (408)
Q Consensus       303 ~  303 (408)
                      .
T Consensus        85 ~   85 (89)
T d1x4da1          85 Y   85 (89)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.60  E-value=9.1e-16  Score=119.08  Aligned_cols=76  Identities=9%  Similarity=0.171  Sum_probs=68.0

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ...+|||+|||+++|+++|+++|+.||.|..+     ...+.++|+|||+|.+.++|++|++ |||..|+|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            35789999999999999999999999987653     3567889999999999999999996 99999999999999985


Q ss_pred             CC
Q 046223          302 PG  303 (408)
Q Consensus       302 ~~  303 (408)
                      ..
T Consensus        86 ~~   87 (103)
T d2cpya1          86 LE   87 (103)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=99.60  E-value=4.9e-16  Score=119.50  Aligned_cols=79  Identities=16%  Similarity=0.186  Sum_probs=65.1

Q ss_pred             CCCCCCEEEEcCCCCC-CCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCccccccccccceecc
Q 046223           78 STGPTRTLVLSYVPGD-VSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNP  156 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~-vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~  156 (408)
                      ...++++|||+|||.+ +|+++|+++|+.||.|.+|.+. +++|||||+|.+.++|.+|++.++...+.+.||  .+++.
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~-~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr--~l~V~   90 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGR--CVKVD   90 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSS--CCEEE
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEe-ecCCcEEEEecchHHHHHHHHHHhcCCceECCE--EEEEE
Confidence            3456789999999985 8999999999999999999987 468999999999999999998654444445577  45555


Q ss_pred             ccC
Q 046223          157 YSS  159 (408)
Q Consensus       157 ~s~  159 (408)
                      |+.
T Consensus        91 ~s~   93 (99)
T d1x4fa1          91 LSE   93 (99)
T ss_dssp             EEC
T ss_pred             EcC
Confidence            654

>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=99.60  E-value=7.2e-16  Score=118.56  Aligned_cols=77  Identities=22%  Similarity=0.225  Sum_probs=68.7

Q ss_pred             CCCceEEEcCCCCC-CcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHH--HhCCceeCCeEEEEEEecC
Q 046223          226 NNQGTIVVFNLDSG-VSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK--EMNGQEIYGKHVVIEFSRP  302 (408)
Q Consensus       226 ~~~~~l~V~nLp~~-~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~--~l~g~~~~g~~l~v~~a~~  302 (408)
                      ..+++|||+|||.+ +|+++|.++|++||.|.++... ..+|+|||+|.+.++|.+|++  .+++..++|+.|+|.||+.
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~-~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~   94 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEe-ecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCC
Confidence            44689999999985 8999999999999999999643 568999999999999999998  5788899999999999965


Q ss_pred             C
Q 046223          303 G  303 (408)
Q Consensus       303 ~  303 (408)
                      +
T Consensus        95 ~   95 (99)
T d1x4fa1          95 Y   95 (99)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.60  E-value=1.6e-15  Score=117.84  Aligned_cols=73  Identities=21%  Similarity=0.353  Sum_probs=60.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee------cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      +..+|||+|||+++||++|+++|+.|| |..++++.      +++|||||+|.+.++|++|+ .||+..|.  +|.  |+
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~--gr~--l~   87 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG--NKR--IR   87 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEET--TEE--CE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEEC--CEE--EE
Confidence            468999999999999999999999999 77776654      35899999999999998777 49998875  774  45


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.++.
T Consensus        88 V~~a~   92 (104)
T d1wi8a_          88 VDVAD   92 (104)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            54543

>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=99.56  E-value=1.6e-15  Score=113.56  Aligned_cols=72  Identities=15%  Similarity=0.156  Sum_probs=60.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEE-EEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRG-VQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~-v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ...+|||+|||++++++||+++|+.||.|.. +.+..    +++|+|||+|.+.++|++|++.|||..|.  ||.|.+.
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~--gr~i~v~   84 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIG--SRKVKLV   84 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEET--TEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            3457999999999999999999999999876 44433    45899999999999999999999999876  7754443

>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=99.56  E-value=2.7e-15  Score=115.53  Aligned_cols=66  Identities=17%  Similarity=0.179  Sum_probs=60.1

Q ss_pred             CCCCCEEEEcC--CCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           79 TGPTRTLVLSY--VPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        79 ~~~~rtlfV~n--Lp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ..++++|||+|  |+.++||++|+++|++||.|..|++. ..+|||||+|.+.++|++|++.|||+.|.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~-~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeec-cCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            45678999955  99999999999999999999999887 46899999999999999999999999874

>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=99.53  E-value=1.8e-16  Score=119.99  Aligned_cols=70  Identities=21%  Similarity=0.348  Sum_probs=62.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeec----------cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----------ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIE  298 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----------~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~  298 (408)
                      ++|||+|||+++|+++|+++|+.||.|..+.          ..+.++|||||+|.+.++|++|++ |||..+.|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            6899999999999999999999999876651          345679999999999999999986 99999999999996


Q ss_pred             E
Q 046223          299 F  299 (408)
Q Consensus       299 ~  299 (408)
                      .
T Consensus        81 r   81 (90)
T d1u2fa_          81 R   81 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=1.9e-14  Score=111.65  Aligned_cols=72  Identities=17%  Similarity=0.074  Sum_probs=59.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      .....+|||+|||+++||+||+++|+.+|.|..+.++.     +++|||||+|.+.++|++|++ +|+..|.  +|.|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~--gR~i~V   88 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIG--HRYIEI   88 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSS--SSCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEc--ceEEEE
Confidence            33556899999999999999999999999888744433     458999999999999999996 8998765  774433

>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=99.52  E-value=4.7e-15  Score=116.67  Aligned_cols=75  Identities=13%  Similarity=0.125  Sum_probs=67.6

Q ss_pred             CCceEEEcCCCCCCcHHHHHHHHhcCCCceee-----ccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       227 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v-----~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      ...+|||+|||+++|++||+++|+.||.|..+     ...+..+|+|||+|.+.++|++|++ |||..|+||.|.|..+.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            45799999999999999999999999987653     4677889999999999999999996 99999999999999875


Q ss_pred             C
Q 046223          302 P  302 (408)
Q Consensus       302 ~  302 (408)
                      .
T Consensus        96 ~   96 (112)
T d1wela1          96 K   96 (112)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.52  E-value=1.1e-14  Score=112.58  Aligned_cols=76  Identities=16%  Similarity=0.139  Sum_probs=61.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      ......+|||+|||+++||+||+++|+.||. ..|.+..    ..+|||||+|.+.++|++|++ ||+..|.  ||.  |
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~--gR~--I   84 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQ--HRY--V   84 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSS--SSC--C
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEEC--CEE--E
Confidence            3445679999999999999999999999984 4555554    448999999999999999996 8998876  774  4


Q ss_pred             eccccC
Q 046223          154 KNPYSS  159 (408)
Q Consensus       154 ~~~~s~  159 (408)
                      +|.++.
T Consensus        85 ~V~~s~   90 (102)
T d1weza_          85 ELFLNS   90 (102)
T ss_dssp             EEEEEC
T ss_pred             EEEEcC
Confidence            444433

>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=99.52  E-value=3.6e-16  Score=118.22  Aligned_cols=69  Identities=14%  Similarity=0.185  Sum_probs=58.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----------cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----------LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----------~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      |+|||+|||.++||++|+++|++||.|..+.+..          +++|||||+|.+.++|++|++ |||..+.  ||.|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~--Gr~l~   78 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQ--GQSLK   78 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSS--SSCCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEEC--CEEEE
Confidence            7899999999999999999999999877654431          569999999999999999995 9998876  77544


Q ss_pred             ee
Q 046223          153 LK  154 (408)
Q Consensus       153 ~~  154 (408)
                      ++
T Consensus        79 V~   80 (90)
T d1u2fa_          79 IR   80 (90)
T ss_dssp             CB
T ss_pred             EC
Confidence            43

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.51  E-value=4e-15  Score=115.19  Aligned_cols=75  Identities=15%  Similarity=0.101  Sum_probs=64.7

Q ss_pred             CCCCEEEEcCCCCCC-CH----HHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDV-SE----TIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~v-te----~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ..+.+|||+||+.++ ++    ++|+++|+.||.|.++++. +++|||||+|.+.++|.+|++.|||..|.  |+  .|+
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~-k~~~~afV~f~~~~~A~~Ai~~lng~~~~--g~--~l~   77 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-KSFKRVRINFSNPLSAADARLRLHKTEFL--GK--EMK   77 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-TTTTEEEEECSSTTHHHHHHHTSTTSEET--TE--ECE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEe-cCCCEEEEEECCHHHHHHHHHHhcccccC--CC--EeE
Confidence            457899999999887 33    5699999999999999987 58999999999999999999999999876  67  466


Q ss_pred             ccccC
Q 046223          155 NPYSS  159 (408)
Q Consensus       155 ~~~s~  159 (408)
                      +.|+.
T Consensus        78 v~~a~   82 (104)
T d1weya_          78 LYFAQ   82 (104)
T ss_dssp             EECCC
T ss_pred             Eeecc
Confidence            66665

>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=99.49  E-value=7.8e-15  Score=113.66  Aligned_cols=72  Identities=13%  Similarity=0.075  Sum_probs=60.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhccCCeEE-EEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccccee
Q 046223           80 GPTRTLVLSYVPGDVSETIVRRDLEVFGEVRG-VQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLK  154 (408)
Q Consensus        80 ~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~-v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~  154 (408)
                      ....+|||+|||+++|+++|+++|+.||.|.. +.+..    +++|||||+|.+.++|++|++ |||..|.  ||.|.+.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~--gr~i~V~   82 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLN--GREAFVH   82 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEET--TEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeEC--CcEEEEE
Confidence            34678999999999999999999999998876 44433    569999999999999999996 9998876  7744443

>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=99.46  E-value=2.9e-14  Score=112.07  Aligned_cols=73  Identities=14%  Similarity=0.035  Sum_probs=60.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEE-EEee----cCccEEEEEECCHHHHHHHHHHhcCccccccccccce
Q 046223           79 TGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGV-QMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGL  153 (408)
Q Consensus        79 ~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v-~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~  153 (408)
                      .....+|||+|||+++|+++|+++|+.||.|..+ .+..    .++|||||+|.+.++|++|++ |||..|.  ||.|.+
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~--gR~i~V   91 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMG--NRFIQV   91 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCST--TSCBEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCC--CEEEEE
Confidence            3456799999999999999999999999988663 2222    559999999999999999996 8998875  775444


Q ss_pred             e
Q 046223          154 K  154 (408)
Q Consensus       154 ~  154 (408)
                      .
T Consensus        92 ~   92 (112)
T d1wela1          92 H   92 (112)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=99.44  E-value=1.1e-13  Score=106.32  Aligned_cols=63  Identities=27%  Similarity=0.432  Sum_probs=57.0

Q ss_pred             CCceEEEcC--CCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCcee
Q 046223          227 NQGTIVVFN--LDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI  290 (408)
Q Consensus       227 ~~~~l~V~n--Lp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~  290 (408)
                      +..+|+|.|  |+.++|+++|+++|++||.|..++.. ..++||||+|.+.++|.+|++.|||+.+
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~-~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeec-cCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            358899955  99999999999999999999998643 5789999999999999999999999987

>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=99.44  E-value=1.3e-13  Score=108.30  Aligned_cols=68  Identities=10%  Similarity=0.040  Sum_probs=60.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCH-HHHHHHHHHhcCcccccccc
Q 046223           81 PTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDL-RHAEMAFKEIREQHMQLQQQ  149 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~-~~A~~Ai~~lng~~i~~~gr  149 (408)
                      ....+|||||+.++||++|+++|++||+|..|.++ +.+|||||.|.+. ++|.+|+..|++..+.+.+.
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~-~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~   78 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNK   78 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC-TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEe-cCCceEEEEecCcHHHHHHHHHHhcCCceecCce
Confidence            35567999999999999999999999999999998 4799999999995 78999999999988774443

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=8e-15  Score=113.45  Aligned_cols=72  Identities=18%  Similarity=0.261  Sum_probs=66.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeec----cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~----~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      ..++|.++..++++++|+++|++||.|.+|+    .++.++|+|||+|.+.++|.+|++.|||++++||.|+|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4578888888999999999999999999993    46788999999999999999999999999999999999985

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=3.1e-13  Score=103.46  Aligned_cols=79  Identities=13%  Similarity=0.217  Sum_probs=67.1

Q ss_pred             CCCceEEEcCC--CCCC---------cHHHHHHHHhcCCCceeec-cCCCCccEEEEEECCHHHHHHHHHHhCCceeCCe
Q 046223          226 NNQGTIVVFNL--DSGV---------SSSTLKEIFQAFGPVKELR-ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK  293 (408)
Q Consensus       226 ~~~~~l~V~nL--p~~~---------t~~~L~~~F~~~G~v~~v~-~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~  293 (408)
                      ..+++|+|.||  +.++         .++||++.|++||.|..|. ..+..+|+|||+|.+.++|.+|+..|||+.++||
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr   85 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR   85 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECCE
Confidence            34689999999  4432         2368999999999999984 3456789999999999999999999999999999


Q ss_pred             EEEEEEecCCC
Q 046223          294 HVVIEFSRPGG  304 (408)
Q Consensus       294 ~l~v~~a~~~~  304 (408)
                      .|+|+|+.++.
T Consensus        86 ~i~v~~~~g~~   96 (99)
T d2dita1          86 QITAQAWDGTT   96 (99)
T ss_dssp             ECEEEECCSCC
T ss_pred             EEEEEEeCCcC
Confidence            99999987653

>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=99.37  E-value=2.8e-13  Score=106.42  Aligned_cols=74  Identities=15%  Similarity=0.148  Sum_probs=64.7

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCH-HHHHHHHHHhCCceeCCeEEEEEEecCC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDV-RDAAKALKEMNGQEIYGKHVVIEFSRPG  303 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~-~~A~~A~~~l~g~~~~g~~l~v~~a~~~  303 (408)
                      ..+|||||+..+|+++|+++|++||.|.+|+.. ..+|||||+|.+. ++|.+|+..|++..+.++.+.|.++...
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~-~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~   86 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   86 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC-TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEe-cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeecc
Confidence            567999999999999999999999999999754 6799999999995 7899999999999988877777776543

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=4.8e-14  Score=108.96  Aligned_cols=67  Identities=19%  Similarity=0.222  Sum_probs=60.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee----cCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      ..++|.++..+++|++|+++|++||+|.+|+|.+    +++|||||+|.+.++|.+|++.|||+.+.  ||.|
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~--gr~i   98 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFN--GQPI   98 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEET--TEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEEC--CEEE
Confidence            4588999999999999999999999999999876    55899999999999999999999999886  7743

>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=99.32  E-value=1.8e-12  Score=110.77  Aligned_cols=76  Identities=12%  Similarity=0.188  Sum_probs=64.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-----cCccEEEEEECCHHHHHHHHHHhcCccccccccccc
Q 046223           78 STGPTRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-----LMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYG  152 (408)
Q Consensus        78 ~~~~~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-----~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~  152 (408)
                      .....++|||+|||.++|+++|+++|+.||.|..+.+..     .++|||||+|.+.++|++|++ +++..|.  |+.  
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~--G~~--  167 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVN--GHN--  167 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEET--TEE--
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeEC--CEE--
Confidence            445678999999999999999999999999999998875     458999999999999999997 6887765  664  


Q ss_pred             eecccc
Q 046223          153 LKNPYS  158 (408)
Q Consensus       153 ~~~~~s  158 (408)
                      ++|.++
T Consensus       168 i~V~~A  173 (183)
T d1u1qa_         168 CEVRKA  173 (183)
T ss_dssp             EEEEEC
T ss_pred             EEEEec
Confidence            444443

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=1.3e-12  Score=99.92  Aligned_cols=78  Identities=15%  Similarity=0.297  Sum_probs=64.8

Q ss_pred             CCCCCCCEEEEcCC--CCCCC---------HHHHHHHhhccCCeEEEEEee-cCccEEEEEECCHHHHHHHHHHhcCccc
Q 046223           77 PSTGPTRTLVLSYV--PGDVS---------ETIVRRDLEVFGEVRGVQMER-LMEGIVTVHFYDLRHAEMAFKEIREQHM  144 (408)
Q Consensus        77 ~~~~~~rtlfV~nL--p~~vt---------e~~L~~~F~~~G~V~~v~~~~-~~kG~afV~F~~~~~A~~Ai~~lng~~i  144 (408)
                      .....+++|+|.||  +.++.         +++|++.|++||.|..|.+.. ..+|+|||+|.+.++|.+|++.|||..|
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            45678999999999  55432         367999999999999998876 4589999999999999999999999988


Q ss_pred             cccccccceecccc
Q 046223          145 QLQQQSYGLKNPYS  158 (408)
Q Consensus       145 ~~~gr~l~~~~~~s  158 (408)
                      .  ||  .|++.|.
T Consensus        83 ~--gr--~i~v~~~   92 (99)
T d2dita1          83 G--GR--QITAQAW   92 (99)
T ss_dssp             T--TE--ECEEEEC
T ss_pred             C--CE--EEEEEEe
Confidence            6  77  4555543

>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=99.31  E-value=1.1e-12  Score=96.06  Aligned_cols=72  Identities=17%  Similarity=0.159  Sum_probs=61.3

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeE-EEEEEecC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH-VVIEFSRP  302 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~-l~v~~a~~  302 (408)
                      .+.|+|+++|++.+++.| +.|++||+|.+++ .+..++||||+|.+.++|++|++ +||..|+|+. |.|.....
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~-~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHV-MSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEE-ECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEE-ecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            377999999999987655 5799999999996 45678999999999999999996 9999999985 56776543

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.27  E-value=2.2e-12  Score=99.58  Aligned_cols=76  Identities=20%  Similarity=0.373  Sum_probs=63.9

Q ss_pred             CCceEEEcCC--CCCC--------cHHHHHHHHhcCCCceeecc-------CCCCccEEEEEECCHHHHHHHHHHhCCce
Q 046223          227 NQGTIVVFNL--DSGV--------SSSTLKEIFQAFGPVKELRE-------TPLKKHQRFIEFYDVRDAAKALKEMNGQE  289 (408)
Q Consensus       227 ~~~~l~V~nL--p~~~--------t~~~L~~~F~~~G~v~~v~~-------~~~~~g~afV~F~~~~~A~~A~~~l~g~~  289 (408)
                      ++++|.|.||  +..+        ..+||++.|++||.|.+|..       .....|++||+|.+.++|.+|+..|||+.
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            3589999999  4433        24679999999999999932       22346899999999999999999999999


Q ss_pred             eCCeEEEEEEecC
Q 046223          290 IYGKHVVIEFSRP  302 (408)
Q Consensus       290 ~~g~~l~v~~a~~  302 (408)
                      ++||.|.|.|+.+
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999864

>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=99.27  E-value=2.6e-12  Score=94.09  Aligned_cols=61  Identities=10%  Similarity=0.105  Sum_probs=54.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      .+.|+|++||++++++.| ++|++||+|.++++. +.+|||||+|.+.++|++|++ +||..|.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~-~~~~~~fV~f~~~~~A~~Al~-~nG~~~~   64 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS-NTGNWMHIRYQSKLQARKALS-KDGRIFG   64 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC-SSSSEEEEEESSHHHHHHHHT-TTTCEET
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEec-CCCCEEEEEEcccHHHHHHHh-cCCCeEC
Confidence            467999999999997666 579999999999886 468999999999999999996 9998875

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.18  E-value=1.1e-11  Score=95.49  Aligned_cols=75  Identities=20%  Similarity=0.351  Sum_probs=61.6

Q ss_pred             CCCCEEEEcCC--CCCCC--------HHHHHHHhhccCCeEEEEEee-------cCccEEEEEECCHHHHHHHHHHhcCc
Q 046223           80 GPTRTLVLSYV--PGDVS--------ETIVRRDLEVFGEVRGVQMER-------LMEGIVTVHFYDLRHAEMAFKEIREQ  142 (408)
Q Consensus        80 ~~~rtlfV~nL--p~~vt--------e~~L~~~F~~~G~V~~v~~~~-------~~kG~afV~F~~~~~A~~Ai~~lng~  142 (408)
                      .++++|.|.||  +.++.        .+||++.|++||.|.+|.+.+       ...|++||+|.+.++|.+|++.|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            46899999999  55543        356899999999999999875       23689999999999999999999999


Q ss_pred             cccccccccceecccc
Q 046223          143 HMQLQQQSYGLKNPYS  158 (408)
Q Consensus       143 ~i~~~gr~l~~~~~~s  158 (408)
                      .+.  ||.  +.+.|.
T Consensus        82 ~f~--gR~--v~v~f~   93 (104)
T d1o0pa_          82 KFA--NRV--VVTKYC   93 (104)
T ss_dssp             CSS--SSC--CEEEEE
T ss_pred             EEC--CeE--EEEEEc
Confidence            886  773  455443

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.61  E-value=0.00013  Score=49.25  Aligned_cols=60  Identities=20%  Similarity=0.390  Sum_probs=50.7

Q ss_pred             HHHHHHHHhcCCCceeeccCCCCc--cEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 046223          242 SSTLKEIFQAFGPVKELRETPLKK--HQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR  301 (408)
Q Consensus       242 ~~~L~~~F~~~G~v~~v~~~~~~~--g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a~  301 (408)
                      .+.|.+.|.++|.|..+.....+.  -.|-|...+..+|.-|+..||.++|++++|.|.++.
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            345677899999999995433333  469999999999999999999999999999999975

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.40  E-value=0.00012  Score=52.02  Aligned_cols=54  Identities=22%  Similarity=0.401  Sum_probs=47.4

Q ss_pred             HHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 046223          243 STLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS  300 (408)
Q Consensus       243 ~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~l~v~~a  300 (408)
                      .+|.+.|..||+|.-||+.   .+...|+|.+-++|.+|++ ++|.+++|+.|+|...
T Consensus        39 ~~Llq~l~~~GeViLvRFv---~d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRIN---QGQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEE---TTEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEe---CCeEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            4688899999999888754   5678999999999999988 9999999999999754

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.10  E-value=0.00096  Score=48.05  Aligned_cols=63  Identities=10%  Similarity=0.099  Sum_probs=54.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEee-------cCccEEEEEECCHHHHHHHHHHhcCcccc
Q 046223           83 RTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMER-------LMEGIVTVHFYDLRHAEMAFKEIREQHMQ  145 (408)
Q Consensus        83 rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~-------~~kG~afV~F~~~~~A~~Ai~~lng~~i~  145 (408)
                      ..|.|+.||+++||+++.+.++..|++.......       ..-.-|||.|.+.++...-.+..+|..+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            4689999999999999999999999988876654       11456999999999999999999998775

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.05  E-value=0.0005  Score=48.81  Aligned_cols=68  Identities=18%  Similarity=0.276  Sum_probs=52.0

Q ss_pred             CCCEEEEcCCCCCCCH---------HHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhcCcccccccccc
Q 046223           81 PTRTLVLSYVPGDVSE---------TIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSY  151 (408)
Q Consensus        81 ~~rtlfV~nLp~~vte---------~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l  151 (408)
                      +.-||.|.=...+..|         .+|.+.|..||+|.-|+++   .+...|+|.+-++|.+|++ ++|.++.  |+.|
T Consensus        14 pDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv---~d~mwVTF~dG~SAL~al~-l~g~~v~--G~~l   87 (95)
T d1ufwa_          14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRIN---QGQMLVTFADSHSALSVLD-VDGMKVK--GRAV   87 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEE---TTEEEEECSCSHHHHHHHH-GGGSEET--TEEE
T ss_pred             CCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEe---CCeEEEEECCcHHHHHHhc-cCCeEEc--ceEE
Confidence            3457888655444433         2478889999999999987   6789999999999999996 8998876  6654


Q ss_pred             cee
Q 046223          152 GLK  154 (408)
Q Consensus       152 ~~~  154 (408)
                      .+.
T Consensus        88 ~It   90 (95)
T d1ufwa_          88 KIS   90 (95)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            443

>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=96.62  E-value=0.0036  Score=44.93  Aligned_cols=63  Identities=14%  Similarity=0.185  Sum_probs=51.7

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhcCCCceeec------cCC-CCccEEEEEECCHHHHHHHHHHhCCceeC
Q 046223          229 GTIVVFNLDSGVSSSTLKEIFQAFGPVKELR------ETP-LKKHQRFIEFYDVRDAAKALKEMNGQEIY  291 (408)
Q Consensus       229 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~------~~~-~~~g~afV~F~~~~~A~~A~~~l~g~~~~  291 (408)
                      .+|.|+.||+.+|++++.+.++..|++....      ..+ ..-.-|+|.|.+.++...-.+..+|..+-
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            5799999999999999999999888877661      111 12246999999999999999999998774

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.81  E-value=0.014  Score=39.13  Aligned_cols=61  Identities=13%  Similarity=0.188  Sum_probs=47.6

Q ss_pred             CCCHHH----HHHHhhccCCeEEEEEeecC--ccEEEEEECCHHHHHHHHHHhcCccccccccccceeccc
Q 046223           93 DVSETI----VRRDLEVFGEVRGVQMERLM--EGIVTVHFYDLRHAEMAFKEIREQHMQLQQQSYGLKNPY  157 (408)
Q Consensus        93 ~vte~~----L~~~F~~~G~V~~v~~~~~~--kG~afV~F~~~~~A~~Ai~~lng~~i~~~gr~l~~~~~~  157 (408)
                      .+++.+    |.+.|.++|.|.+|.+...+  .-.|-|...+..+|..|+..|+..+|.  +|  ++.+.|
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG--~K--RI~Vs~   69 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIG--SK--KILVSL   69 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEET--TE--EEEEEE
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcC--Ce--EEEEEE
Confidence            345555    56789999999999987644  446999999999999999999998875  44  345444

>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=94.03  E-value=0.15  Score=36.39  Aligned_cols=56  Identities=9%  Similarity=0.168  Sum_probs=47.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhccCCeEEEEEeecCccEEEEEECCHHHHHHHHHHhc
Q 046223           82 TRTLVLSYVPGDVSETIVRRDLEVFGEVRGVQMERLMEGIVTVHFYDLRHAEMAFKEIR  140 (408)
Q Consensus        82 ~rtlfV~nLp~~vte~~L~~~F~~~G~V~~v~~~~~~kG~afV~F~~~~~A~~Ai~~ln  140 (408)
                      ...||.-..|..+...||.++|+.||.|.--.|.   ---|||...+.++|+.++..+.
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswId---dTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWID---DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEE---TTEEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEec---CceEEEEecCHHHHHHHHHHhc
Confidence            3459999999999999999999999987665553   4579999999999999987654

>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=93.32  E-value=0.13  Score=36.75  Aligned_cols=56  Identities=14%  Similarity=0.264  Sum_probs=45.8

Q ss_pred             CceEEEcCCCCCCcHHHHHHHHhcCCCceeeccCCCCccEEEEEECCHHHHHHHHHHhC
Q 046223          228 QGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMN  286 (408)
Q Consensus       228 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~g~afV~F~~~~~A~~A~~~l~  286 (408)
                      ...||.-..|..+...||.++|+.||.|.--..   ..--|||...+.++|+.+++.+.
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI---ddTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE---ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEe---cCceEEEEecCHHHHHHHHHHhc
Confidence            466888889999999999999999998743322   34479999999999999988664